Starting phenix.real_space_refine on Sat Feb 24 02:50:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfp_33796/02_2024/7yfp_33796_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfp_33796/02_2024/7yfp_33796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfp_33796/02_2024/7yfp_33796.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfp_33796/02_2024/7yfp_33796.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfp_33796/02_2024/7yfp_33796_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfp_33796/02_2024/7yfp_33796_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 31 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 168 5.16 5 C 26357 2.51 5 N 6867 2.21 5 O 7554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D GLU 332": "OE1" <-> "OE2" Residue "D ARG 343": "NH1" <-> "NH2" Residue "D GLU 572": "OE1" <-> "OE2" Residue "D GLU 609": "OE1" <-> "OE2" Residue "D ARG 618": "NH1" <-> "NH2" Residue "D GLU 653": "OE1" <-> "OE2" Residue "D GLU 689": "OE1" <-> "OE2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "D ARG 756": "NH1" <-> "NH2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "F GLU 525": "OE1" <-> "OE2" Residue "F ARG 593": "NH1" <-> "NH2" Residue "F ARG 641": "NH1" <-> "NH2" Residue "T ARG 288": "NH1" <-> "NH2" Residue "T ARG 352": "NH1" <-> "NH2" Residue "T ARG 474": "NH1" <-> "NH2" Residue "T GLU 498": "OE1" <-> "OE2" Residue "T GLU 516": "OE1" <-> "OE2" Residue "T GLU 629": "OE1" <-> "OE2" Residue "T GLU 705": "OE1" <-> "OE2" Residue "T GLU 711": "OE1" <-> "OE2" Residue "T ARG 712": "NH1" <-> "NH2" Residue "T ARG 813": "NH1" <-> "NH2" Residue "T ARG 817": "NH1" <-> "NH2" Residue "T GLU 856": "OE1" <-> "OE2" Residue "T ARG 1054": "NH1" <-> "NH2" Residue "T GLU 1084": "OE1" <-> "OE2" Residue "T ARG 1123": "NH1" <-> "NH2" Residue "T ARG 1170": "NH1" <-> "NH2" Residue "T GLU 1182": "OE1" <-> "OE2" Residue "T ARG 1304": "NH1" <-> "NH2" Residue "T GLU 1427": "OE1" <-> "OE2" Residue "T ARG 1437": "NH1" <-> "NH2" Residue "T ARG 1520": "NH1" <-> "NH2" Residue "T ARG 1585": "NH1" <-> "NH2" Residue "T TYR 1610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1650": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1673": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 1729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 1760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 1851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 1861": "NH1" <-> "NH2" Residue "T PHE 1889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 1911": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1918": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 1996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 2093": "NH1" <-> "NH2" Residue "T PHE 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 2172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 2227": "OE1" <-> "OE2" Residue "T GLU 2229": "OE1" <-> "OE2" Residue "T GLU 2249": "OE1" <-> "OE2" Residue "T GLU 2302": "OE1" <-> "OE2" Residue "T ARG 2415": "NH1" <-> "NH2" Residue "T ARG 2432": "NH1" <-> "NH2" Residue "T ARG 2445": "NH1" <-> "NH2" Residue "T ARG 2456": "NH1" <-> "NH2" Residue "T ARG 2482": "NH1" <-> "NH2" Residue "T GLU 2614": "OE1" <-> "OE2" Residue "T ARG 2681": "NH1" <-> "NH2" Residue "T ARG 2715": "NH1" <-> "NH2" Residue "T ARG 2807": "NH1" <-> "NH2" Residue "T ARG 2887": "NH1" <-> "NH2" Residue "T ARG 2938": "NH1" <-> "NH2" Residue "T GLU 2942": "OE1" <-> "OE2" Residue "T ARG 2969": "NH1" <-> "NH2" Residue "T ARG 3034": "NH1" <-> "NH2" Residue "T GLU 3070": "OE1" <-> "OE2" Residue "T ARG 3172": "NH1" <-> "NH2" Residue "T GLU 3243": "OE1" <-> "OE2" Residue "T ARG 3313": "NH1" <-> "NH2" Residue "T ARG 3320": "NH1" <-> "NH2" Residue "T ARG 3373": "NH1" <-> "NH2" Residue "T ARG 3382": "NH1" <-> "NH2" Residue "T ARG 3424": "NH1" <-> "NH2" Residue "T ARG 3438": "NH1" <-> "NH2" Residue "T ARG 3545": "NH1" <-> "NH2" Residue "T ARG 3689": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40949 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2904 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Chain: "B" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3172 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 382} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3777 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1668 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1023 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 28374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3475, 28374 Classifications: {'peptide': 3475} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 13} Link IDs: {'CIS': 3, 'PTRANS': 146, 'TRANS': 3325} Chain breaks: 14 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.08, per 1000 atoms: 0.49 Number of scatterers: 40949 At special positions: 0 Unit cell: (138.6, 168.96, 248.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 168 16.00 P 3 15.00 O 7554 8.00 N 6867 7.00 C 26357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 17.57 Conformation dependent library (CDL) restraints added in 7.5 seconds 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 221 helices and 15 sheets defined 57.5% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 17.65 Creating SS restraints... Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 79 through 91 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 127 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 182 through 196 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 262 removed outlier: 5.688A pdb=" N ALA A 257 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 338 through 348 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 359 through 365 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'B' and resid 59 through 62 No H-bonds generated for 'chain 'B' and resid 59 through 62' Processing helix chain 'B' and resid 83 through 97 removed outlier: 4.464A pdb=" N GLU B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 Processing helix chain 'B' and resid 142 through 150 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.920A pdb=" N PHE B 239 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 245 " --> pdb=" O GLU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 259 through 262 No H-bonds generated for 'chain 'B' and resid 259 through 262' Processing helix chain 'B' and resid 282 through 293 removed outlier: 4.151A pdb=" N ALA B 289 " --> pdb=" O ARG B 285 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 Processing helix chain 'B' and resid 401 through 406 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 472 through 478 Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'D' and resid 26 through 47 Processing helix chain 'D' and resid 70 through 73 No H-bonds generated for 'chain 'D' and resid 70 through 73' Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 300 through 305 Proline residue: D 304 - end of helix No H-bonds generated for 'chain 'D' and resid 300 through 305' Processing helix chain 'D' and resid 312 through 335 Processing helix chain 'D' and resid 358 through 397 Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 639 through 644 removed outlier: 4.902A pdb=" N GLN D 643 " --> pdb=" O ARG D 640 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN D 644 " --> pdb=" O TYR D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 665 Processing helix chain 'D' and resid 669 through 676 Processing helix chain 'D' and resid 693 through 703 Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 715 through 734 removed outlier: 4.477A pdb=" N HIS D 718 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLN D 734 " --> pdb=" O GLN D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 771 removed outlier: 4.354A pdb=" N TRP D 757 " --> pdb=" O ARG D 753 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU D 762 " --> pdb=" O ALA D 758 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS D 766 " --> pdb=" O GLU D 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 102 No H-bonds generated for 'chain 'E' and resid 99 through 102' Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 166 through 176 removed outlier: 4.191A pdb=" N LEU E 175 " --> pdb=" O TYR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 Processing helix chain 'E' and resid 198 through 216 Processing helix chain 'E' and resid 221 through 225 Processing helix chain 'E' and resid 230 through 245 Processing helix chain 'E' and resid 248 through 265 Processing helix chain 'E' and resid 271 through 283 removed outlier: 6.280A pdb=" N LEU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 307 Processing helix chain 'F' and resid 521 through 534 removed outlier: 4.093A pdb=" N GLU F 525 " --> pdb=" O GLN F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 578 Processing helix chain 'T' and resid 4 through 13 removed outlier: 4.669A pdb=" N SER T 12 " --> pdb=" O GLU T 8 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG T 13 " --> pdb=" O GLN T 9 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 26 No H-bonds generated for 'chain 'T' and resid 23 through 26' Processing helix chain 'T' and resid 29 through 33 Processing helix chain 'T' and resid 48 through 60 Proline residue: T 53 - end of helix Processing helix chain 'T' and resid 73 through 84 Processing helix chain 'T' and resid 93 through 106 removed outlier: 4.868A pdb=" N LEU T 100 " --> pdb=" O ALA T 96 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU T 101 " --> pdb=" O MET T 97 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE T 102 " --> pdb=" O GLU T 98 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL T 106 " --> pdb=" O PHE T 102 " (cutoff:3.500A) Processing helix chain 'T' and resid 116 through 130 Processing helix chain 'T' and resid 137 through 157 removed outlier: 3.761A pdb=" N ILE T 141 " --> pdb=" O ASP T 138 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG T 142 " --> pdb=" O SER T 139 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE T 143 " --> pdb=" O PHE T 140 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR T 151 " --> pdb=" O TYR T 148 " (cutoff:3.500A) Proline residue: T 152 - end of helix Processing helix chain 'T' and resid 219 through 222 No H-bonds generated for 'chain 'T' and resid 219 through 222' Processing helix chain 'T' and resid 232 through 243 removed outlier: 4.731A pdb=" N SER T 237 " --> pdb=" O THR T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 250 through 257 Processing helix chain 'T' and resid 292 through 315 Proline residue: T 315 - end of helix Processing helix chain 'T' and resid 324 through 334 Processing helix chain 'T' and resid 342 through 356 removed outlier: 3.831A pdb=" N GLU T 346 " --> pdb=" O SER T 342 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 368 removed outlier: 4.094A pdb=" N LEU T 364 " --> pdb=" O LYS T 361 " (cutoff:3.500A) Proline residue: T 365 - end of helix Processing helix chain 'T' and resid 375 through 377 No H-bonds generated for 'chain 'T' and resid 375 through 377' Processing helix chain 'T' and resid 381 through 402 removed outlier: 4.993A pdb=" N THR T 386 " --> pdb=" O THR T 382 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU T 387 " --> pdb=" O MET T 383 " (cutoff:3.500A) Proline residue: T 389 - end of helix Processing helix chain 'T' and resid 408 through 423 Processing helix chain 'T' and resid 430 through 452 removed outlier: 4.078A pdb=" N GLU T 444 " --> pdb=" O LEU T 440 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG T 445 " --> pdb=" O ASN T 441 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 503 Proline residue: T 458 - end of helix removed outlier: 3.502A pdb=" N ASN T 473 " --> pdb=" O SER T 470 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP T 483 " --> pdb=" O ARG T 480 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS T 487 " --> pdb=" O THR T 484 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU T 493 " --> pdb=" O GLY T 490 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS T 502 " --> pdb=" O LYS T 499 " (cutoff:3.500A) Processing helix chain 'T' and resid 512 through 521 Processing helix chain 'T' and resid 563 through 566 No H-bonds generated for 'chain 'T' and resid 563 through 566' Processing helix chain 'T' and resid 579 through 603 removed outlier: 4.371A pdb=" N LYS T 602 " --> pdb=" O ILE T 598 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL T 603 " --> pdb=" O HIS T 599 " (cutoff:3.500A) Processing helix chain 'T' and resid 608 through 611 No H-bonds generated for 'chain 'T' and resid 608 through 611' Processing helix chain 'T' and resid 628 through 647 removed outlier: 3.928A pdb=" N LYS T 646 " --> pdb=" O ILE T 642 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N PHE T 647 " --> pdb=" O ILE T 643 " (cutoff:3.500A) Processing helix chain 'T' and resid 677 through 692 removed outlier: 4.358A pdb=" N GLN T 692 " --> pdb=" O PHE T 688 " (cutoff:3.500A) Processing helix chain 'T' and resid 695 through 714 removed outlier: 4.160A pdb=" N GLN T 704 " --> pdb=" O GLU T 700 " (cutoff:3.500A) Proline residue: T 707 - end of helix Processing helix chain 'T' and resid 718 through 728 Processing helix chain 'T' and resid 733 through 750 removed outlier: 4.712A pdb=" N LYS T 749 " --> pdb=" O LYS T 745 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP T 750 " --> pdb=" O GLY T 746 " (cutoff:3.500A) Processing helix chain 'T' and resid 756 through 775 Processing helix chain 'T' and resid 782 through 785 No H-bonds generated for 'chain 'T' and resid 782 through 785' Processing helix chain 'T' and resid 788 through 801 removed outlier: 3.592A pdb=" N THR T 801 " --> pdb=" O LYS T 797 " (cutoff:3.500A) Processing helix chain 'T' and resid 805 through 818 Processing helix chain 'T' and resid 832 through 843 Processing helix chain 'T' and resid 856 through 863 Processing helix chain 'T' and resid 880 through 888 Processing helix chain 'T' and resid 894 through 904 Processing helix chain 'T' and resid 912 through 931 Proline residue: T 915 - end of helix Proline residue: T 919 - end of helix removed outlier: 5.884A pdb=" N ASP T 922 " --> pdb=" O PRO T 919 " (cutoff:3.500A) Processing helix chain 'T' and resid 939 through 951 Processing helix chain 'T' and resid 971 through 973 No H-bonds generated for 'chain 'T' and resid 971 through 973' Processing helix chain 'T' and resid 997 through 1005 Processing helix chain 'T' and resid 1011 through 1033 removed outlier: 4.616A pdb=" N SER T1031 " --> pdb=" O LEU T1027 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER T1032 " --> pdb=" O MET T1028 " (cutoff:3.500A) Processing helix chain 'T' and resid 1039 through 1051 removed outlier: 3.673A pdb=" N LYS T1044 " --> pdb=" O THR T1040 " (cutoff:3.500A) Processing helix chain 'T' and resid 1069 through 1091 removed outlier: 4.027A pdb=" N SER T1091 " --> pdb=" O PHE T1087 " (cutoff:3.500A) Processing helix chain 'T' and resid 1096 through 1124 Processing helix chain 'T' and resid 1144 through 1154 Proline residue: T1150 - end of helix Processing helix chain 'T' and resid 1158 through 1179 