Starting phenix.real_space_refine on Thu Mar 21 19:51:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6p_11102/03_2024/6z6p_11102.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6p_11102/03_2024/6z6p_11102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6p_11102/03_2024/6z6p_11102.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6p_11102/03_2024/6z6p_11102.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6p_11102/03_2024/6z6p_11102.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z6p_11102/03_2024/6z6p_11102.pdb" } resolution = 4.43 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= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 288 5.49 5 S 100 5.16 5 C 18784 2.51 5 N 5486 2.21 5 O 6455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "K ASP 113": "OD1" <-> "OD2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K GLU 153": "OE1" <-> "OE2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 190": "OE1" <-> "OE2" Residue "K ARG 201": "NH1" <-> "NH2" Residue "K ASP 243": "OD1" <-> "OD2" Residue "K TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 404": "OD1" <-> "OD2" Residue "K ASP 418": "OD1" <-> "OD2" Residue "K TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 543": "OD1" <-> "OD2" Residue "K PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 635": "OD1" <-> "OD2" Residue "K TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 685": "OE1" <-> "OE2" Residue "K GLU 689": "OE1" <-> "OE2" Residue "K PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 105": "OD1" <-> "OD2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 175": "NH1" <-> "NH2" Residue "L GLU 183": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 234": "OE1" <-> "OE2" Residue "L PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 289": "OE1" <-> "OE2" Residue "L GLU 310": "OE1" <-> "OE2" Residue "L TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 404": "OD1" <-> "OD2" Residue "L GLU 444": "OE1" <-> "OE2" Residue "L PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 487": "OD1" <-> "OD2" Residue "L ASP 511": "OD1" <-> "OD2" Residue "L ASP 543": "OD1" <-> "OD2" Residue "L PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 561": "OD1" <-> "OD2" Residue "L TYR 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 640": "OE1" <-> "OE2" Residue "L ASP 676": "OD1" <-> "OD2" Residue "L ARG 687": "NH1" <-> "NH2" Residue "L PHE 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 43": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 128": "OE1" <-> "OE2" Residue "M TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 147": "OE1" <-> "OE2" Residue "M ASP 210": "OD1" <-> "OD2" Residue "M TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 297": "OE1" <-> "OE2" Residue "M GLU 323": "OE1" <-> "OE2" Residue "M PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 431": "OD1" <-> "OD2" Residue "M TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 460": "OD1" <-> "OD2" Residue "M GLU 466": "OE1" <-> "OE2" Residue "M GLU 468": "OE1" <-> "OE2" Residue "M GLU 476": "OE1" <-> "OE2" Residue "M GLU 483": "OE1" <-> "OE2" Residue "M GLU 487": "OE1" <-> "OE2" Residue "M GLU 503": "OE1" <-> "OE2" Residue "M ASP 531": "OD1" <-> "OD2" Residue "M GLU 532": "OE1" <-> "OE2" Residue "M ARG 543": "NH1" <-> "NH2" Residue "M ASP 544": "OD1" <-> "OD2" Residue "M TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 559": "OD1" <-> "OD2" Residue "M GLU 563": "OE1" <-> "OE2" Residue "M GLU 587": "OE1" <-> "OE2" Residue "M GLU 598": "OE1" <-> "OE2" Residue "N ASP 24": "OD1" <-> "OD2" Residue "N ASP 78": "OD1" <-> "OD2" Residue "N ASP 93": "OD1" <-> "OD2" Residue "N GLU 107": "OE1" <-> "OE2" Residue "N TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 217": "OD1" <-> "OD2" Residue "N TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 259": "OD1" <-> "OD2" Residue "N PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 329": "OE1" <-> "OE2" Residue "N GLU 362": "OE1" <-> "OE2" Residue "N PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 420": "OE1" <-> "OE2" Residue "N ASP 431": "OD1" <-> "OD2" Residue "N ASP 434": "OD1" <-> "OD2" Residue "N GLU 450": "OE1" <-> "OE2" Residue "N ASP 458": "OD1" <-> "OD2" Residue "N ASP 541": "OD1" <-> "OD2" Residue "N GLU 566": "OE1" <-> "OE2" Residue "N GLU 580": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31115 Number of models: 1 Model: "" Number of chains: 16 Chain: "K" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5178 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 615} Chain breaks: 2 Chain: "L" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5245 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "M" Number of atoms: 4376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4376 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 16, 'TRANS': 517} Chain breaks: 3 Chain: "N" Number of atoms: 4416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4416 Classifications: {'peptide': 541} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 520} Chain breaks: 6 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.02, per 1000 atoms: 0.51 Number of scatterers: 31115 At special positions: 0 Unit cell: (127.68, 149.811, 264.723, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 100 16.00 P 288 15.00 O 6455 8.00 N 5486 7.00 C 18784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 359 " - pdb=" SG CYS N 366 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 13.83 Conformation dependent library (CDL) restraints added in 4.