Processing helix chain 'T' and resid 1182 through 1187 Processing helix chain 'T' and resid 1190 through 1202 Processing helix chain 'T' and resid 1206 through 1225 removed outlier: 5.381A pdb=" N SER T1225 " --> pdb=" O ASP T1221 " (cutoff:3.500A) Processing helix chain 'T' and resid 1228 through 1247 removed outlier: 6.427A pdb=" N TYR T1235 " --> pdb=" O LYS T1231 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN T1236 " --> pdb=" O LYS T1232 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU T1237 " --> pdb=" O TYR T1233 " (cutoff:3.500A) Processing helix chain 'T' and resid 1254 through 1272 Processing helix chain 'T' and resid 1284 through 1295 Processing helix chain 'T' and resid 1301 through 1316 Processing helix chain 'T' and resid 1322 through 1339 removed outlier: 4.753A pdb=" N HIS T1328 " --> pdb=" O LYS T1324 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N SER T1329 " --> pdb=" O LEU T1325 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N GLN T1331 " --> pdb=" O ASP T1327 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N PHE T1332 " --> pdb=" O HIS T1328 " (cutoff:3.500A) Proline residue: T1336 - end of helix Processing helix chain 'T' and resid 1347 through 1362 Processing helix chain 'T' and resid 1372 through 1383 Processing helix chain 'T' and resid 1404 through 1424 Processing helix chain 'T' and resid 1437 through 1449 Processing helix chain 'T' and resid 1453 through 1468 Processing helix chain 'T' and resid 1478 through 1489 Proline residue: T1484 - end of helix Processing helix chain 'T' and resid 1497 through 1508 removed outlier: 3.576A pdb=" N GLU T1508 " --> pdb=" O SER T1504 " (cutoff:3.500A) Processing helix chain 'T' and resid 1518 through 1529 removed outlier: 3.571A pdb=" N ASP T1524 " --> pdb=" O ARG T1520 " (cutoff:3.500A) Processing helix chain 'T' and resid 1532 through 1538 Processing helix chain 'T' and resid 1543 through 1545 No H-bonds generated for 'chain 'T' and resid 1543 through 1545' Processing helix chain 'T' and resid 1547 through 1561 removed outlier: 3.590A pdb=" N ILE T1558 " --> pdb=" O SER T1554 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE T1559 " --> pdb=" O ILE T1555 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N HIS T1560 " --> pdb=" O ILE T1556 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU T1561 " --> pdb=" O ASN T1557 " (cutoff:3.500A) Processing helix chain 'T' and resid 1569 through 1584 Processing helix chain 'T' and resid 1591 through 1603 removed outlier: 3.963A pdb=" N THR T1594 " --> pdb=" O PRO T1591 " (cutoff:3.500A) Proline residue: T1595 - end of helix Processing helix chain 'T' and resid 1606 through 1613 Processing helix chain 'T' and resid 1618 through 1629 Processing helix chain 'T' and resid 1635 through 1642 Processing helix chain 'T' and resid 1644 through 1658 Proline residue: T1656 - end of helix Processing helix chain 'T' and resid 1662 through 1679 Processing helix chain 'T' and resid 1690 through 1708 Processing helix chain 'T' and resid 1716 through 1735 Processing helix chain 'T' and resid 1739 through 1749 removed outlier: 3.714A pdb=" N LEU T1743 " --> pdb=" O ASP T1739 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU T1744 " --> pdb=" O GLN T1740 " (cutoff:3.500A) Processing helix chain 'T' and resid 1762 through 1768 Processing helix chain 'T' and resid 1778 through 1791 Processing helix chain 'T' and resid 1797 through 1817 Processing helix chain 'T' and resid 1833 through 1843 Processing helix chain 'T' and resid 1859 through 1874 removed outlier: 3.768A pdb=" N LEU T1865 " --> pdb=" O ARG T1861 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE T1871 " --> pdb=" O LEU T1867 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE T1872 " --> pdb=" O SER T1868 " (cutoff:3.500A) Processing helix chain 'T' and resid 1880 through 1895 removed outlier: 4.212A pdb=" N PHE T1893 " --> pdb=" O PHE T1889 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE T1894 " --> pdb=" O CYS T1890 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS T1895 " --> pdb=" O TRP T1891 " (cutoff:3.500A) Processing helix chain 'T' and resid 1899 through 1915 Processing helix chain 'T' and resid 1920 through 1931 removed outlier: 3.501A pdb=" N GLN T1925 " --> pdb=" O LYS T1921 " (cutoff:3.500A) Processing helix chain 'T' and resid 1939 through 1956 Proline residue: T1951 - end of helix Processing helix chain 'T' and resid 1965 through 1975 Processing helix chain 'T' and resid 1981 through 1992 Processing helix chain 'T' and resid 2002 through 2015 removed outlier: 3.828A pdb=" N ASN T2012 " --> pdb=" O ILE T2008 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS T2013 " --> pdb=" O HIS T2009 " (cutoff:3.500A) Processing helix chain 'T' and resid 2024 through 2042 Processing helix chain 'T' and resid 2091 through 2106 Processing helix chain 'T' and resid 2116 through 2128 removed outlier: 3.598A pdb=" N GLU T2126 " --> pdb=" O ASN T2122 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU T2127 " --> pdb=" O ILE T2123 " (cutoff:3.500A) Processing helix chain 'T' and resid 2141 through 2145 removed outlier: 3.564A pdb=" N LYS T2145 " --> pdb=" O VAL T2141 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 2141 through 2145' Processing helix chain 'T' and resid 2156 through 2173 removed outlier: 3.528A pdb=" N TYR T2169 " --> pdb=" O LEU T2165 " (cutoff:3.500A) Processing helix chain 'T' and resid 2181 through 2200 Proline residue: T2185 - end of helix removed outlier: 4.375A pdb=" N LYS T2193 " --> pdb=" O ASN T2189 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS T2194 " --> pdb=" O LEU T2190 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP T2198 " --> pdb=" O CYS T2194 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N HIS T2199 " --> pdb=" O ILE T2195 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N HIS T2200 " --> pdb=" O LYS T2196 " (cutoff:3.500A) Processing helix chain 'T' and resid 2203 through 2217 removed outlier: 3.597A pdb=" N GLN T2211 " --> pdb=" O GLN T2207 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL T2212 " --> pdb=" O LYS T2208 " (cutoff:3.500A) Processing helix chain 'T' and resid 2222 through 2225 No H-bonds generated for 'chain 'T' and resid 2222 through 2225' Processing helix chain 'T' and resid 2230 through 2245 Processing helix chain 'T' and resid 2250 through 2266 removed outlier: 3.526A pdb=" N LEU T2263 " --> pdb=" O LEU T2259 " (cutoff:3.500A) Processing helix chain 'T' and resid 2273 through 2294 Proline residue: T2277 - end of helix removed outlier: 3.950A pdb=" N GLN T2294 " --> pdb=" O LEU T2290 " (cutoff:3.500A) Processing helix chain 'T' and resid 2302 through 2321 Processing helix chain 'T' and resid 2327 through 2341 removed outlier: 3.812A pdb=" N ARG T2330 " --> pdb=" O ASP T2327 " (cutoff:3.500A) Proline residue: T2331 - end of helix Processing helix chain 'T' and resid 2346 through 2360 removed outlier: 4.519A pdb=" N SER T2358 " --> pdb=" O ASN T2354 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP T2359 " --> pdb=" O MET T2355 " (cutoff:3.500A) Processing helix chain 'T' and resid 2369 through 2385 removed outlier: 4.355A pdb=" N LEU T2380 " --> pdb=" O LEU T2376 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ALA T2381 " --> pdb=" O THR T2377 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N PHE T2382 " --> pdb=" O LYS T2378 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLU T2383 " --> pdb=" O MET T2379 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE T2384 " --> pdb=" O LEU T2380 " (cutoff:3.500A) Processing helix chain 'T' and resid 2388 through 2404 Processing helix chain 'T' and resid 2413 through 2424 Proline residue: T2419 - end of helix removed outlier: 4.451A pdb=" N VAL T2422 " --> pdb=" O GLN T2418 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR T2424 " --> pdb=" O PHE T2420 " (cutoff:3.500A) Processing helix chain 'T' and resid 2429 through 2441 removed outlier: 3.689A pdb=" N ARG T2434 " --> pdb=" O GLY T2430 " (cutoff:3.500A) Processing helix chain 'T' and resid 2447 through 2456 Processing helix chain 'T' and resid 2468 through 2479 Processing helix chain 'T' and resid 2497 through 2502 removed outlier: 5.418A pdb=" N GLU T2502 " --> pdb=" O SER T2498 " (cutoff:3.500A) Processing helix chain 'T' and resid 2519 through 2534 Processing helix chain 'T' and resid 2538 through 2550 removed outlier: 4.189A pdb=" N ASP T2543 " --> pdb=" O SER T2539 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE T2548 " --> pdb=" O SER T2544 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR T2550 " --> pdb=" O ILE T2546 " (cutoff:3.500A) Processing helix chain 'T' and resid 2553 through 2569 Proline residue: T2565 - end of helix Processing helix chain 'T' and resid 2576 through 2587 removed outlier: 3.801A pdb=" N THR T2585 " --> pdb=" O ARG T2581 " (cutoff:3.500A) Processing helix chain 'T' and resid 2603 through 2613 removed outlier: 3.671A pdb=" N LYS T2612 " --> pdb=" O ASP T2608 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE T2613 " --> pdb=" O SER T2609 " (cutoff:3.500A) Processing helix chain 'T' and resid 2633 through 2645 removed outlier: 3.897A pdb=" N ILE T2639 " --> pdb=" O GLN T2635 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN T2644 " --> pdb=" O LEU T2640 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER T2645 " --> pdb=" O GLU T2641 " (cutoff:3.500A) Processing helix chain 'T' and resid 2653 through 2668 Processing helix chain 'T' and resid 2672 through 2682 removed outlier: 4.822A pdb=" N GLY T2677 " --> pdb=" O ASP T2673 " (cutoff:3.500A) Processing helix chain 'T' and resid 2686 through 2697 Processing helix chain 'T' and resid 2700 through 2713 Processing helix chain 'T' and resid 2725 through 2740 Processing helix chain 'T' and resid 2745 through 2752 removed outlier: 3.868A pdb=" N LEU T2749 " --> pdb=" O VAL T2745 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N HIS T2752 " --> pdb=" O GLU T2748 " (cutoff:3.500A) Processing helix chain 'T' and resid 2755 through 2760 Processing helix chain 'T' and resid 2773 through 2782 Processing helix chain 'T' and resid 2789 through 2805 removed outlier: 4.165A pdb=" N PHE T2794 " --> pdb=" O ARG T2790 " (cutoff:3.500A) Processing helix chain 'T' and resid 2812 through 2829 removed outlier: 4.609A pdb=" N CYS T2817 " --> pdb=" O ARG T2814 " (cutoff:3.500A) Processing helix chain 'T' and resid 2839 through 2864 removed outlier: 4.479A pdb=" N GLN T2847 " --> pdb=" O LEU T2843 " (cutoff:3.500A) Processing helix chain 'T' and resid 2874 through 2886 removed outlier: 3.610A pdb=" N ALA T2883 " --> pdb=" O ARG T2879 " (cutoff:3.500A) Processing helix chain 'T' and resid 2896 through 2919 removed outlier: 4.776A pdb=" N ALA T2908 " --> pdb=" O TRP T2904 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE T2909 " --> pdb=" O ARG T2905 " (cutoff:3.500A) Proline residue: T2918 - end of helix Processing helix chain 'T' and resid 2942 through 2957 Processing helix chain 'T' and resid 2960 through 2971 removed outlier: 3.983A pdb=" N ALA T2968 " --> pdb=" O ILE T2964 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG T2969 " --> pdb=" O SER T2965 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ILE T2970 " --> pdb=" O GLN T2966 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR T2971 " --> pdb=" O LEU T2967 " (cutoff:3.500A) Processing helix chain 'T' and resid 2980 through 2992 Processing helix chain 'T' and resid 2998 through 3002 Processing helix chain 'T' and resid 3017 through 3032 removed outlier: 4.098A pdb=" N GLU T3021 " --> pdb=" O VAL T3017 " (cutoff:3.500A) Processing helix chain 'T' and resid 3037 through 3050 removed outlier: 4.060A pdb=" N ASP T3050 " --> pdb=" O ALA T3046 " (cutoff:3.500A) Processing helix chain 'T' and resid 3055 through 3070 removed outlier: 3.541A pdb=" N GLN T3059 " --> pdb=" O LYS T3055 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN T3064 " --> pdb=" O TRP T3060 " (cutoff:3.500A) Processing helix chain 'T' and resid 3079 through 3091 removed outlier: 4.172A pdb=" N LEU T3086 " --> pdb=" O ILE T3082 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN T3087 " --> pdb=" O SER T3083 " (cutoff:3.500A) Processing helix chain 'T' and resid 3098 through 3108 Processing helix chain 'T' and resid 3116 through 3121 Processing helix chain 'T' and resid 3130 through 3145 removed outlier: 3.699A pdb=" N ILE T3134 " --> pdb=" O VAL T3130 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR T3135 " --> pdb=" O TRP T3131 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE T3136 " --> pdb=" O TYR T3132 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE T3137 " --> pdb=" O TRP T3133 " (cutoff:3.500A) Proline residue: T3138 - end of helix Processing helix chain 'T' and resid 3152 through 3162 removed outlier: 3.926A pdb=" N ARG T3158 " --> pdb=" O HIS T3154 " (cutoff:3.500A) Processing helix chain 'T' and resid 3165 through 3181 removed outlier: 4.420A pdb=" N PHE T3169 " --> pdb=" O GLN T3165 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLN T3170 " --> pdb=" O ALA T3166 " (cutoff:3.500A) Processing helix chain 'T' and resid 3204 through 3217 Processing helix chain 'T' and resid 3220 through 3235 removed outlier: 3.671A pdb=" N ALA T3231 " --> pdb=" O GLU T3227 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN T3232 " --> pdb=" O SER T3228 " (cutoff:3.500A) Processing helix chain 'T' and resid 3241 through 3263 removed outlier: 4.487A pdb=" N LEU T3263 " --> pdb=" O ASN T3259 " (cutoff:3.500A) Processing helix chain 'T' and resid 3274 through 3284 removed outlier: 3.784A pdb=" N SER T3284 " --> pdb=" O LEU T3280 " (cutoff:3.500A) Processing helix chain 'T' and resid 3289 through 3300 removed outlier: 3.805A pdb=" N ARG T3293 " --> pdb=" O ALA T3289 " (cutoff:3.500A) Proline residue: T3294 - end of helix Processing helix chain 'T' and resid 3309 through 3327 Processing helix chain 'T' and resid 3334 through 3346 Proline residue: T3339 - end of helix removed outlier: 3.966A pdb=" N PHE T3344 " --> pdb=" O HIS T3340 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N HIS T3345 " --> pdb=" O LEU T3341 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N HIS T3346 " --> pdb=" O SER T3342 " (cutoff:3.500A) Processing helix chain 'T' and resid 3411 through 3432 removed outlier: 3.549A pdb=" N TYR T3423 " --> pdb=" O PHE T3420 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE T3426 " --> pdb=" O TYR T3423 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS T3428 " --> pdb=" O LEU T3425 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS T3432 " --> pdb=" O SER T3429 " (cutoff:3.500A) Processing helix chain 'T' and resid 3467 through 3477 Processing helix chain 'T' and resid 3482 through 3497 removed outlier: 3.954A pdb=" N GLN T3486 " --> pdb=" O PRO T3482 " (cutoff:3.500A) Processing helix chain 'T' and resid 3507 through 3520 removed outlier: 3.655A pdb=" N THR T3519 " --> pdb=" O ASN T3515 " (cutoff:3.500A) Processing helix chain 'T' and resid 3526 through 3534 Processing helix chain 'T' and resid 3541 through 3560 removed outlier: 3.987A pdb=" N SER T3550 " --> pdb=" O LYS T3546 " (cutoff:3.500A) Processing helix chain 'T' and resid 3626 through 3631 Processing helix chain 'T' and resid 3634 through 3639 Processing helix chain 'T' and resid 3641 through 3653 removed outlier: 4.572A pdb=" N PHE T3646 " --> pdb=" O ALA T3642 " (cutoff:3.500A) Processing helix chain 'T' and resid 3659 through 3677 removed outlier: 4.190A pdb=" N ALA T3664 " --> pdb=" O ASN T3660 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG T3668 " --> pdb=" O ALA T3664 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP T3669 " --> pdb=" O LEU T3665 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU T3670 " --> pdb=" O PHE T3666 " (cutoff:3.500A) Processing helix chain 'T' and resid 3686 through 3706 removed outlier: 3.917A pdb=" N LEU T3706 " --> pdb=" O LYS T3702 " (cutoff:3.500A) Processing helix chain 'T' and resid 3718 through 3728 Processing helix chain 'T' and resid 3730 through 3734 Processing sheet with id= A, first strand: chain 'A' and resid 16 through 19 removed outlier: 3.527A pdb=" N PHE A 31 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 298 through 300 Processing sheet with id= D, first strand: chain 'A' and resid 238 through 242 Processing sheet with id= E, first strand: chain 'B' and resid 136 through 141 removed outlier: 6.629A pdb=" N VAL B 17 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR B 111 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE B 19 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 43 through 47 Processing sheet with id= G, first strand: chain 'B' and resid 166 through 170 Processing sheet with id= H, first strand: chain 'B' and resid 209 through 212 removed outlier: 6.265A pdb=" N ILE B 217 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 268 through 274 Processing sheet with id= J, first strand: chain 'E' and resid 78 through 83 Processing sheet with id= K, first strand: chain 'F' and resid 636 through 642 removed outlier: 3.900A pdb=" N ARG F 639 " --> pdb=" O ASP F 651 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 977 through 980 Processing sheet with id= M, first strand: chain 'T' and resid 3379 through 3382 removed outlier: 4.235A pdb=" N ARG T3389 " --> pdb=" O VAL T3405 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET T3458 " --> pdb=" O ALA T3404 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'T' and resid 3464 through 3466 removed outlier: 3.670A pdb=" N ASN T3580 " --> pdb=" O ASP T3575 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'T' and resid 3371 through 3374 removed outlier: 7.020A pdb=" N ARG T3394 " --> pdb=" O ALA T3372 " (cutoff:3.500A) 1891 hydrogen bonds defined for protein. 5196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 17.94 Time building geometry restraints manager: 18.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9983 1.33 - 1.45: 8290 1.45 - 1.58: 23285 1.58 - 1.70: 5 1.70 - 1.82: 282 Bond restraints: 41845 Sorted by residual: bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.75e+01 bond pdb=" C5 ATP B 501 " pdb=" C6 ATP B 501 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.41e+01 bond pdb=" C4 ATP B 501 " pdb=" N9 ATP B 501 " ideal model delta sigma weight residual 1.374 1.324 0.050 1.00e-02 1.00e+04 2.49e+01 bond pdb=" C5 ATP B 501 " pdb=" N7 ATP B 501 " ideal model delta sigma weight residual 1.387 1.341 0.046 1.00e-02 1.00e+04 2.08e+01 bond pdb=" C8 ATP B 501 " pdb=" N7 ATP B 501 " ideal model delta sigma weight residual 1.310 1.353 -0.043 1.00e-02 1.00e+04 1.81e+01 ... (remaining 41840 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.66: 1171 106.66 - 113.98: 24145 113.98 - 121.30: 21741 121.30 - 128.62: 9298 128.62 - 135.94: 309 Bond angle restraints: 56664 Sorted by residual: angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 119.74 20.13 1.00e+00 1.00e+00 4.05e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 117.03 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" C5 ATP B 501 " pdb=" C4 ATP B 501 " pdb=" N3 ATP B 501 " ideal model delta sigma weight residual 126.80 118.93 7.87 1.00e+00 1.00e+00 6.20e+01 angle pdb=" N3 ATP B 501 " pdb=" C4 ATP B 501 " pdb=" N9 ATP B 501 " ideal model delta sigma weight residual 127.04 135.00 -7.96 1.15e+00 7.59e-01 4.80e+01 angle pdb=" N PRO T3592 " pdb=" CA PRO T3592 " pdb=" CB PRO T3592 " ideal model delta sigma weight residual 103.25 110.23 -6.98 1.05e+00 9.07e-01 4.42e+01 ... (remaining 56659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 22748 17.99 - 35.98: 2308 35.98 - 53.97: 302 53.97 - 71.96: 59 71.96 - 89.94: 33 Dihedral angle restraints: 25450 sinusoidal: 10517 harmonic: 14933 Sorted by residual: dihedral pdb=" CA ALA D 540 " pdb=" C ALA D 540 " pdb=" N PRO D 541 " pdb=" CA PRO D 541 " ideal model delta harmonic sigma weight residual -180.00 -138.68 -41.32 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA SER D 535 " pdb=" C SER D 535 " pdb=" N LYS D 536 " pdb=" CA LYS D 536 " ideal model delta harmonic sigma weight residual 180.00 141.89 38.11 0 5.00e+00 4.00e-02 5.81e+01 dihedral pdb=" CA THR T1366 " pdb=" C THR T1366 " pdb=" N PHE T1367 " pdb=" CA PHE T1367 " ideal model delta harmonic sigma weight residual 180.00 143.08 36.92 0 5.00e+00 4.00e-02 5.45e+01 ... (remaining 25447 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 5597 0.092 - 0.184: 688 0.184 - 0.276: 104 0.276 - 0.368: 5 0.368 - 0.460: 2 Chirality restraints: 6396 Sorted by residual: chirality pdb=" CA PHE T1988 " pdb=" N PHE T1988 " pdb=" C PHE T1988 " pdb=" CB PHE T1988 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.28e+00 chirality pdb=" CA ASN T1557 " pdb=" N ASN T1557 " pdb=" C ASN T1557 " pdb=" CB ASN T1557 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA TYR T1851 " pdb=" N TYR T1851 " pdb=" C TYR T1851 " pdb=" CB TYR T1851 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 6393 not shown) Planarity restraints: 7199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN T1958 " -0.014 2.00e-02 2.50e+03 3.02e-02 9.14e+00 pdb=" C ASN T1958 " 0.052 2.00e-02 2.50e+03 pdb=" O ASN T1958 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA T1959 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU T1796 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.14e+00 pdb=" C LEU T1796 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU T1796 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP T1797 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU T2719 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.06e+00 pdb=" N PRO T2720 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO T2720 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO T2720 " -0.039 5.00e-02 4.00e+02 ... (remaining 7196 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 64 2.23 - 2.90: 18255 2.90 - 3.56: 67171 3.56 - 4.23: 94045 4.23 - 4.90: 153428 Nonbonded interactions: 332963 Sorted by model distance: nonbonded pdb=" CE2 PHE T 381 " pdb=" ND1 HIS T1857 " model vdw 1.562 3.420 nonbonded pdb=" OD2 ASP T 694 " pdb=" NH2 ARG T1585 " model vdw 1.729 2.520 nonbonded pdb=" CZ PHE T 381 " pdb=" ND1 HIS T1857 " model vdw 1.837 3.420 nonbonded pdb=" CD1 LEU T2320 " pdb=" CB MET T2355 " model vdw 1.855 3.860 nonbonded pdb=" CB ARG T 480 " pdb=" CZ TYR T1760 " model vdw 1.860 3.660 ... (remaining 332958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.030 Extract box with map and model: 28.300 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 109.350 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 41845 Z= 0.433 Angle : 0.932 20.129 56664 Z= 0.630 Chirality : 0.062 0.460 6396 Planarity : 0.005 0.071 7199 Dihedral : 14.318 89.944 15710 Min Nonbonded Distance : 1.562 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.31 % Favored : 88.47 % Rotamer: Outliers : 1.60 % Allowed : 9.60 % Favored : 88.80 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.11), residues: 4978 helix: -0.79 (0.09), residues: 2950 sheet: -3.12 (0.31), residues: 175 loop : -3.91 (0.12), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 469 HIS 0.008 0.001 HIS T2592 PHE 0.029 0.002 PHE T 10 TYR 0.020 0.002 TYR F 584 ARG 0.008 0.000 ARG T 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 686 time to evaluate : 5.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 ASN cc_start: 0.7428 (t0) cc_final: 0.6710 (t0) REVERT: A 190 MET cc_start: 0.9544 (ttm) cc_final: 0.9183 (tmm) REVERT: A 313 MET cc_start: 0.9223 (tpp) cc_final: 0.8827 (mmp) REVERT: A 361 GLU cc_start: 0.9442 (tp30) cc_final: 0.9168 (tp30) REVERT: B 98 LEU cc_start: 0.9621 (mt) cc_final: 0.9231 (mt) REVERT: D 285 LEU cc_start: 0.9201 (mt) cc_final: 0.8738 (tt) REVERT: D 287 LEU cc_start: 0.9416 (tp) cc_final: 0.9215 (tt) REVERT: D 573 ARG cc_start: 0.8802 (ptt180) cc_final: 0.8487 (ptm-80) REVERT: D 609 GLU cc_start: 0.9094 (tp30) cc_final: 0.8542 (tm-30) REVERT: D 656 GLN cc_start: 0.9201 (tp-100) cc_final: 0.8758 (tm-30) REVERT: D 682 TYR cc_start: 0.9085 (t80) cc_final: 0.8780 (t80) REVERT: D 689 GLU cc_start: 0.8556 (tp30) cc_final: 0.8323 (tp30) REVERT: E 223 LEU cc_start: 0.8701 (mt) cc_final: 0.8240 (mp) REVERT: F 525 GLU cc_start: 0.9194 (mp0) cc_final: 0.8992 (mp0) REVERT: F 586 LYS cc_start: 0.8248 (mppt) cc_final: 0.7728 (mmtm) REVERT: F 621 ASP cc_start: 0.9144 (t0) cc_final: 0.8144 (t0) REVERT: T 83 PHE cc_start: 0.8407 (m-80) cc_final: 0.8044 (m-80) REVERT: T 304 PHE cc_start: 0.8507 (m-10) cc_final: 0.8245 (m-80) REVERT: T 307 TYR cc_start: 0.8427 (m-10) cc_final: 0.7976 (m-80) REVERT: T 432 GLN cc_start: 0.8793 (mt0) cc_final: 0.8555 (mt0) REVERT: T 691 MET cc_start: 0.9195 (mmm) cc_final: 0.8750 (mmm) REVERT: T 711 GLU cc_start: 0.9765 (tp30) cc_final: 0.9457 (tp30) REVERT: T 749 LYS cc_start: 0.8969 (mmtt) cc_final: 0.8696 (tppt) REVERT: T 771 MET cc_start: 0.8551 (mmt) cc_final: 0.8273 (mmt) REVERT: T 775 LEU cc_start: 0.8951 (pp) cc_final: 0.8699 (pp) REVERT: T 840 GLN cc_start: 0.8446 (pt0) cc_final: 0.8103 (tm-30) REVERT: T 845 MET cc_start: 0.8639 (ttm) cc_final: 0.8351 (ttp) REVERT: T 965 ASP cc_start: 0.8969 (p0) cc_final: 0.8748 (p0) REVERT: T 1084 GLU cc_start: 0.8656 (pp20) cc_final: 0.8399 (pp20) REVERT: T 1147 ASP cc_start: 0.8995 (t0) cc_final: 0.8625 (t70) REVERT: T 1242 LEU cc_start: 0.9578 (mt) cc_final: 0.9357 (mt) REVERT: T 1246 LYS cc_start: 0.9637 (mtmt) cc_final: 0.9390 (mtpp) REVERT: T 1266 ASP cc_start: 0.9493 (m-30) cc_final: 0.9270 (m-30) REVERT: T 1326 MET cc_start: 0.9124 (mtp) cc_final: 0.8463 (ppp) REVERT: T 1375 PHE cc_start: 0.9417 (m-10) cc_final: 0.9206 (m-80) REVERT: T 1487 MET cc_start: 0.5839 (mmp) cc_final: 0.5433 (ptp) REVERT: T 1550 LYS cc_start: 0.9122 (mtmt) cc_final: 0.8886 (mtmm) REVERT: T 1565 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6699 (pm20) REVERT: T 1618 ARG cc_start: 0.8563 (tpt170) cc_final: 0.8194 (tpt170) REVERT: T 1691 MET cc_start: 0.8065 (mtt) cc_final: 0.7830 (mtt) REVERT: T 1718 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9243 (pp) REVERT: T 1724 LYS cc_start: 0.9542 (ttmt) cc_final: 0.9323 (tppt) REVERT: T 1729 TYR cc_start: 0.8801 (t80) cc_final: 0.8566 (t80) REVERT: T 1744 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9239 (pp) REVERT: T 1750 PHE cc_start: 0.9626 (OUTLIER) cc_final: 0.8895 (p90) REVERT: T 1779 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8257 (pm20) REVERT: T 1799 ARG cc_start: 0.9415 (OUTLIER) cc_final: 0.8990 (mmp80) REVERT: T 1813 TYR cc_start: 0.9290 (t80) cc_final: 0.8990 (t80) REVERT: T 1860 PHE cc_start: 0.9352 (t80) cc_final: 0.9124 (t80) REVERT: T 1927 PHE cc_start: 0.7335 (OUTLIER) cc_final: 0.6974 (p90) REVERT: T 1969 TRP cc_start: 0.8532 (m100) cc_final: 0.7819 (m100) REVERT: T 2144 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.9036 (pp20) REVERT: T 2163 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7467 (p0) REVERT: T 2171 PHE cc_start: 0.9001 (m-10) cc_final: 0.8594 (m-10) REVERT: T 2189 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8933 (m-40) REVERT: T 2215 LYS cc_start: 0.8669 (mttt) cc_final: 0.8300 (mttt) REVERT: T 2279 MET cc_start: 0.9720 (mmm) cc_final: 0.9389 (mmm) REVERT: T 2305 ARG cc_start: 0.9239 (mpt-90) cc_final: 0.8692 (mmp80) REVERT: T 2316 TYR cc_start: 0.9180 (m-80) cc_final: 0.8675 (m-80) REVERT: T 2416 MET cc_start: 0.7095 (mpp) cc_final: 0.6706 (mpp) REVERT: T 2446 ASP cc_start: 0.8980 (t0) cc_final: 0.8760 (t70) REVERT: T 2470 ASN cc_start: 0.8859 (m-40) cc_final: 0.8650 (p0) REVERT: T 2605 MET cc_start: 0.8044 (mtm) cc_final: 0.7596 (mtm) REVERT: T 2643 ILE cc_start: 0.9380 (tt) cc_final: 0.9065 (tt) REVERT: T 2695 GLU cc_start: 0.8901 (tp30) cc_final: 0.8645 (tp30) REVERT: T 2730 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8437 (tm-30) REVERT: T 2773 ARG cc_start: 0.9218 (ptm160) cc_final: 0.8753 (ttp80) REVERT: T 2784 MET cc_start: 0.8940 (tpp) cc_final: 0.8535 (tpp) REVERT: T 2897 MET cc_start: 0.8499 (ttm) cc_final: 0.8239 (ttm) REVERT: T 2959 MET cc_start: 0.9374 (pmm) cc_final: 0.9057 (pmm) REVERT: T 3022 PHE cc_start: 0.9034 (m-10) cc_final: 0.8751 (m-80) REVERT: T 3248 LEU cc_start: 0.9647 (tp) cc_final: 0.9446 (tt) REVERT: T 3558 MET cc_start: 0.8673 (mtp) cc_final: 0.8384 (mtp) REVERT: T 3562 MET cc_start: 0.9234 (ttp) cc_final: 0.8883 (ptm) outliers start: 73 outliers final: 26 residues processed: 753 average time/residue: 0.5617 time to fit residues: 698.5074 Evaluate side-chains 522 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 486 time to evaluate : 4.