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 801 " pdb="ZN ZN K 801 " - pdb=" NE2 HIS K 205 " pdb=" ZN L 801 " pdb="ZN ZN L 801 " - pdb=" ND1 HIS L 247 " 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5950 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 13 sheets defined 54.0% alpha, 5.7% beta 126 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 12.04 Creating SS restraints... Processing helix chain 'K' and resid 76 through 81 removed outlier: 3.797A pdb=" N ILE K 80 " --> pdb=" O TYR K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 99 removed outlier: 4.098A pdb=" N ARG K 92 " --> pdb=" O ARG K 88 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE K 93 " --> pdb=" O ARG K 89 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA K 98 " --> pdb=" O TYR K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 134 Processing helix chain 'K' and resid 136 through 146 removed outlier: 3.619A pdb=" N THR K 146 " --> pdb=" O PHE K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 161 removed outlier: 3.653A pdb=" N LEU K 154 " --> pdb=" O SER K 150 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 190 removed outlier: 3.546A pdb=" N ARG K 175 " --> pdb=" O TYR K 171 " (cutoff:3.500A) Proline residue: K 177 - end of helix removed outlier: 3.787A pdb=" N ALA K 187 " --> pdb=" O GLU K 183 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU K 190 " --> pdb=" O LYS K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 232 removed outlier: 3.750A pdb=" N LEU K 229 " --> pdb=" O ALA K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 254 removed outlier: 4.214A pdb=" N LYS K 254 " --> pdb=" O ASN K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 257 No H-bonds generated for 'chain 'K' and resid 255 through 257' Processing helix chain 'K' and resid 289 through 293 removed outlier: 3.566A pdb=" N GLU K 293 " --> pdb=" O GLY K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 326 removed outlier: 3.903A pdb=" N TYR K 311 " --> pdb=" O GLY K 307 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N MET K 320 " --> pdb=" O GLU K 316 " (cutoff:3.500A) Proline residue: K 321 - end of helix Processing helix chain 'K' and resid 351 through 366 removed outlier: 3.692A pdb=" N TYR K 355 " --> pdb=" O THR K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 396 removed outlier: 4.238A pdb=" N ARG K 385 " --> pdb=" O ASP K 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER K 386 " --> pdb=" O ALA K 382 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS K 392 " --> pdb=" O LEU K 388 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL K 393 " --> pdb=" O SER K 389 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 415 removed outlier: 3.764A pdb=" N ILE K 414 " --> pdb=" O LYS K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 428 Processing helix chain 'K' and resid 429 through 432 Processing helix chain 'K' and resid 458 through 472 removed outlier: 3.686A pdb=" N ARG K 462 " --> pdb=" O GLN K 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 534 through 544 removed outlier: 3.565A pdb=" N ILE K 538 " --> pdb=" O SER K 534 " (cutoff:3.500A) Processing helix chain 'K' and resid 562 through 578 Processing helix chain 'K' and resid 598 through 607 removed outlier: 4.270A pdb=" N ILE K 602 " --> pdb=" O SER K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 645 Processing helix chain 'K' and resid 679 through 687 removed outlier: 3.591A pdb=" N ILE K 683 " --> pdb=" O GLY K 679 " (cutoff:3.500A) Processing helix chain 'K' and resid 687 through 699 removed outlier: 4.039A pdb=" N LEU K 696 " --> pdb=" O THR K 692 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 68 removed outlier: 3.506A pdb=" N MET L 66 " --> pdb=" O ASP L 63 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR L 68 " --> pdb=" O ARG L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 100 removed outlier: 3.645A pdb=" N ASN L 100 " --> pdb=" O ILE L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 Processing helix chain 'L' and resid 136 through 147 removed outlier: 3.604A pdb=" N