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 1506 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1614 ASN Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1644 LEU Chi-restraints excluded: chain T residue 1660 VAL Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1718 LEU Chi-restraints excluded: chain T residue 1744 LEU Chi-restraints excluded: chain T residue 1750 PHE Chi-restraints excluded: chain T residue 1779 GLN Chi-restraints excluded: chain T residue 1790 VAL Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1859 LEU Chi-restraints excluded: chain T residue 1900 LEU Chi-restraints excluded: chain T residue 1920 ILE Chi-restraints excluded: chain T residue 1927 PHE Chi-restraints excluded: chain T residue 1941 LEU Chi-restraints excluded: chain T residue 1949 LEU Chi-restraints excluded: chain T residue 1995 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2144 GLU Chi-restraints excluded: chain T residue 2163 ASN Chi-restraints excluded: chain T residue 2182 GLU Chi-restraints excluded: chain T residue 2189 ASN Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2236 ILE Chi-restraints excluded: chain T residue 2278 LEU Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2325 LEU Chi-restraints excluded: chain T residue 2556 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 423 optimal weight: 2.9990 chunk 379 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 256 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 392 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 292 optimal weight: 9.9990 chunk 454 optimal weight: 0.0970 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 GLN A 49 GLN A 87 HIS A 137 GLN A 372 HIS B 60 GLN B 95 GLN B 103 ASN B 248 HIS B 275 ASN B 406 HIS D 262 ASN D 360 ASN D 644 ASN D 728 HIS ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 580 HIS F 624 GLN T 6 GLN T 39 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 615 ASN T 639 HIS ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 896 GLN T1105 ASN T1287 ASN T1300 ASN T1312 HIS T1407 GLN T1432 GLN T1470 ASN T1493 GLN ** T1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1571 ASN T1659 GLN ** T1768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T1781 ASN T1838 HIS T1903 GLN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1981 GLN ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1992 HIS ** T1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2122 ASN T2174 ASN T2188 GLN T2189 ASN T2200 HIS T2207 GLN T2245 GLN T2266 ASN ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2418 GLN T2507 ASN ** T2592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2651 ASN ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2704 GLN T2742 HIS T2811 GLN T2848 GLN T2863 HIS T2948 ASN T2957 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3073 ASN T3154 HIS T3357 GLN ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3644 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 41845 Z= 0.300 Angle : 0.767 12.259 56664 Z= 0.384 Chirality : 0.045 0.229 6396 Planarity : 0.005 0.074 7199 Dihedral : 6.663 55.292 5549 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.49 % Favored : 89.43 % Rotamer: Outliers : 3.11 % Allowed : 16.28 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.11), residues: 4978 helix: -0.33 (0.09), residues: 2927 sheet: -2.60 (0.33), residues: 187 loop : -3.40 (0.13), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 469 HIS 0.010 0.001 HIS T2010 PHE 0.046 0.002 PHE T1801 TYR 0.026 0.002 TYR E 304 ARG 0.007 0.001 ARG T2599 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 549 time to evaluate : 5.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.5917 (ppp) cc_final: 0.5233 (ppp) REVERT: A 190 MET cc_start: 0.9550 (ttm) cc_final: 0.9194 (tmm) REVERT: A 361 GLU cc_start: 0.9441 (tp30) cc_final: 0.9164 (tp30) REVERT: B 98 LEU cc_start: 0.9603 (mt) cc_final: 0.9193 (mt) REVERT: B 282 ASN cc_start: 0.9364 (OUTLIER) cc_final: 0.9155 (m-40) REVERT: D 536 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.6837 (mmmt) REVERT: D 573 ARG cc_start: 0.8776 (ptt180) cc_final: 0.8476 (ptm-80) REVERT: D 609 GLU cc_start: 0.9109 (tp30) cc_final: 0.8544 (tm-30) REVERT: D 622 PHE cc_start: 0.8467 (m-10) cc_final: 0.8080 (m-10) REVERT: D 656 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8719 (tm-30) REVERT: D 689 GLU cc_start: 0.8570 (tp30) cc_final: 0.8341 (tp30) REVERT: E 223 LEU cc_start: 0.8739 (mt) cc_final: 0.8264 (mp) REVERT: E 266 MET cc_start: 0.9010 (mtt) cc_final: 0.8701 (mtm) REVERT: F 586 LYS cc_start: 0.8241 (mppt) cc_final: 0.7671 (mmtm) REVERT: F 621 ASP cc_start: 0.8849 (t0) cc_final: 0.8617 (t0) REVERT: T 560 MET cc_start: 0.7816 (tmm) cc_final: 0.6493 (tmm) REVERT: T 689 MET cc_start: 0.9055 (mtt) cc_final: 0.8749 (mpp) REVERT: T 691 MET cc_start: 0.9217 (mmm) cc_final: 0.8709 (mmm) REVERT: T 711 GLU cc_start: 0.9739 (tp30) cc_final: 0.9412 (tp30) REVERT: T 749 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8638 (tppt) REVERT: T 771 MET cc_start: 0.8548 (mmt) cc_final: 0.8278 (mmt) REVERT: T 775 LEU cc_start: 0.8944 (pp) cc_final: 0.8639 (pp) REVERT: T 840 GLN cc_start: 0.8471 (pt0) cc_final: 0.7856 (tm-30) REVERT: T 844 GLN cc_start: 0.8884 (pm20) cc_final: 0.8619 (pm20) REVERT: T 853 HIS cc_start: 0.8083 (m90) cc_final: 0.7521 (m90) REVERT: T 856 GLU cc_start: 0.8740 (pp20) cc_final: 0.8490 (pp20) REVERT: T 965 ASP cc_start: 0.8964 (p0) cc_final: 0.8751 (p0) REVERT: T 1071 ASP cc_start: 0.9507 (OUTLIER) cc_final: 0.9293 (t0) REVERT: T 1084 GLU cc_start: 0.8673 (pp20) cc_final: 0.8418 (pp20) REVERT: T 1113 LEU cc_start: 0.9447 (mt) cc_final: 0.9240 (mt) REVERT: T 1130 ASN cc_start: 0.8700 (t0) cc_final: 0.8494 (t0) REVERT: T 1133 LEU cc_start: 0.9096 (tp) cc_final: 0.8728 (tp) REVERT: T 1147 ASP cc_start: 0.8958 (t0) cc_final: 0.8391 (t70) REVERT: T 1246 LYS cc_start: 0.9645 (mtmt) cc_final: 0.9347 (mtpp) REVERT: T 1266 ASP cc_start: 0.9490 (m-30) cc_final: 0.9267 (m-30) REVERT: T 1487 MET cc_start: 0.6040 (mmp) cc_final: 0.5760 (ptp) REVERT: T 1565 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.6736 (pm20) REVERT: T 1568 MET cc_start: 0.8455 (tmm) cc_final: 0.8188 (tmm) REVERT: T 1767 PHE cc_start: 0.8789 (t80) cc_final: 0.8562 (m-80) REVERT: T 1779 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8968 (pm20) REVERT: T 1813 TYR cc_start: 0.9321 (t80) cc_final: 0.8987 (t80) REVERT: T 2034 LEU cc_start: 0.9513 (tt) cc_final: 0.9241 (pp) REVERT: T 2171 PHE cc_start: 0.9022 (m-10) cc_final: 0.8680 (m-80) REVERT: T 2215 LYS cc_start: 0.8720 (mttt) cc_final: 0.8508 (mttt) REVERT: T 2279 MET cc_start: 0.9624 (mmm) cc_final: 0.9219 (mmm) REVERT: T 2312 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8543 (mt-10) REVERT: T 2359 TRP cc_start: 0.7874 (m100) cc_final: 0.7611 (m100) REVERT: T 2416 MET cc_start: 0.7278 (mpp) cc_final: 0.6754 (mpp) REVERT: T 2604 ASN cc_start: 0.8433 (m110) cc_final: 0.8151 (t0) REVERT: T 2605 MET cc_start: 0.8031 (mtm) cc_final: 0.7598 (mtm) REVERT: T 2635 GLN cc_start: 0.9306 (mp10) cc_final: 0.8828 (mp10) REVERT: T 2695 GLU cc_start: 0.8894 (tp30) cc_final: 0.8618 (tp30) REVERT: T 2773 ARG cc_start: 0.9158 (ptm160) cc_final: 0.8583 (ttp80) REVERT: T 2784 MET cc_start: 0.8895 (tpp) cc_final: 0.8520 (tpp) REVERT: T 2897 MET cc_start: 0.8489 (ttm) cc_final: 0.8207 (ttm) REVERT: T 2959 MET cc_start: 0.9386 (pmm) cc_final: 0.9072 (pmm) REVERT: T 3022 PHE cc_start: 0.9080 (m-10) cc_final: 0.8680 (m-80) REVERT: T 3028 MET cc_start: 0.9524 (mtp) cc_final: 0.9166 (mtp) REVERT: T 3077 PHE cc_start: 0.9042 (m-80) cc_final: 0.8803 (m-80) REVERT: T 3283 PHE cc_start: 0.8871 (m-80) cc_final: 0.8653 (t80) REVERT: T 3391 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8831 (pt) REVERT: T 3558 MET cc_start: 0.8722 (mtp) cc_final: 0.8455 (mtp) outliers start: 142 outliers final: 84 residues processed: 651 average time/residue: 0.5597 time to fit residues: 615.8365 Evaluate side-chains 560 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 470 time to evaluate : 4.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 582 PHE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 693 MET Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 964 THR Chi-restraints excluded: chain T residue 979 ASP Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1171 ILE Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1588 LEU Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1623 PHE Chi-restraints excluded: chain T residue 1663 VAL Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1718 LEU Chi-restraints excluded: chain T residue 1779 GLN Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1803 LEU Chi-restraints excluded: chain T residue 1900 LEU Chi-restraints excluded: chain T residue 1941 LEU Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2025 HIS Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2315 LEU Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2617 GLU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2961 ASP Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3391 LEU Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3529 ASP Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3640 ILE Chi-restraints excluded: chain T residue 3649 SER Chi-restraints excluded: chain T residue 3653 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 252 optimal weight: 4.9990 chunk 141 optimal weight: 8.9990 chunk 378 optimal weight: 0.9990 chunk 309 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 455 optimal weight: 10.0000 chunk 492 optimal weight: 2.9990 chunk 405 optimal weight: 5.9990 chunk 451 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 365 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 87 HIS D 359 GLN D 360 ASN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 983 ASN T1074 ASN ** T1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T2646 ASN ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3644 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41845 Z= 0.242 Angle : 0.723 11.738 56664 Z= 0.361 Chirality : 0.044 0.290 6396 Planarity : 0.005 0.066 7199 Dihedral : 6.217 54.764 5506 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 20.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.14 % Favored : 89.80 % Rotamer: Outliers : 3.26 % Allowed : 18.90 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.12), residues: 4978 helix: -0.02 (0.09), residues: 2914 sheet: -2.37 (0.34), residues: 181 loop : -3.14 (0.13), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T2460 HIS 0.012 0.001 HIS T1992 PHE 0.059 0.002 PHE T1927 TYR 0.023 0.002 TYR D 258 ARG 0.011 0.000 ARG T1932 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 529 time to evaluate : 4.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9551 (ttm) cc_final: 0.9173 (tmm) REVERT: A 227 MET cc_start: 0.9125 (mmm) cc_final: 0.8831 (mmm) REVERT: A 361 GLU cc_start: 0.9447 (tp30) cc_final: 0.9146 (tp30) REVERT: B 98 LEU cc_start: 0.9575 (mt) cc_final: 0.9168 (mt) REVERT: D 285 LEU cc_start: 0.9343 (tt) cc_final: 0.9120 (mt) REVERT: D 536 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6861 (mmmt) REVERT: D 573 ARG cc_start: 0.8764 (ptt180) cc_final: 0.8465 (ptm-80) REVERT: D 609 GLU cc_start: 0.9134 (tp30) cc_final: 0.8563 (tm-30) REVERT: D 656 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8612 (tm-30) REVERT: D 689 GLU cc_start: 0.8585 (tp30) cc_final: 0.8256 (tp30) REVERT: E 223 LEU cc_start: 0.8741 (mt) cc_final: 0.8347 (mp) REVERT: F 586 LYS cc_start: 0.8237 (mppt) cc_final: 0.7821 (mmtm) REVERT: F 621 ASP cc_start: 0.8835 (t0) cc_final: 0.8608 (t0) REVERT: T 560 MET cc_start: 0.7952 (tmm) cc_final: 0.6463 (tmm) REVERT: T 691 MET cc_start: 0.9213 (mmm) cc_final: 0.8689 (mmm) REVERT: T 711 GLU cc_start: 0.9732 (tp30) cc_final: 0.9396 (tp30) REVERT: T 749 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8690 (tppt) REVERT: T 771 MET cc_start: 0.8601 (mmt) cc_final: 0.8297 (mmt) REVERT: T 775 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8662 (pp) REVERT: T 840 GLN cc_start: 0.8464 (pt0) cc_final: 0.7867 (tm-30) REVERT: T 844 GLN cc_start: 0.8936 (pm20) cc_final: 0.8628 (pm20) REVERT: T 1084 GLU cc_start: 0.8636 (pp20) cc_final: 0.8366 (pp20) REVERT: T 1113 LEU cc_start: 0.9405 (mt) cc_final: 0.9202 (mt) REVERT: T 1130 ASN cc_start: 0.8607 (t0) cc_final: 0.8370 (t0) REVERT: T 1133 LEU cc_start: 0.9073 (tp) cc_final: 0.8599 (tp) REVERT: T 1147 ASP cc_start: 0.8953 (t0) cc_final: 0.8431 (t70) REVERT: T 1246 LYS cc_start: 0.9636 (mtmt) cc_final: 0.9392 (mtpp) REVERT: T 1266 ASP cc_start: 0.9484 (m-30) cc_final: 0.9253 (m-30) REVERT: T 1487 MET cc_start: 0.6013 (mmp) cc_final: 0.5649 (ptt) REVERT: T 1506 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5506 (pp) REVERT: T 1565 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6707 (pm20) REVERT: T 1568 MET cc_start: 0.8520 (tmm) cc_final: 0.8302 (tmm) REVERT: T 1586 LEU cc_start: 0.9394 (mp) cc_final: 0.8970 (tt) REVERT: T 1767 PHE cc_start: 0.8819 (t80) cc_final: 0.8489 (m-80) REVERT: T 1779 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8981 (pm20) REVERT: T 1813 TYR cc_start: 0.9335 (t80) cc_final: 0.8983 (t80) REVERT: T 1969 TRP cc_start: 0.8549 (m100) cc_final: 0.8337 (m100) REVERT: T 2171 PHE cc_start: 0.9030 (m-10) cc_final: 0.8695 (m-80) REVERT: T 2215 LYS cc_start: 0.8691 (mttt) cc_final: 0.8270 (mtmt) REVERT: T 2279 MET cc_start: 0.9646 (mmm) cc_final: 0.9285 (mmm) REVERT: T 2312 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8437 (mt-10) REVERT: T 2316 TYR cc_start: 0.8801 (m-10) cc_final: 0.8458 (m-80) REVERT: T 2359 TRP cc_start: 0.7958 (m100) cc_final: 0.7691 (m100) REVERT: T 2416 MET cc_start: 0.7311 (mpp) cc_final: 0.6750 (mpp) REVERT: T 2604 ASN cc_start: 0.8449 (m110) cc_final: 0.8103 (t0) REVERT: T 2605 MET cc_start: 0.7971 (mtm) cc_final: 0.7561 (mtm) REVERT: T 2695 GLU cc_start: 0.8865 (tp30) cc_final: 0.8577 (tp30) REVERT: T 2704 GLN cc_start: 0.9394 (OUTLIER) cc_final: 0.8628 (tm-30) REVERT: T 2773 ARG cc_start: 0.9097 (ptm160) cc_final: 0.8637 (ttp80) REVERT: T 2784 MET cc_start: 0.8868 (tpp) cc_final: 0.8520 (tpp) REVERT: T 2897 MET cc_start: 0.8457 (ttm) cc_final: 0.8205 (ttm) REVERT: T 2959 MET cc_start: 0.9334 (pmm) cc_final: 0.8956 (pmm) REVERT: T 3022 PHE cc_start: 0.8999 (m-10) cc_final: 0.8635 (m-80) REVERT: T 3028 MET cc_start: 0.9516 (mtp) cc_final: 0.9180 (mtp) REVERT: T 3248 LEU cc_start: 0.9551 (tp) cc_final: 0.9141 (tt) outliers start: 149 outliers final: 88 residues processed: 640 average time/residue: 0.5170 time to fit residues: 564.5899 Evaluate side-chains 568 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 474 time to evaluate : 5.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 740 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 778 ASN Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 964 THR Chi-restraints excluded: chain T residue 1062 ASP Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1171 ILE Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1506 LEU Chi-restraints excluded: chain T residue 1543 LEU Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1779 GLN Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1854 LEU Chi-restraints excluded: chain T residue 1860 PHE Chi-restraints excluded: chain T residue 1900 LEU Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2025 HIS Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2263 LEU Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2611 SER Chi-restraints excluded: chain T residue 2617 GLU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2704 GLN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2961 ASP Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3529 ASP Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3649 SER Chi-restraints excluded: chain T residue 3653 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 450 optimal weight: 2.9990 chunk 342 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 217 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 457 optimal weight: 0.4980 chunk 484 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 433 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1781 ASN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2009 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2907 HIS ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T3073 ASN ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3644 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41845 Z= 0.283 Angle : 0.731 11.975 56664 Z= 0.365 Chirality : 0.044 0.268 6396 Planarity : 0.005 0.073 7199 Dihedral : 6.144 54.940 5498 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.59 % Favored : 89.37 % Rotamer: Outliers : 4.05 % Allowed : 20.43 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.12), residues: 4978 helix: 0.09 (0.09), residues: 2910 sheet: -1.94 (0.34), residues: 199 loop : -3.06 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP T2179 HIS 0.016 0.001 HIS T2010 PHE 0.043 0.002 PHE T1927 TYR 0.018 0.002 TYR T2492 ARG 0.007 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 498 time to evaluate : 4.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9549 (ttm) cc_final: 0.9170 (tmm) REVERT: A 361 GLU cc_start: 0.9457 (tp30) cc_final: 0.9142 (tp30) REVERT: B 98 LEU cc_start: 0.9564 (mt) cc_final: 0.9194 (mt) REVERT: B 425 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8959 (tpp) REVERT: D 45 CYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8955 (t) REVERT: D 536 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7048 (mmmt) REVERT: D 573 ARG cc_start: 0.8763 (ptt180) cc_final: 0.8459 (ptm-80) REVERT: D 609 GLU cc_start: 0.9156 (tp30) cc_final: 0.8591 (tm-30) REVERT: D 656 GLN cc_start: 0.9156 (tp-100) cc_final: 0.8577 (tm-30) REVERT: D 657 GLU cc_start: 0.9429 (tt0) cc_final: 0.9189 (tt0) REVERT: D 689 GLU cc_start: 0.8625 (tp30) cc_final: 0.8387 (tp30) REVERT: E 266 MET cc_start: 0.8988 (mtt) cc_final: 0.8742 (mtm) REVERT: E 269 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8496 (pptt) REVERT: F 586 LYS cc_start: 0.8275 (mppt) cc_final: 0.7843 (mmtm) REVERT: F 621 ASP cc_start: 0.8897 (t0) cc_final: 0.8665 (t0) REVERT: T 83 PHE cc_start: 0.8481 (m-80) cc_final: 0.8078 (m-10) REVERT: T 352 ARG cc_start: 0.9166 (ptt-90) cc_final: 0.8827 (ptm-80) REVERT: T 560 MET cc_start: 0.7939 (tmm) cc_final: 0.6924 (tmm) REVERT: T 591 MET cc_start: 0.9483 (mmt) cc_final: 0.8744 (ttp) REVERT: T 691 MET cc_start: 0.9241 (mmm) cc_final: 0.8729 (mmm) REVERT: T 711 GLU cc_start: 0.9729 (tp30) cc_final: 0.9399 (tp30) REVERT: T 749 LYS cc_start: 0.9050 (mmtt) cc_final: 0.8723 (tppt) REVERT: T 771 MET cc_start: 0.8617 (mmt) cc_final: 0.8319 (mmt) REVERT: T 775 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8648 (pp) REVERT: T 840 GLN cc_start: 0.8461 (pt0) cc_final: 0.8212 (tm-30) REVERT: T 889 GLN cc_start: 0.8408 (mp10) cc_final: 0.8196 (mp10) REVERT: T 965 ASP cc_start: 0.8913 (p0) cc_final: 0.8711 (p0) REVERT: T 1077 ASN cc_start: 0.9421 (m-40) cc_final: 0.9218 (t0) REVERT: T 1084 GLU cc_start: 0.8662 (pp20) cc_final: 0.8386 (pp20) REVERT: T 1113 LEU cc_start: 0.9400 (mt) cc_final: 0.9171 (mt) REVERT: T 1130 ASN cc_start: 0.8602 (t0) cc_final: 0.8358 (t0) REVERT: T 1133 LEU cc_start: 0.9117 (tp) cc_final: 0.8644 (tp) REVERT: T 1147 ASP cc_start: 0.8963 (t0) cc_final: 0.8416 (t70) REVERT: T 1246 LYS cc_start: 0.9635 (mtmt) cc_final: 0.9323 (mtpp) REVERT: T 1248 THR cc_start: 0.8280 (OUTLIER) cc_final: 0.8064 (p) REVERT: T 1266 ASP cc_start: 0.9475 (m-30) cc_final: 0.9245 (m-30) REVERT: T 1487 MET cc_start: 0.5999 (mmp) cc_final: 0.5611 (ptt) REVERT: T 1565 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6627 (pm20) REVERT: T 1586 LEU cc_start: 0.9432 (mp) cc_final: 0.8814 (tt) REVERT: T 1760 TYR cc_start: 0.7997 (m-80) cc_final: 0.7744 (m-80) REVERT: T 1813 TYR cc_start: 0.9335 (t80) cc_final: 0.8986 (t80) REVERT: T 2034 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9174 (pp) REVERT: T 2171 PHE cc_start: 0.9030 (m-10) cc_final: 0.8718 (m-80) REVERT: T 2215 LYS cc_start: 0.8636 (mttt) cc_final: 0.8272 (mtmt) REVERT: T 2279 MET cc_start: 0.9657 (mmm) cc_final: 0.9295 (mmm) REVERT: T 2316 TYR cc_start: 0.8820 (m-10) cc_final: 0.8478 (m-80) REVERT: T 2359 TRP cc_start: 0.8026 (m100) cc_final: 0.7777 (m100) REVERT: T 2416 MET cc_start: 0.7426 (mpp) cc_final: 0.6904 (mpp) REVERT: T 2604 ASN cc_start: 0.8475 (m110) cc_final: 0.8111 (t0) REVERT: T 2605 MET cc_start: 0.8057 (mtm) cc_final: 0.7602 (mtm) REVERT: T 2624 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8573 (mmmm) REVERT: T 2695 GLU cc_start: 0.8872 (tp30) cc_final: 0.8605 (tp30) REVERT: T 2704 GLN cc_start: 0.9424 (OUTLIER) cc_final: 0.8650 (tm-30) REVERT: T 2773 ARG cc_start: 0.9075 (ptm160) cc_final: 0.8637 (ttp80) REVERT: T 2784 MET cc_start: 0.8832 (tpp) cc_final: 0.8455 (tpp) REVERT: T 2792 GLN cc_start: 0.9399 (tt0) cc_final: 0.9031 (tt0) REVERT: T 2897 MET cc_start: 0.8469 (ttm) cc_final: 0.8223 (ttm) REVERT: T 2959 MET cc_start: 0.9309 (pmm) cc_final: 0.9053 (pmm) REVERT: T 3022 PHE cc_start: 0.9039 (m-10) cc_final: 0.8599 (m-80) REVERT: T 3028 MET cc_start: 0.9526 (mtp) cc_final: 0.9151 (mtp) REVERT: T 3099 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7693 (tm-30) REVERT: T 3283 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8748 (t80) outliers start: 185 outliers final: 125 residues processed: 634 average time/residue: 0.5378 time to fit residues: 582.3140 Evaluate side-chains 598 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 463 time to evaluate : 4.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 382 THR Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 740 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 778 ASN Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 964 THR Chi-restraints excluded: chain T residue 979 ASP Chi-restraints excluded: chain T residue 1062 ASP Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1171 ILE Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1854 LEU Chi-restraints excluded: chain T residue 1860 PHE Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2025 HIS Chi-restraints excluded: chain T residue 2034 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2263 LEU Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2611 SER Chi-restraints excluded: chain T residue 2617 GLU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2656 GLU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2700 TRP Chi-restraints excluded: chain T residue 2704 GLN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2796 THR Chi-restraints excluded: chain T residue 2961 ASP Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3241 THR Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3529 ASP Chi-restraints excluded: chain T residue 3574 VAL Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3649 SER Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 403 optimal weight: 0.9990 chunk 274 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 360 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 413 optimal weight: 0.7980 chunk 334 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 434 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2009 HIS T2270 ASN ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3644 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41845 Z= 0.252 Angle : 0.718 14.107 56664 Z= 0.358 Chirality : 0.044 0.362 6396 Planarity : 0.005 0.063 7199 Dihedral : 6.014 53.412 5491 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 21.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.22 % Favored : 89.71 % Rotamer: Outliers : 4.27 % Allowed : 21.70 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.12), residues: 4978 helix: 0.18 (0.10), residues: 2920 sheet: -1.81 (0.34), residues: 200 loop : -2.99 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP T2179 HIS 0.017 0.001 HIS T2010 PHE 0.053 0.002 PHE T 593 TYR 0.023 0.002 TYR D 258 ARG 0.011 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 501 time to evaluate : 5.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9549 (ttm) cc_final: 0.9172 (tmm) REVERT: A 227 MET cc_start: 0.9027 (mmm) cc_final: 0.8711 (mmm) REVERT: A 305 MET cc_start: 0.9037 (mpp) cc_final: 0.8657 (mpp) REVERT: A 361 GLU cc_start: 0.9457 (tp30) cc_final: 0.9119 (tp30) REVERT: B 98 LEU cc_start: 0.9581 (mt) cc_final: 0.9145 (mt) REVERT: B 425 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8960 (tpp) REVERT: D 36 ARG cc_start: 0.8272 (pmt-80) cc_final: 0.7707 (pmt-80) REVERT: D 45 CYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8953 (t) REVERT: D 536 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.6922 (mmmt) REVERT: D 573 ARG cc_start: 0.8757 (ptt180) cc_final: 0.8443 (ptm-80) REVERT: D 609 GLU cc_start: 0.9164 (tp30) cc_final: 0.8595 (tm-30) REVERT: D 656 GLN cc_start: 0.9147 (tp-100) cc_final: 0.8551 (tm-30) REVERT: D 689 GLU cc_start: 0.8644 (tp30) cc_final: 0.8399 (tp30) REVERT: E 266 MET cc_start: 0.8994 (mtt) cc_final: 0.8676 (mtm) REVERT: F 586 LYS cc_start: 0.8246 (mppt) cc_final: 0.7884 (mmtm) REVERT: F 621 ASP cc_start: 0.8896 (t0) cc_final: 0.8641 (t0) REVERT: F 625 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: T 691 MET cc_start: 0.9282 (mmm) cc_final: 0.8789 (mmm) REVERT: T 711 GLU cc_start: 0.9725 (tp30) cc_final: 0.9389 (tp30) REVERT: T 749 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8640 (tppt) REVERT: T 771 MET cc_start: 0.8672 (mmt) cc_final: 0.8359 (mmt) REVERT: T 775 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8671 (pp) REVERT: T 840 GLN cc_start: 0.8375 (pt0) cc_final: 0.8130 (tm-30) REVERT: T 965 ASP cc_start: 0.8984 (p0) cc_final: 0.8714 (p0) REVERT: T 1077 ASN cc_start: 0.9405 (m-40) cc_final: 0.9198 (t0) REVERT: T 1084 GLU cc_start: 0.8678 (pp20) cc_final: 0.8409 (pp20) REVERT: T 1130 ASN cc_start: 0.8542 (t0) cc_final: 0.8276 (t0) REVERT: T 1133 LEU cc_start: 0.9117 (tp) cc_final: 0.8638 (tp) REVERT: T 1147 ASP cc_start: 0.8946 (t0) cc_final: 0.8353 (t70) REVERT: T 1246 LYS cc_start: 0.9634 (mtmt) cc_final: 0.9324 (mtpp) REVERT: T 1248 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7942 (p) REVERT: T 1266 ASP cc_start: 0.9456 (m-30) cc_final: 0.9218 (m-30) REVERT: T 1487 MET cc_start: 0.6048 (mmp) cc_final: 0.5627 (ptt) REVERT: T 1565 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6485 (pt0) REVERT: T 1586 LEU cc_start: 0.9298 (mp) cc_final: 0.8849 (tt) REVERT: T 1615 MET cc_start: 0.6960 (mtp) cc_final: 0.6707 (mtp) REVERT: T 1760 TYR cc_start: 0.8058 (m-80) cc_final: 0.7796 (m-80) REVERT: T 1813 TYR cc_start: 0.9322 (t80) cc_final: 0.8999 (t80) REVERT: T 1957 MET cc_start: 0.7307 (ppp) cc_final: 0.6963 (ppp) REVERT: T 1969 TRP cc_start: 0.8582 (m100) cc_final: 0.8381 (m100) REVERT: T 2034 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9125 (pp) REVERT: T 2169 TYR cc_start: 0.8827 (t80) cc_final: 0.8528 (t80) REVERT: T 2171 PHE cc_start: 0.9003 (m-10) cc_final: 0.8685 (m-80) REVERT: T 2215 LYS cc_start: 0.8654 (mttt) cc_final: 0.8368 (mttt) REVERT: T 2279 MET cc_start: 0.9664 (mmm) cc_final: 0.9300 (mmm) REVERT: T 2316 TYR cc_start: 0.8848 (m-10) cc_final: 0.8590 (m-80) REVERT: T 2359 TRP cc_start: 0.8042 (m100) cc_final: 0.7824 (m100) REVERT: T 2416 MET cc_start: 0.7476 (mpp) cc_final: 0.6937 (mpp) REVERT: T 2604 ASN cc_start: 0.8481 (m110) cc_final: 0.8072 (t0) REVERT: T 2605 MET cc_start: 0.8015 (mtm) cc_final: 0.7557 (mtm) REVERT: T 2624 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8551 (mmmm) REVERT: T 2695 GLU cc_start: 0.8865 (tp30) cc_final: 0.8625 (tp30) REVERT: T 2704 GLN cc_start: 0.9428 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: T 2773 ARG cc_start: 0.9062 (ptm160) cc_final: 0.8638 (ttp80) REVERT: T 2792 GLN cc_start: 0.9385 (tt0) cc_final: 0.9025 (tt0) REVERT: T 2897 MET cc_start: 0.8465 (ttm) cc_final: 0.8217 (ttm) REVERT: T 2959 MET cc_start: 0.9231 (pmm) cc_final: 0.8916 (pmm) REVERT: T 3022 PHE cc_start: 0.9011 (m-10) cc_final: 0.8589 (m-80) REVERT: T 3028 MET cc_start: 0.9516 (mtp) cc_final: 0.9135 (mtp) REVERT: T 3283 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8771 (t80) outliers start: 195 outliers final: 139 residues processed: 640 average time/residue: 0.5631 time to fit residues: 618.4371 Evaluate side-chains 616 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 467 time to evaluate : 4.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 603 VAL Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 740 LEU Chi-restraints excluded: chain T residue 758 THR Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 778 ASN Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 964 THR Chi-restraints excluded: chain T residue 979 ASP Chi-restraints excluded: chain T residue 1062 ASP Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1590 SER Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1854 LEU Chi-restraints excluded: chain T residue 1860 PHE Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2025 HIS Chi-restraints excluded: chain T residue 2034 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2263 LEU Chi-restraints excluded: chain T residue 2265 MET Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2414 VAL Chi-restraints excluded: chain T residue 2436 MET Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2611 SER Chi-restraints excluded: chain T residue 2617 GLU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2656 GLU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2700 TRP Chi-restraints excluded: chain T residue 2704 GLN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2796 THR Chi-restraints excluded: chain T residue 2961 ASP Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3137 ILE Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3465 THR Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3519 THR Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3648 ILE Chi-restraints excluded: chain T residue 3649 SER Chi-restraints excluded: chain T residue 3653 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 162 optimal weight: 8.9990 chunk 436 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 284 optimal weight: 30.0000 chunk 119 optimal weight: 1.9990 chunk 484 optimal weight: 5.9990 chunk 402 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 254 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 401 ASN ** T 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 889 GLN T1546 GLN ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T2839 HIS ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3644 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 41845 Z= 0.319 Angle : 0.746 12.880 56664 Z= 0.373 Chirality : 0.044 0.294 6396 Planarity : 0.005 0.067 7199 Dihedral : 6.072 53.629 5491 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.81 % Favored : 89.15 % Rotamer: Outliers : 4.79 % Allowed : 22.10 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.12), residues: 4978 helix: 0.17 (0.09), residues: 2920 sheet: -1.90 (0.35), residues: 189 loop : -2.97 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP T2179 HIS 0.019 0.001 HIS T2010 PHE 0.046 0.002 PHE T1767 TYR 0.021 0.002 TYR T2492 ARG 0.007 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 472 time to evaluate : 5.