LEU L 140 " --> pdb=" O THR L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 161 Processing helix chain 'L' and resid 170 through 184 removed outlier: 3.972A pdb=" N ARG L 175 " --> pdb=" O TYR L 171 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU L 176 " --> pdb=" O ALA L 172 " (cutoff:3.500A) Proline residue: L 177 - end of helix Processing helix chain 'L' and resid 184 through 191 removed outlier: 3.686A pdb=" N VAL L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 226 Processing helix chain 'L' and resid 226 through 232 Processing helix chain 'L' and resid 249 through 254 removed outlier: 3.622A pdb=" N LYS L 254 " --> pdb=" O ASN L 250 " (cutoff:3.500A) Processing helix chain 'L' and resid 271 through 274 removed outlier: 3.687A pdb=" N LYS L 274 " --> pdb=" O GLU L 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 271 through 274' Processing helix chain 'L' and resid 307 through 318 removed outlier: 3.864A pdb=" N TYR L 311 " --> pdb=" O GLY L 307 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU L 316 " --> pdb=" O MET L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 318 through 327 removed outlier: 3.539A pdb=" N MET L 322 " --> pdb=" O VAL L 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 340 No H-bonds generated for 'chain 'L' and resid 338 through 340' Processing helix chain 'L' and resid 351 through 361 removed outlier: 3.534A pdb=" N TYR L 355 " --> pdb=" O THR L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 381 through 395 Processing helix chain 'L' and resid 410 through 421 removed outlier: 3.864A pdb=" N ILE L 414 " --> pdb=" O LYS L 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 422 through 427 removed outlier: 3.741A pdb=" N SER L 425 " --> pdb=" O ARG L 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 456 through 474 removed outlier: 3.575A pdb=" N ALA L 460 " --> pdb=" O PRO L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 532 through 543 removed outlier: 3.932A pdb=" N ASP L 536 " --> pdb=" O ASP L 532 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE L 537 " --> pdb=" O ASN L 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 580 Processing helix chain 'L' and resid 581 through 584 removed outlier: 3.768A pdb=" N PHE L 584 " --> pdb=" O ILE L 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 581 through 584' Processing helix chain 'L' and resid 599 through 609 Processing helix chain 'L' and resid 637 through 645 Processing helix chain 'L' and resid 681 through 699 removed outlier: 5.151A pdb=" N GLU L 689 " --> pdb=" O GLU L 685 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU L 690 " --> pdb=" O GLU L 686 " (cutoff:3.500A) Processing helix chain 'M' and resid 38 through 43 Processing helix chain 'M' and resid 44 through 52 removed outlier: 3.762A pdb=" N HIS M 52 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 61 removed outlier: 4.172A pdb=" N ARG M 58 " --> pdb=" O SER M 54 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR M 59 " --> pdb=" O ASP M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 87 removed outlier: 3.950A pdb=" N SER M 82 " --> pdb=" O CYS M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 91 Processing helix chain 'M' and resid 104 through 113 Processing helix chain 'M' and resid 114 through 124 removed outlier: 3.647A pdb=" N ASP M 121 " --> pdb=" O SER M 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 150 removed outlier: 3.737A pdb=" N LEU M 146 " --> pdb=" O THR M 142 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 150 " --> pdb=" O LEU M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 221 removed outlier: 3.946A pdb=" N GLN M 217 " --> pdb=" O GLN M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 255 removed outlier: 3.517A pdb=" N CYS M 247 " --> pdb=" O SER M 243 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS M 253 " --> pdb=" O LEU M 249 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS M 254 " --> pdb=" O PHE M 250 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 275 removed outlier: 4.012A pdb=" N VAL M 271 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE M 272 " --> pdb=" O ALA M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 289 Processing helix chain 'M' and resid 295 through 300 Processing helix chain 'M' and resid 318 through 328 Processing helix chain 'M' and resid 405 through 441 removed outlier: 4.491A pdb=" N ASN M 409 " --> pdb=" O SER M 405 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS M 419 " --> pdb=" O GLY M 415 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS M 420 " --> pdb=" O ILE M 416 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU M 427 " --> pdb=" O GLN M 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 449 through 465 removed outlier: 4.341A pdb=" N ASN M 458 " --> pdb=" O