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9551 (ttm) cc_final: 0.9177 (tmm) REVERT: A 227 MET cc_start: 0.9118 (mmm) cc_final: 0.8826 (mmm) REVERT: A 305 MET cc_start: 0.9041 (mpp) cc_final: 0.8665 (mpp) REVERT: A 361 GLU cc_start: 0.9480 (tp30) cc_final: 0.9141 (tp30) REVERT: B 425 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8988 (tpp) REVERT: B 444 HIS cc_start: 0.8625 (OUTLIER) cc_final: 0.8347 (m170) REVERT: D 36 ARG cc_start: 0.8257 (pmt-80) cc_final: 0.7874 (pmt-80) REVERT: D 45 CYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8987 (t) REVERT: D 536 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7011 (mmmt) REVERT: D 573 ARG cc_start: 0.8734 (ptt180) cc_final: 0.8429 (ptm-80) REVERT: D 609 GLU cc_start: 0.9184 (tp30) cc_final: 0.8621 (tm-30) REVERT: D 656 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8532 (tm-30) REVERT: D 689 GLU cc_start: 0.8649 (tp30) cc_final: 0.8412 (tp30) REVERT: E 302 GLN cc_start: 0.9394 (tp-100) cc_final: 0.9163 (tp-100) REVERT: F 530 GLU cc_start: 0.9363 (mm-30) cc_final: 0.9094 (mm-30) REVERT: F 621 ASP cc_start: 0.8941 (t0) cc_final: 0.8619 (t0) REVERT: F 625 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: T 35 MET cc_start: 0.5232 (ttp) cc_final: 0.4869 (ttp) REVERT: T 83 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8256 (t80) REVERT: T 591 MET cc_start: 0.9349 (mmt) cc_final: 0.8860 (ptp) REVERT: T 691 MET cc_start: 0.9287 (mmm) cc_final: 0.8900 (mtp) REVERT: T 711 GLU cc_start: 0.9728 (tp30) cc_final: 0.9400 (tp30) REVERT: T 749 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8637 (tppt) REVERT: T 771 MET cc_start: 0.8735 (mmt) cc_final: 0.8404 (mmt) REVERT: T 775 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8711 (pp) REVERT: T 840 GLN cc_start: 0.8387 (pt0) cc_final: 0.8179 (tm-30) REVERT: T 965 ASP cc_start: 0.8997 (p0) cc_final: 0.8697 (p0) REVERT: T 1034 GLU cc_start: 0.9024 (pt0) cc_final: 0.8766 (pm20) REVERT: T 1077 ASN cc_start: 0.9430 (m-40) cc_final: 0.9211 (t0) REVERT: T 1084 GLU cc_start: 0.8710 (pp20) cc_final: 0.8435 (pp20) REVERT: T 1130 ASN cc_start: 0.8560 (t0) cc_final: 0.8297 (t0) REVERT: T 1133 LEU cc_start: 0.9172 (tp) cc_final: 0.8696 (tp) REVERT: T 1147 ASP cc_start: 0.8968 (t0) cc_final: 0.8368 (t70) REVERT: T 1246 LYS cc_start: 0.9630 (mtmt) cc_final: 0.9319 (mtpp) REVERT: T 1248 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7993 (p) REVERT: T 1266 ASP cc_start: 0.9442 (m-30) cc_final: 0.9216 (m-30) REVERT: T 1487 MET cc_start: 0.6091 (mmp) cc_final: 0.5635 (ptt) REVERT: T 1565 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.6482 (pt0) REVERT: T 1586 LEU cc_start: 0.9280 (mp) cc_final: 0.8838 (tt) REVERT: T 1615 MET cc_start: 0.6972 (mtp) cc_final: 0.6713 (mtp) REVERT: T 1813 TYR cc_start: 0.9334 (t80) cc_final: 0.9023 (t80) REVERT: T 1957 MET cc_start: 0.7301 (ppp) cc_final: 0.7100 (ppp) REVERT: T 2169 TYR cc_start: 0.8878 (t80) cc_final: 0.8561 (t80) REVERT: T 2215 LYS cc_start: 0.8695 (mttt) cc_final: 0.8415 (mttt) REVERT: T 2279 MET cc_start: 0.9674 (mmm) cc_final: 0.9311 (mmm) REVERT: T 2316 TYR cc_start: 0.8882 (m-10) cc_final: 0.8637 (m-80) REVERT: T 2416 MET cc_start: 0.7615 (mpp) cc_final: 0.6939 (mpp) REVERT: T 2604 ASN cc_start: 0.8491 (m110) cc_final: 0.8086 (t0) REVERT: T 2605 MET cc_start: 0.8070 (mtm) cc_final: 0.7592 (mtm) REVERT: T 2624 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8593 (mmmm) REVERT: T 2773 ARG cc_start: 0.9083 (ptm160) cc_final: 0.8665 (ttp80) REVERT: T 2792 GLN cc_start: 0.9423 (tt0) cc_final: 0.9000 (tt0) REVERT: T 2852 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: T 2897 MET cc_start: 0.8480 (ttm) cc_final: 0.8234 (ttm) REVERT: T 2959 MET cc_start: 0.9232 (pmm) cc_final: 0.8981 (pmm) REVERT: T 3022 PHE cc_start: 0.9001 (m-10) cc_final: 0.8635 (m-80) REVERT: T 3028 MET cc_start: 0.9531 (mtp) cc_final: 0.9178 (mtp) REVERT: T 3283 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8822 (t80) REVERT: T 3435 GLU cc_start: 0.8212 (tp30) cc_final: 0.7968 (tp30) outliers start: 219 outliers final: 166 residues processed: 632 average time/residue: 0.5481 time to fit residues: 593.7670 Evaluate side-chains 630 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 453 time to evaluate : 4.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 289 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 681 THR Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 546 VAL Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 577 ASN Chi-restraints excluded: chain T residue 587 TYR Chi-restraints excluded: chain T residue 603 VAL Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 693 MET Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 739 ILE Chi-restraints excluded: chain T residue 758 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 778 ASN Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 938 ASN Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 964 THR Chi-restraints excluded: chain T residue 979 ASP Chi-restraints excluded: chain T residue 1062 ASP Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1160 VAL Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1534 VAL Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1590 SER Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1676 MET Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1854 LEU Chi-restraints excluded: chain T residue 1860 PHE Chi-restraints excluded: chain T residue 1872 ILE Chi-restraints excluded: chain T residue 1904 SER Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2025 HIS Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2190 LEU Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2263 LEU Chi-restraints excluded: chain T residue 2265 MET Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2360 ILE Chi-restraints excluded: chain T residue 2384 ILE Chi-restraints excluded: chain T residue 2414 VAL Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2656 GLU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2700 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2796 THR Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2961 ASP Chi-restraints excluded: chain T residue 2999 LEU Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3137 ILE Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3241 THR Chi-restraints excluded: chain T residue 3283 PHE Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3436 THR Chi-restraints excluded: chain T residue 3457 ILE Chi-restraints excluded: chain T residue 3462 VAL Chi-restraints excluded: chain T residue 3465 THR Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3519 THR Chi-restraints excluded: chain T residue 3529 ASP Chi-restraints excluded: chain T residue 3574 VAL Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3648 ILE Chi-restraints excluded: chain T residue 3649 SER Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 467 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 276 optimal weight: 5.9990 chunk 353 optimal weight: 1.9990 chunk 274 optimal weight: 20.0000 chunk 408 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 482 optimal weight: 0.8980 chunk 302 optimal weight: 10.0000 chunk 294 optimal weight: 0.3980 chunk 222 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1365 ASN ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T2418 GLN ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T3471 HIS ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3644 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41845 Z= 0.217 Angle : 0.721 15.126 56664 Z= 0.353 Chirality : 0.044 0.244 6396 Planarity : 0.005 0.070 7199 Dihedral : 5.934 53.625 5491 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.84 % Favored : 90.14 % Rotamer: Outliers : 4.57 % Allowed : 22.93 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.12), residues: 4978 helix: 0.33 (0.10), residues: 2909 sheet: -1.66 (0.34), residues: 199 loop : -2.88 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP T2179 HIS 0.024 0.001 HIS T2010 PHE 0.050 0.002 PHE T1767 TYR 0.018 0.001 TYR T 828 ARG 0.007 0.000 ARG T2599 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 720 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 511 time to evaluate : 7.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9553 (ttm) cc_final: 0.9166 (tmm) REVERT: A 227 MET cc_start: 0.9163 (mmm) cc_final: 0.8878 (mmm) REVERT: A 305 MET cc_start: 0.8991 (mpp) cc_final: 0.8603 (mpp) REVERT: A 361 GLU cc_start: 0.9453 (tp30) cc_final: 0.9095 (tp30) REVERT: B 82 ASP cc_start: 0.8703 (m-30) cc_final: 0.8338 (m-30) REVERT: B 98 LEU cc_start: 0.9574 (mt) cc_final: 0.9141 (mt) REVERT: B 425 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8959 (tpp) REVERT: B 444 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.8337 (m170) REVERT: D 36 ARG cc_start: 0.8164 (pmt-80) cc_final: 0.7883 (pmt-80) REVERT: D 45 CYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8917 (t) REVERT: D 285 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9050 (tt) REVERT: D 536 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6966 (mmmt) REVERT: D 573 ARG cc_start: 0.8728 (ptt180) cc_final: 0.8476 (ptm-80) REVERT: D 609 GLU cc_start: 0.9156 (tp30) cc_final: 0.8592 (tm-30) REVERT: D 656 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8510 (tm-30) REVERT: D 657 GLU cc_start: 0.9442 (tt0) cc_final: 0.9026 (tm-30) REVERT: D 676 MET cc_start: 0.8444 (mmt) cc_final: 0.8202 (mmm) REVERT: D 689 GLU cc_start: 0.8652 (tp30) cc_final: 0.8417 (tp30) REVERT: E 302 GLN cc_start: 0.9375 (tp-100) cc_final: 0.9087 (tt0) REVERT: F 530 GLU cc_start: 0.9342 (mm-30) cc_final: 0.9084 (mm-30) REVERT: F 592 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8317 (pt) REVERT: F 621 ASP cc_start: 0.8908 (t0) cc_final: 0.8600 (t0) REVERT: F 625 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: T 35 MET cc_start: 0.5084 (ttp) cc_final: 0.4721 (ttp) REVERT: T 83 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8207 (t80) REVERT: T 691 MET cc_start: 0.9281 (mmm) cc_final: 0.8894 (mtp) REVERT: T 711 GLU cc_start: 0.9721 (tp30) cc_final: 0.9397 (tp30) REVERT: T 749 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8645 (tppt) REVERT: T 771 MET cc_start: 0.8670 (mmt) cc_final: 0.8461 (tmm) REVERT: T 840 GLN cc_start: 0.8393 (pt0) cc_final: 0.8169 (tm-30) REVERT: T 965 ASP cc_start: 0.8992 (p0) cc_final: 0.8701 (p0) REVERT: T 1077 ASN cc_start: 0.9403 (m-40) cc_final: 0.9190 (t0) REVERT: T 1084 GLU cc_start: 0.8676 (pp20) cc_final: 0.8380 (pp20) REVERT: T 1130 ASN cc_start: 0.8445 (t0) cc_final: 0.8174 (t0) REVERT: T 1133 LEU cc_start: 0.9151 (tp) cc_final: 0.8660 (tp) REVERT: T 1246 LYS cc_start: 0.9635 (mtmt) cc_final: 0.9313 (mtpp) REVERT: T 1248 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7871 (p) REVERT: T 1266 ASP cc_start: 0.9439 (m-30) cc_final: 0.9207 (m-30) REVERT: T 1565 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6537 (pt0) REVERT: T 1586 LEU cc_start: 0.9267 (mp) cc_final: 0.8831 (tt) REVERT: T 1615 MET cc_start: 0.6909 (mtp) cc_final: 0.6680 (mtp) REVERT: T 1760 TYR cc_start: 0.8114 (m-80) cc_final: 0.7813 (m-80) REVERT: T 1789 PHE cc_start: 0.9337 (OUTLIER) cc_final: 0.9082 (t80) REVERT: T 1813 TYR cc_start: 0.9323 (t80) cc_final: 0.9028 (t80) REVERT: T 1957 MET cc_start: 0.7244 (ppp) cc_final: 0.6966 (ppp) REVERT: T 1969 TRP cc_start: 0.8596 (m100) cc_final: 0.8388 (m100) REVERT: T 2215 LYS cc_start: 0.8680 (mttt) cc_final: 0.8425 (mttt) REVERT: T 2279 MET cc_start: 0.9672 (mmm) cc_final: 0.9311 (mmm) REVERT: T 2344 MET cc_start: 0.8372 (mmm) cc_final: 0.8019 (mpp) REVERT: T 2416 MET cc_start: 0.7507 (mpp) cc_final: 0.6896 (mpp) REVERT: T 2604 ASN cc_start: 0.8479 (m110) cc_final: 0.8020 (t0) REVERT: T 2605 MET cc_start: 0.7950 (mtm) cc_final: 0.7503 (mtm) REVERT: T 2624 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8578 (mmmm) REVERT: T 2773 ARG cc_start: 0.9061 (ptm160) cc_final: 0.8641 (ttp80) REVERT: T 2792 GLN cc_start: 0.9399 (tt0) cc_final: 0.9002 (tt0) REVERT: T 2852 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: T 2897 MET cc_start: 0.8460 (ttm) cc_final: 0.8212 (ttm) REVERT: T 3022 PHE cc_start: 0.9037 (m-10) cc_final: 0.8697 (m-80) REVERT: T 3091 LEU cc_start: 0.9506 (OUTLIER) cc_final: 0.9292 (tt) outliers start: 209 outliers final: 153 residues processed: 668 average time/residue: 0.5167 time to fit residues: 590.9928 Evaluate side-chains 639 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 473 time to evaluate : 4.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 587 LYS Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 592 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain T residue 117 LEU Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 577 ASN Chi-restraints excluded: chain T residue 587 TYR Chi-restraints excluded: chain T residue 590 LEU Chi-restraints excluded: chain T residue 603 VAL Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 739 ILE Chi-restraints excluded: chain T residue 758 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 778 ASN Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 938 ASN Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 964 THR Chi-restraints excluded: chain T residue 979 ASP Chi-restraints excluded: chain T residue 1062 ASP Chi-restraints excluded: chain T residue 1071 ASP Chi-restraints excluded: chain T residue 1086 VAL Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1200 LEU Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1365 ASN Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1534 VAL Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1590 SER Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1676 MET Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1789 PHE Chi-restraints excluded: chain T residue 1799 ARG Chi-restraints excluded: chain T residue 1872 ILE Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2025 HIS Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2190 LEU Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2263 LEU Chi-restraints excluded: chain T residue 2265 MET Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2360 ILE Chi-restraints excluded: chain T residue 2384 ILE Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2436 MET Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2656 GLU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2700 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2796 THR Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2961 ASP Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3091 LEU Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3436 THR Chi-restraints excluded: chain T residue 3462 VAL Chi-restraints excluded: chain T residue 3465 THR Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3519 THR Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3653 ILE Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3720 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 298 optimal weight: 30.0000 chunk 192 optimal weight: 9.9990 chunk 288 optimal weight: 40.0000 chunk 145 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 306 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 238 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 379 optimal weight: 7.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1754 ASN ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3644 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 41845 Z= 0.361 Angle : 0.786 16.103 56664 Z= 0.391 Chirality : 0.045 0.378 6396 Planarity : 0.005 0.096 7199 Dihedral : 6.105 55.066 5491 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.03 % Favored : 88.93 % Rotamer: Outliers : 4.83 % Allowed : 23.50 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.12), residues: 4978 helix: 0.19 (0.10), residues: 2919 sheet: -1.80 (0.36), residues: 187 loop : -2.91 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP T2179 HIS 0.024 0.001 HIS T2010 PHE 0.051 0.002 PHE T1767 TYR 0.029 0.002 TYR T2316 ARG 0.008 0.000 ARG T1070 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 462 time to evaluate : 5.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 MET cc_start: 0.9552 (ttm) cc_final: 0.9174 (tmm) REVERT: A 227 MET cc_start: 0.9183 (mmm) cc_final: 0.8886 (mmm) REVERT: A 305 MET cc_start: 0.9023 (mpp) cc_final: 0.8659 (mpp) REVERT: B 425 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8995 (tpp) REVERT: B 444 HIS cc_start: 0.8614 (OUTLIER) cc_final: 0.8369 (m170) REVERT: D 45 CYS cc_start: 0.9272 (OUTLIER) cc_final: 0.9022 (t) REVERT: D 297 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8426 (mm) REVERT: D 536 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7031 (mmmt) REVERT: D 573 ARG cc_start: 0.8729 (ptt180) cc_final: 0.8497 (ptm-80) REVERT: D 609 GLU cc_start: 0.9191 (tp30) cc_final: 0.8634 (tm-30) REVERT: D 656 GLN cc_start: 0.9188 (tp-100) cc_final: 0.8563 (tm-30) REVERT: D 657 GLU cc_start: 0.9466 (tt0) cc_final: 0.9018 (tm-30) REVERT: D 676 MET cc_start: 0.8562 (mmt) cc_final: 0.8279 (mmm) REVERT: D 689 GLU cc_start: 0.8662 (tp30) cc_final: 0.8437 (tp30) REVERT: E 266 MET cc_start: 0.8654 (mtm) cc_final: 0.8406 (mtm) REVERT: E 302 GLN cc_start: 0.9397 (tp-100) cc_final: 0.9192 (tp-100) REVERT: F 530 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9095 (mm-30) REVERT: F 549 MET cc_start: 0.8755 (mmm) cc_final: 0.8407 (mtt) REVERT: F 621 ASP cc_start: 0.8982 (t0) cc_final: 0.8606 (t0) REVERT: F 625 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7210 (pm20) REVERT: T 35 MET cc_start: 0.5183 (ttp) cc_final: 0.4878 (ttp) REVERT: T 83 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.8178 (t80) REVERT: T 390 LEU cc_start: 0.9218 (mm) cc_final: 0.8869 (pp) REVERT: T 480 ARG cc_start: 0.9558 (mtt180) cc_final: 0.9185 (mpp80) REVERT: T 691 MET cc_start: 0.9306 (mmm) cc_final: 0.8872 (mtp) REVERT: T 711 GLU cc_start: 0.9733 (tp30) cc_final: 0.9431 (tp30) REVERT: T 749 LYS cc_start: 0.9058 (mmtt) cc_final: 0.8652 (tppt) REVERT: T 771 MET cc_start: 0.8710 (mmt) cc_final: 0.8426 (tmm) REVERT: T 775 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.7700 (pp) REVERT: T 965 ASP cc_start: 0.9038 (p0) cc_final: 0.8756 (p0) REVERT: T 1077 ASN cc_start: 0.9430 (m-40) cc_final: 0.9226 (t0) REVERT: T 1084 GLU cc_start: 0.8738 (pp20) cc_final: 0.8488 (pp20) REVERT: T 1130 ASN cc_start: 0.8520 (t0) cc_final: 0.8271 (t0) REVERT: T 1133 LEU cc_start: 0.9211 (tp) cc_final: 0.8744 (tp) REVERT: T 1246 LYS cc_start: 0.9628 (mtmt) cc_final: 0.9318 (mtpp) REVERT: T 1248 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7972 (p) REVERT: T 1266 ASP cc_start: 0.9429 (m-30) cc_final: 0.9201 (m-30) REVERT: T 1565 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.6610 (pt0) REVERT: T 1586 LEU cc_start: 0.9279 (mp) cc_final: 0.8838 (tt) REVERT: T 1615 MET cc_start: 0.7003 (mtp) cc_final: 0.6793 (mtp) REVERT: T 1760 TYR cc_start: 0.8104 (m-80) cc_final: 0.7420 (m-80) REVERT: T 1813 TYR cc_start: 0.9348 (t80) cc_final: 0.9074 (t80) REVERT: T 1957 MET cc_start: 0.7269 (ppp) cc_final: 0.6936 (ppp) REVERT: T 2215 LYS cc_start: 0.8716 (mttt) cc_final: 0.8468 (mttt) REVERT: T 2279 MET cc_start: 0.9677 (mmm) cc_final: 0.9310 (mmm) REVERT: T 2316 TYR cc_start: 0.8887 (m-80) cc_final: 0.8647 (m-80) REVERT: T 2416 MET cc_start: 0.7657 (mpp) cc_final: 0.6944 (mpp) REVERT: T 2604 ASN cc_start: 0.8517 (m110) cc_final: 0.8021 (t0) REVERT: T 2605 MET cc_start: 0.8085 (mtm) cc_final: 0.7588 (mtm) REVERT: T 2624 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8606 (mmmm) REVERT: T 2773 ARG cc_start: 0.9086 (ptm160) cc_final: 0.8511 (ttp80) REVERT: T 2852 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: T 2897 MET cc_start: 0.8482 (ttm) cc_final: 0.8236 (ttm) REVERT: T 2957 HIS cc_start: 0.9520 (OUTLIER) cc_final: 0.9008 (t-90) REVERT: T 3022 PHE cc_start: 0.9041 (m-10) cc_final: 0.8657 (m-80) REVERT: T 3028 MET cc_start: 0.9548 (mtp) cc_final: 0.9180 (mtp) REVERT: T 3091 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9343 (tt) outliers start: 221 outliers final: 176 residues processed: 626 average time/residue: 0.5304 time to fit residues: 565.9027 Evaluate side-chains 640 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 451 time to evaluate : 4.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 562 ASP Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 594 ASP Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 636 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 685 LEU Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 117 HIS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 269 LYS Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain F residue 642 VAL Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain T residue 117 LEU Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 400 HIS Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 443 VAL Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 577 ASN Chi-restraints excluded: chain T residue 587 TYR Chi-restraints excluded: chain T residue 590 LEU Chi-restraints excluded: chain T residue 603 VAL Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 709 VAL Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 739 ILE Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 778 ASN Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 789 ASN Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 938 ASN Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 964 THR Chi-restraints excluded: chain T residue 973 ASP Chi-restraints excluded: chain T residue 979 ASP Chi-restraints excluded: chain T residue 1062 ASP Chi-restraints excluded: chain T residue 1086 VAL Chi-restraints excluded: chain T residue 1117 THR Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1200 LEU Chi-restraints excluded: chain T residue 1235 TYR Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1473 LEU Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1534 VAL Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1590 SER Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1676 MET Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 1860 PHE Chi-restraints excluded: chain T residue 1872 ILE Chi-restraints excluded: chain T residue 1904 SER Chi-restraints excluded: chain T residue 1952 VAL Chi-restraints excluded: chain T residue 2025 HIS Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2250 THR Chi-restraints excluded: chain T residue 2263 LEU Chi-restraints excluded: chain T residue 2265 MET Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2360 ILE Chi-restraints excluded: chain T residue 2384 ILE Chi-restraints excluded: chain T residue 2414 VAL Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2436 MET Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2552 ASP Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2567 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2600 THR Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2642 SER Chi-restraints excluded: chain T residue 2656 GLU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2700 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2709 VAL Chi-restraints excluded: chain T residue 2734 ILE Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2760 LEU Chi-restraints excluded: chain T residue 2796 THR Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2957 HIS Chi-restraints excluded: chain T residue 2961 ASP Chi-restraints excluded: chain T residue 2999 LEU Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3091 LEU Chi-restraints excluded: chain T residue 3111 ASP Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3137 ILE Chi-restraints excluded: chain T residue 3156 LEU Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3352 ILE Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3462 VAL Chi-restraints excluded: chain T residue 3465 THR Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3511 VAL Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3519 THR Chi-restraints excluded: chain T residue 3563 MET Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3581 VAL Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3648 ILE Chi-restraints excluded: chain T residue 3712 THR Chi-restraints excluded: chain T residue 3720 ILE Chi-restraints excluded: chain T residue 3738 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 439 optimal weight: 9.9990 chunk 462 optimal weight: 0.8980 chunk 422 optimal weight: 2.9990 chunk 449 optimal weight: 1.9990 chunk 270 optimal weight: 0.9990 chunk 196 optimal weight: 0.5980 chunk 353 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 406 optimal weight: 0.9990 chunk 425 optimal weight: 1.9990 chunk 448 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 889 GLN ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41845 Z= 0.191 Angle : 0.753 16.380 56664 Z= 0.365 Chirality : 0.044 0.295 6396 Planarity : 0.005 0.080 7199 Dihedral : 5.854 58.869 5491 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.24 % Favored : 90.72 % Rotamer: Outliers : 3.33 % Allowed : 24.94 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.12), residues: 4978 helix: 0.36 (0.10), residues: 2916 sheet: -1.51 (0.36), residues: 193 loop : -2.78 (0.14), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP T2179 HIS 0.030 0.001 HIS T2010 PHE 0.052 0.002 PHE T1767 TYR 0.031 0.001 TYR T2316 ARG 0.026 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 523 time to evaluate : 5.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8891 (mmm) cc_final: 0.8373 (tpp) REVERT: A 190 MET cc_start: 0.9557 (ttm) cc_final: 0.9161 (tmm) REVERT: A 227 MET cc_start: 0.9218 (mmm) cc_final: 0.8951 (mmm) REVERT: A 305 MET cc_start: 0.8974 (mpp) cc_final: 0.8550 (mpp) REVERT: A 361 GLU cc_start: 0.9441 (tp30) cc_final: 0.9058 (tp30) REVERT: B 82 ASP cc_start: 0.8681 (m-30) cc_final: 0.8316 (m-30) REVERT: B 98 LEU cc_start: 0.9552 (mt) cc_final: 0.9129 (mt) REVERT: B 444 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.8327 (m170) REVERT: D 45 CYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8874 (t) REVERT: D 369 MET cc_start: 0.9016 (tpt) cc_final: 0.8794 (tpt) REVERT: D 375 GLU cc_start: 0.8740 (mm-30) cc_final: 0.6868 (mm-30) REVERT: D 536 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6949 (mmmt) REVERT: D 609 GLU cc_start: 0.9128 (tp30) cc_final: 0.8567 (tm-30) REVERT: D 656 GLN cc_start: 0.9093 (tp-100) cc_final: 0.8498 (tm-30) REVERT: D 657 GLU cc_start: 0.9444 (tt0) cc_final: 0.8993 (tm-30) REVERT: D 658 LEU cc_start: 0.9717 (tt) cc_final: 0.9481 (tp) REVERT: E 266 MET cc_start: 0.8581 (mtm) cc_final: 0.8359 (mtm) REVERT: E 302 GLN cc_start: 0.9356 (tp-100) cc_final: 0.9090 (tt0) REVERT: F 530 GLU cc_start: 0.9290 (mm-30) cc_final: 0.9076 (mm-30) REVERT: F 549 MET cc_start: 0.8706 (mmm) cc_final: 0.8408 (mtt) REVERT: F 586 LYS cc_start: 0.8179 (mppt) cc_final: 0.7845 (mmtm) REVERT: F 621 ASP cc_start: 0.8900 (t0) cc_final: 0.8654 (t0) REVERT: F 625 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7055 (pm20) REVERT: T 35 MET cc_start: 0.5094 (ttp) cc_final: 0.4785 (ttp) REVERT: T 83 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8173 (t80) REVERT: T 477 THR cc_start: 0.9658 (p) cc_final: 0.9222 (p) REVERT: T 480 ARG cc_start: 0.9531 (mtt180) cc_final: 0.9167 (mpp80) REVERT: T 570 LEU cc_start: 0.8854 (pt) cc_final: 0.8652 (pt) REVERT: T 683 MET cc_start: 0.8970 (ptp) cc_final: 0.8594 (ptp) REVERT: T 704 GLN cc_start: 0.9040 (pt0) cc_final: 0.8632 (tp40) REVERT: T 711 GLU cc_start: 0.9712 (tp30) cc_final: 0.9397 (tp30) REVERT: T 749 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8590 (tppt) REVERT: T 771 MET cc_start: 0.8637 (mmt) cc_final: 0.8410 (tmm) REVERT: T 775 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.7564 (pp) REVERT: T 836 GLN cc_start: 0.9528 (mm110) cc_final: 0.8960 (tm-30) REVERT: T 965 ASP cc_start: 0.8986 (p0) cc_final: 0.8702 (p0) REVERT: T 1077 ASN cc_start: 0.9342 (m-40) cc_final: 0.9126 (t0) REVERT: T 1084 GLU cc_start: 0.8638 (pp20) cc_final: 0.8343 (pp20) REVERT: T 1100 MET cc_start: 0.9294 (tpp) cc_final: 0.9048 (tpp) REVERT: T 1130 ASN cc_start: 0.8299 (t0) cc_final: 0.8043 (t0) REVERT: T 1133 LEU cc_start: 0.9135 (tp) cc_final: 0.8647 (tp) REVERT: T 1246 LYS cc_start: 0.9625 (mtmt) cc_final: 0.9390 (mtpp) REVERT: T 1248 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7666 (p) REVERT: T 1266 ASP cc_start: 0.9435 (m-30) cc_final: 0.9214 (m-30) REVERT: T 1487 MET cc_start: 0.6184 (mmp) cc_final: 0.5749 (ptt) REVERT: T 1565 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6574 (pt0) REVERT: T 1760 TYR cc_start: 0.8087 (m-80) cc_final: 0.7375 (m-80) REVERT: T 1789 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.9108 (t80) REVERT: T 1813 TYR cc_start: 0.9316 (t80) cc_final: 0.9017 (t80) REVERT: T 1957 MET cc_start: 0.7170 (ppp) cc_final: 0.6837 (ppp) REVERT: T 1969 TRP cc_start: 0.8562 (m100) cc_final: 0.8362 (m100) REVERT: T 2215 LYS cc_start: 0.8653 (mttt) cc_final: 0.8418 (mtmt) REVERT: T 2279 MET cc_start: 0.9670 (mmm) cc_final: 0.9290 (mmm) REVERT: T 2316 TYR cc_start: 0.8858 (m-80) cc_final: 0.8620 (m-80) REVERT: T 2344 MET cc_start: 0.8388 (mmm) cc_final: 0.8048 (mpp) REVERT: T 2416 MET cc_start: 0.7420 (mpp) cc_final: 0.6858 (mpp) REVERT: T 2605 MET cc_start: 0.7824 (mtm) cc_final: 0.7429 (mtm) REVERT: T 2624 LYS cc_start: 0.8787 (mmmm) cc_final: 0.8456 (mmmm) REVERT: T 2692 LEU cc_start: 0.9163 (mt) cc_final: 0.8850 (tt) REVERT: T 2704 GLN cc_start: 0.9385 (OUTLIER) cc_final: 0.8575 (tm-30) REVERT: T 2731 ASP cc_start: 0.8800 (m-30) cc_final: 0.8577 (m-30) REVERT: T 2744 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.8167 (t0) REVERT: T 2773 ARG cc_start: 0.9027 (ptm160) cc_final: 0.8487 (ttp80) REVERT: T 2792 GLN cc_start: 0.9375 (tt0) cc_final: 0.8963 (tt0) REVERT: T 2852 PHE cc_start: 0.8884 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: T 2897 MET cc_start: 0.8416 (ttm) cc_final: 0.8182 (ttm) REVERT: T 2957 HIS cc_start: 0.9468 (OUTLIER) cc_final: 0.8973 (t-90) REVERT: T 3022 PHE cc_start: 0.9043 (m-10) cc_final: 0.8700 (m-80) REVERT: T 3091 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9288 (tt) REVERT: T 3576 LYS cc_start: 0.9307 (mtmt) cc_final: 0.9047 (mtmm) outliers start: 152 outliers final: 115 residues processed: 633 average time/residue: 0.5284 time to fit residues: 569.6227 Evaluate side-chains 617 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 488 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 373 PHE Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 597 PHE Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 