LYS M 454 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP M 460 " --> pdb=" O PHE M 456 " (cutoff:3.500A) Processing helix chain 'M' and resid 466 through 515 removed outlier: 3.877A pdb=" N ASN M 474 " --> pdb=" O VAL M 470 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN M 475 " --> pdb=" O LEU M 471 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS M 482 " --> pdb=" O LEU M 478 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN M 489 " --> pdb=" O GLU M 485 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE M 495 " --> pdb=" O LYS M 491 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY M 513 " --> pdb=" O LEU M 509 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU M 514 " --> pdb=" O MET M 510 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR M 515 " --> pdb=" O ALA M 511 " (cutoff:3.500A) Processing helix chain 'M' and resid 525 through 631 removed outlier: 4.181A pdb=" N THR M 545 " --> pdb=" O VAL M 541 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N GLU M 546 " --> pdb=" O SER M 542 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU M 571 " --> pdb=" O GLU M 567 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU M 584 " --> pdb=" O SER M 580 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE M 591 " --> pdb=" O GLU M 587 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU M 596 " --> pdb=" O SER M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 634 through 639 Processing helix chain 'N' and resid 20 through 34 removed outlier: 4.026A pdb=" N LEU N 25 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N SER N 26 " --> pdb=" O GLN N 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU N 27 " --> pdb=" O LYS N 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS N 33 " --> pdb=" O LEU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 35 through 42 Processing helix chain 'N' and resid 69 through 86 removed outlier: 3.966A pdb=" N ILE N 84 " --> pdb=" O ASN N 80 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN N 86 " --> pdb=" O ARG N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.685A pdb=" N LEU N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 103 removed outlier: 3.696A pdb=" N ARG N 102 " --> pdb=" O GLN N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 110 Processing helix chain 'N' and resid 113 through 128 removed outlier: 3.690A pdb=" N GLN N 117 " --> pdb=" O SER N 113 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU N 119 " --> pdb=" O LYS N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 147 through 154 removed outlier: 3.785A pdb=" N LEU N 151 " --> pdb=" O SER N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 155 through 159 removed outlier: 3.653A pdb=" N ILE N 158 " --> pdb=" O GLU N 155 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU N 159 " --> pdb=" O GLY N 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 155 through 159' Processing helix chain 'N' and resid 221 through 228 removed outlier: 3.719A pdb=" N LYS N 228 " --> pdb=" O LYS N 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 249 Processing helix chain 'N' and resid 272 through 280 removed outlier: 4.386A pdb=" N ASN N 280 " --> pdb=" O GLN N 276 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 307 Processing helix chain 'N' and resid 326 through 341 Processing helix chain 'N' and resid 354 through 362 Processing helix chain 'N' and resid 415 through 437 removed outlier: 4.269A pdb=" N HIS N 423 " --> pdb=" O THR N 419 " (cutoff:3.500A) Processing helix chain 'N' and resid 439 through 511 removed outlier: 4.302A pdb=" N LEU N 443 " --> pdb=" O GLY N 439 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER N 463 " --> pdb=" O GLU N 459 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY N 465 " --> pdb=" O LYS N 461 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS N 476 " --> pdb=" O GLN N 472 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER N 477 " --> pdb=" O GLU N 473 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE N 478 " --> pdb=" O VAL N 474 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS N 483 " --> pdb=" O ASN N 479 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU N 508 " --> pdb=" O LYS N 504 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU N 509 " --> pdb=" O ASN N 505 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN N 511 " --> pdb=" O GLN N 507 " (cutoff:3.500A) Processing helix chain 'N' and resid 517 through 523 Processing helix chain 'N' and resid 524 through 595 removed outlier: 4.047A pdb=" N ALA N 556 " --> pdb=" O GLU N 552 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER N 561 " --> pdb=" O ASN N 557 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS N 562 " --> pdb=" O ALA N 558 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU N 563 " --> pdb=" O GLU N 559 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU N 574 " --> pdb=" O LYS N 570 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER N 576 " --> pdb=" O GLN N 572 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS N 577 " --> pdb=" O ILE N 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.518A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.857A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.591A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.651A pdb=" N THR B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 70 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.973A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 74 removed outlier: 4.038A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.939A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.701A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 119 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.849A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.820A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.001A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 77 Processing helix chain 'F' and resid 82 through 91 removed outlier: 3.516A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.587A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 90 removed outlier: 3.987A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 82 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.847A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 Processing sheet with id=AA1, first strand: chain 'K' and resid 118 through 120 removed outlier: 6.330A pdb=" N THR K 58 " --> pdb=" O LEU K 119 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER K 196 " --> pdb=" O VAL K 372 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU K 374 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA K 198 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY K 376 " --> pdb=" O ALA K 198 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS K 371 " --> pdb=" O VAL K 331 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N PHE K 337 " --> pdb=" O GLU K 375 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY K 377 " --> pdb=" O PHE K 337 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET K 240 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N SER K 334 " --> pdb=" O MET K 240 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU K 242 " --> pdb=" O SER K 334 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N GLY K 336 " --> pdb=" O LEU K 242 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ILE K 239 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL K 265 " --> pdb=" O ILE K 239 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE K 241 " --> pdb=" O VAL K 265 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU K 267 " --> pdb=" O ILE K 241 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP K 243 " --> pdb=" O LEU K 267 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS K 297 " --> pdb=" O VAL K 262 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR K 264 " --> pdb=" O CYS K 297 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ILE K 299 " --> pdb=" O TYR K 264 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER K 266 " --> pdb=" O ILE K 299 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 476 through 477 removed outlier: 6.089A pdb=" N PHE K 592 " --> pdb=" O ILE K 619 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE K 621 " --> pdb=" O PHE K 592 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY K 594 " --> pdb=" O PHE K 621 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLY K 623 " --> pdb=" O GLY K 594 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU K 647 " --> pdb=" O ILE K 619 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N PHE K 621 " --> pdb=" O LEU K 647 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE K 649 " --> pdb=" O PHE K 621 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEU K 673 " --> pdb=" O SER K 646 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE K 648 " --> pdb=" O LEU K 673 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 511 through 516 removed outlier: 3.827A pdb=" N LYS K 515 " --> pdb=" O SER K 527 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N SER K 527 " --> pdb=" O LYS K 515 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 58 through 61 removed outlier: 5.976A pdb=" N THR L 58 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE L 121 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU L 60 " --> pdb=" O ILE L 121 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'L' and resid 296 through 301 removed outlier: 6.069A pdb=" N ILE L 239 " --> pdb=" O LEU L 263 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL L 265 " --> pdb=" O