627 LEU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain T residue 117 LEU Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 587 TYR Chi-restraints excluded: chain T residue 590 LEU Chi-restraints excluded: chain T residue 603 VAL Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 714 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 739 ILE Chi-restraints excluded: chain T residue 758 THR Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 778 ASN Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 856 GLU Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 964 THR Chi-restraints excluded: chain T residue 967 THR Chi-restraints excluded: chain T residue 979 ASP Chi-restraints excluded: chain T residue 1062 ASP Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1144 LEU Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1329 SER Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1473 LEU Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1534 VAL Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1789 PHE Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2384 ILE Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2436 MET Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2667 VAL Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2679 TRP Chi-restraints excluded: chain T residue 2700 TRP Chi-restraints excluded: chain T residue 2704 GLN Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2744 ASP Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2957 HIS Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3091 LEU Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3519 THR Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3720 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 295 optimal weight: 30.0000 chunk 475 optimal weight: 2.9990 chunk 290 optimal weight: 20.0000 chunk 225 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 499 optimal weight: 2.9990 chunk 459 optimal weight: 6.9990 chunk 397 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 chunk 307 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS D 644 ASN ** D 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T1239 ASN ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T3644 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 41845 Z= 0.271 Angle : 0.777 15.619 56664 Z= 0.380 Chirality : 0.045 0.326 6396 Planarity : 0.005 0.082 7199 Dihedral : 5.873 59.567 5491 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.06 % Favored : 89.92 % Rotamer: Outliers : 3.13 % Allowed : 25.22 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.12), residues: 4978 helix: 0.37 (0.10), residues: 2916 sheet: -1.61 (0.37), residues: 181 loop : -2.78 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP T2179 HIS 0.031 0.001 HIS T2010 PHE 0.053 0.002 PHE T1767 TYR 0.035 0.002 TYR T1235 ARG 0.014 0.000 ARG T3689 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9956 Ramachandran restraints generated. 4978 Oldfield, 0 Emsley, 4978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 481 time to evaluate : 5.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8860 (mmm) cc_final: 0.8349 (tpp) REVERT: A 190 MET cc_start: 0.9551 (ttm) cc_final: 0.9159 (tmm) REVERT: A 227 MET cc_start: 0.9229 (mmm) cc_final: 0.8950 (mmm) REVERT: A 305 MET cc_start: 0.8988 (mpp) cc_final: 0.8574 (mpp) REVERT: B 82 ASP cc_start: 0.8751 (m-30) cc_final: 0.8371 (m-30) REVERT: B 98 LEU cc_start: 0.9576 (mt) cc_final: 0.9119 (mt) REVERT: B 425 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8988 (tpp) REVERT: B 444 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.8336 (m170) REVERT: D 45 CYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8955 (t) REVERT: D 536 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.7105 (mmmt) REVERT: D 656 GLN cc_start: 0.9168 (tp-100) cc_final: 0.8605 (tm-30) REVERT: D 657 GLU cc_start: 0.9444 (tt0) cc_final: 0.9016 (tm-30) REVERT: D 676 MET cc_start: 0.8461 (mmm) cc_final: 0.7998 (mmm) REVERT: E 302 GLN cc_start: 0.9384 (tp-100) cc_final: 0.9182 (tp-100) REVERT: F 530 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9059 (mm-30) REVERT: F 549 MET cc_start: 0.8702 (mmm) cc_final: 0.8399 (mtt) REVERT: F 621 ASP cc_start: 0.8954 (t0) cc_final: 0.8567 (t0) REVERT: F 625 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: T 35 MET cc_start: 0.5208 (ttp) cc_final: 0.4818 (ttp) REVERT: T 83 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8173 (t80) REVERT: T 390 LEU cc_start: 0.9219 (mm) cc_final: 0.8879 (pp) REVERT: T 480 ARG cc_start: 0.9518 (mtt180) cc_final: 0.9158 (mpp80) REVERT: T 570 LEU cc_start: 0.8858 (pt) cc_final: 0.8655 (pt) REVERT: T 683 MET cc_start: 0.8987 (ptp) cc_final: 0.8618 (ptp) REVERT: T 691 MET cc_start: 0.9233 (mmm) cc_final: 0.8892 (mtp) REVERT: T 704 GLN cc_start: 0.9074 (pt0) cc_final: 0.8695 (tp40) REVERT: T 711 GLU cc_start: 0.9725 (tp30) cc_final: 0.9402 (tp30) REVERT: T 749 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8590 (tppt) REVERT: T 771 MET cc_start: 0.8659 (mmt) cc_final: 0.8397 (tmm) REVERT: T 775 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.7679 (pp) REVERT: T 836 GLN cc_start: 0.9566 (mm110) cc_final: 0.8974 (tm-30) REVERT: T 959 PHE cc_start: 0.8518 (p90) cc_final: 0.8308 (p90) REVERT: T 965 ASP cc_start: 0.9003 (p0) cc_final: 0.8730 (p0) REVERT: T 1084 GLU cc_start: 0.8711 (pp20) cc_final: 0.8413 (pp20) REVERT: T 1100 MET cc_start: 0.9333 (tpp) cc_final: 0.9087 (tpp) REVERT: T 1130 ASN cc_start: 0.8351 (t0) cc_final: 0.8076 (t0) REVERT: T 1133 LEU cc_start: 0.9180 (tp) cc_final: 0.8694 (tp) REVERT: T 1246 LYS cc_start: 0.9628 (mtmt) cc_final: 0.9404 (mtpp) REVERT: T 1248 THR cc_start: 0.7942 (OUTLIER) cc_final: 0.7705 (p) REVERT: T 1266 ASP cc_start: 0.9422 (m-30) cc_final: 0.9194 (m-30) REVERT: T 1448 MET cc_start: 0.7740 (mmm) cc_final: 0.7534 (mmp) REVERT: T 1487 MET cc_start: 0.6212 (mmp) cc_final: 0.5753 (ptt) REVERT: T 1565 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: T 1760 TYR cc_start: 0.8100 (m-80) cc_final: 0.7400 (m-80) REVERT: T 1813 TYR cc_start: 0.9332 (t80) cc_final: 0.9034 (t80) REVERT: T 1957 MET cc_start: 0.7221 (ppp) cc_final: 0.6914 (ppp) REVERT: T 1969 TRP cc_start: 0.8599 (m100) cc_final: 0.8389 (m100) REVERT: T 2279 MET cc_start: 0.9677 (mmm) cc_final: 0.9294 (mmm) REVERT: T 2316 TYR cc_start: 0.8893 (m-80) cc_final: 0.8660 (m-80) REVERT: T 2344 MET cc_start: 0.8461 (mmm) cc_final: 0.8137 (mpp) REVERT: T 2416 MET cc_start: 0.7500 (mpp) cc_final: 0.6857 (mpp) REVERT: T 2605 MET cc_start: 0.7942 (mtm) cc_final: 0.7461 (mtm) REVERT: T 2624 LYS cc_start: 0.8872 (mmmm) cc_final: 0.8539 (mmmm) REVERT: T 2731 ASP cc_start: 0.8824 (m-30) cc_final: 0.8512 (m-30) REVERT: T 2744 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8240 (t0) REVERT: T 2773 ARG cc_start: 0.9053 (ptm160) cc_final: 0.8515 (ttp80) REVERT: T 2852 PHE cc_start: 0.8969 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: T 2897 MET cc_start: 0.8420 (ttm) cc_final: 0.8192 (ttm) REVERT: T 2957 HIS cc_start: 0.9484 (OUTLIER) cc_final: 0.9013 (t-90) REVERT: T 3022 PHE cc_start: 0.9041 (m-10) cc_final: 0.8631 (m-80) outliers start: 143 outliers final: 122 residues processed: 583 average time/residue: 0.5108 time to fit residues: 511.7036 Evaluate side-chains 610 residues out of total 4598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 476 time to evaluate : 4.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 280 PHE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain B residue 444 HIS Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 469 TRP Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 80 PHE Chi-restraints excluded: chain D residue 292 TYR Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 536 LYS Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 567 ASN Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 619 ARG Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain D residue 752 HIS Chi-restraints excluded: chain D residue 755 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 173 PHE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain F residue 540 ASP Chi-restraints excluded: chain F residue 550 SER Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 625 GLU Chi-restraints excluded: chain F residue 629 ILE Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain T residue 117 LEU Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 296 LEU Chi-restraints excluded: chain T residue 310 ILE Chi-restraints excluded: chain T residue 398 PHE Chi-restraints excluded: chain T residue 440 LEU Chi-restraints excluded: chain T residue 467 ILE Chi-restraints excluded: chain T residue 563 ILE Chi-restraints excluded: chain T residue 571 LEU Chi-restraints excluded: chain T residue 574 THR Chi-restraints excluded: chain T residue 587 TYR Chi-restraints excluded: chain T residue 590 LEU Chi-restraints excluded: chain T residue 603 VAL Chi-restraints excluded: chain T residue 637 LEU Chi-restraints excluded: chain T residue 727 LEU Chi-restraints excluded: chain T residue 732 THR Chi-restraints excluded: chain T residue 739 ILE Chi-restraints excluded: chain T residue 765 LEU Chi-restraints excluded: chain T residue 775 LEU Chi-restraints excluded: chain T residue 778 ASN Chi-restraints excluded: chain T residue 783 VAL Chi-restraints excluded: chain T residue 789 ASN Chi-restraints excluded: chain T residue 834 ILE Chi-restraints excluded: chain T residue 856 GLU Chi-restraints excluded: chain T residue 924 VAL Chi-restraints excluded: chain T residue 938 ASN Chi-restraints excluded: chain T residue 949 LEU Chi-restraints excluded: chain T residue 964 THR Chi-restraints excluded: chain T residue 979 ASP Chi-restraints excluded: chain T residue 1062 ASP Chi-restraints excluded: chain T residue 1131 ILE Chi-restraints excluded: chain T residue 1132 ASP Chi-restraints excluded: chain T residue 1248 THR Chi-restraints excluded: chain T residue 1263 LEU Chi-restraints excluded: chain T residue 1275 VAL Chi-restraints excluded: chain T residue 1284 VAL Chi-restraints excluded: chain T residue 1295 GLU Chi-restraints excluded: chain T residue 1348 THR Chi-restraints excluded: chain T residue 1473 LEU Chi-restraints excluded: chain T residue 1522 LEU Chi-restraints excluded: chain T residue 1534 VAL Chi-restraints excluded: chain T residue 1565 GLN Chi-restraints excluded: chain T residue 1616 THR Chi-restraints excluded: chain T residue 1676 MET Chi-restraints excluded: chain T residue 1716 LEU Chi-restraints excluded: chain T residue 1796 LEU Chi-restraints excluded: chain T residue 2092 LEU Chi-restraints excluded: chain T residue 2103 TYR Chi-restraints excluded: chain T residue 2194 CYS Chi-restraints excluded: chain T residue 2201 ASP Chi-restraints excluded: chain T residue 2212 VAL Chi-restraints excluded: chain T residue 2224 VAL Chi-restraints excluded: chain T residue 2240 THR Chi-restraints excluded: chain T residue 2263 LEU Chi-restraints excluded: chain T residue 2276 THR Chi-restraints excluded: chain T residue 2305 ARG Chi-restraints excluded: chain T residue 2360 ILE Chi-restraints excluded: chain T residue 2384 ILE Chi-restraints excluded: chain T residue 2427 GLU Chi-restraints excluded: chain T residue 2436 MET Chi-restraints excluded: chain T residue 2443 LEU Chi-restraints excluded: chain T residue 2469 LEU Chi-restraints excluded: chain T residue 2556 ILE Chi-restraints excluded: chain T residue 2561 VAL Chi-restraints excluded: chain T residue 2599 ARG Chi-restraints excluded: chain T residue 2602 VAL Chi-restraints excluded: chain T residue 2604 ASN Chi-restraints excluded: chain T residue 2607 LEU Chi-restraints excluded: chain T residue 2618 LEU Chi-restraints excluded: chain T residue 2656 GLU Chi-restraints excluded: chain T residue 2673 ASP Chi-restraints excluded: chain T residue 2700 TRP Chi-restraints excluded: chain T residue 2706 LEU Chi-restraints excluded: chain T residue 2741 GLN Chi-restraints excluded: chain T residue 2744 ASP Chi-restraints excluded: chain T residue 2852 PHE Chi-restraints excluded: chain T residue 2900 ASP Chi-restraints excluded: chain T residue 2957 HIS Chi-restraints excluded: chain T residue 2999 LEU Chi-restraints excluded: chain T residue 3009 THR Chi-restraints excluded: chain T residue 3012 VAL Chi-restraints excluded: chain T residue 3068 LEU Chi-restraints excluded: chain T residue 3111 ASP Chi-restraints excluded: chain T residue 3128 ILE Chi-restraints excluded: chain T residue 3219 TYR Chi-restraints excluded: chain T residue 3222 LEU Chi-restraints excluded: chain T residue 3364 ASN Chi-restraints excluded: chain T residue 3365 ASN Chi-restraints excluded: chain T residue 3366 VAL Chi-restraints excluded: chain T residue 3378 VAL Chi-restraints excluded: chain T residue 3462 VAL Chi-restraints excluded: chain T residue 3466 THR Chi-restraints excluded: chain T residue 3517 ILE Chi-restraints excluded: chain T residue 3519 THR Chi-restraints excluded: chain T residue 3564 ILE Chi-restraints excluded: chain T residue 3618 GLU Chi-restraints excluded: chain T residue 3631 LEU Chi-restraints excluded: chain T residue 3645 LEU Chi-restraints excluded: chain T residue 3720 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 315 optimal weight: 20.0000 chunk 423 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 398 optimal weight: 1.9990 chunk 166 optimal weight: 50.0000 chunk 408 optimal weight: 9.9990 chunk 50 optimal weight: 0.4980 chunk 73 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1700 ASN ** T1805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T1944 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T1987 GLN ** T2237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3010 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3064 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3580 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T3629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.091914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063249 restraints weight = 172053.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065035 restraints weight = 98712.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066051 restraints weight = 62693.888| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 41845 Z= 0.208 Angle : 0.772 15.848 56664 Z= 0.373 Chirality : 0.045 0.324 6396 Planarity : 0.005 0.076 7199 Dihedral : 5.763 57.506 5491 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.10 % Favored : 90.88 % Rotamer: Outliers : 2.93 % Allowed : 25.66 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.91 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.12), residues: 4978 helix: 0.40 (0.10), residues: 2911 sheet: -1.42 (0.36), residues: 193 loop : -2.72 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP T2179 HIS 0.032 0.001 HIS T2010 PHE 0.065 0.002 PHE T2235 TYR 0.033 0.001 TYR T1235 ARG 0.011 0.000 ARG D 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10264.17 seconds wall clock time: 187 minutes 42.88 seconds (11262.88 seconds total)