ILE L 239 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ILE L 241 " --> pdb=" O VAL L 265 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU L 267 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASP L 243 " --> pdb=" O LEU L 267 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N ARG L 269 " --> pdb=" O ASP L 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 476 through 477 Processing sheet with id=AA7, first strand: chain 'L' and resid 547 through 548 Processing sheet with id=AA8, first strand: chain 'L' and resid 547 through 548 removed outlier: 4.303A pdb=" N ILE L 502 " --> pdb=" O LYS L 589 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP L 508 " --> pdb=" O ILE L 595 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE L 619 " --> pdb=" O ILE L 590 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE L 592 " --> pdb=" O ILE L 619 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N PHE L 621 " --> pdb=" O PHE L 592 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLY L 594 " --> pdb=" O PHE L 621 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY L 623 " --> pdb=" O GLY L 594 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASN L 620 " --> pdb=" O PHE L 649 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE L 648 " --> pdb=" O LEU L 673 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 31 through 35 removed outlier: 7.388A pdb=" N TYR M 31 " --> pdb=" O ARG M 237 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL M 239 " --> pdb=" O TYR M 31 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU M 33 " --> pdb=" O VAL M 239 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL M 136 " --> pdb=" O ILE M 203 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 13 removed outlier: 5.675A pdb=" N ALA N 142 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU N 238 " --> pdb=" O ARG N 164 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU N 240 " --> pdb=" O LYS N 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.347A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 83 through 84 removed outlier: 8.077A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 1162 hydrogen bonds defined for protein. 3435 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 576 hydrogen bond angles 0 basepair planarities 126 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 13.67 Time building geometry restraints manager: 14.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5382 1.32 - 1.45: 9512 1.45 - 1.57: 16674 1.57 - 1.70: 576 1.70 - 1.82: 158 Bond restraints: 32302 Sorted by residual: bond pdb=" C MET L 320 " pdb=" N PRO L 321 " ideal model delta sigma weight residual 1.336 1.413 -0.077 1.20e-02 6.94e+03 4.11e+01 bond pdb=" CA CYS K 430 " pdb=" C CYS K 430 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.34e-02 5.57e+03 1.24e+01 bond pdb=" C GLU L 208 " pdb=" N PRO L 209 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.30e-02 5.92e+03 1.04e+01 bond pdb=" C3' DC I 66 " pdb=" O3' DC I 66 " ideal model delta sigma weight residual 1.422 1.518 -0.096 3.00e-02 1.11e+03 1.03e+01 bond pdb=" C3' DA J -55 " pdb=" O3' DA J -55 " ideal model delta sigma weight residual 1.422 1.327 0.095 3.00e-02 1.11e+03 9.96e+00 ... (remaining 32297 not shown) Histogram of bond angle deviations from ideal: 93.91 - 103.01: 782 103.01 - 112.11: 15571 112.11 - 121.21: 19583 121.21 - 130.31: 8733 130.31 - 139.42: 231 Bond angle restraints: 44900 Sorted by residual: angle pdb=" C THR N 440 " pdb=" N VAL N 441 " pdb=" CA VAL N 441 " ideal model delta sigma weight residual 120.24 126.79 -6.55 6.30e-01 2.52e+00 1.08e+02 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 94.30 9.70 1.50e+00 4.44e-01 4.18e+01 angle pdb=" C3' DG I -53 " pdb=" O3' DG I -53 " pdb=" P DG I -52 " ideal model delta sigma weight residual 120.20 129.88 -9.68 1.50e+00 4.44e-01 4.17e+01 angle pdb=" C LEU L 555 " pdb=" N THR L 556 " pdb=" CA THR L 556 " ideal model delta sigma weight residual 121.54 133.48 -11.94 1.91e+00 2.74e-01 3.91e+01 angle pdb=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.58 128.76 -8.18 1.32e+00 5.74e-01 3.84e+01 ... (remaining 44895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.15: 16529 31.15 - 62.30: 2186 62.30 - 93.45: 122 93.45 - 124.60: 13 124.60 - 155.75: 4 Dihedral angle restraints: 18854 sinusoidal: 9662 harmonic: 9192 Sorted by residual: dihedral pdb=" CA SER K 54 " pdb=" C SER K 54 " pdb=" N PRO K 55 " pdb=" CA PRO K 55 " ideal model delta harmonic sigma weight residual 180.00 123.48 56.52 0 5.00e+00 4.00e-02 1.28e+02 dihedral pdb=" CA ILE N 306 " pdb=" C ILE N 306 " pdb=" N LYS N 307 " pdb=" CA LYS N 307 " ideal model delta harmonic sigma weight residual -180.00 -134.21 -45.79 0 5.00e+00 4.00e-02 8.39e+01 dihedral pdb=" CA PHE N 512 " pdb=" C PHE N 512 " pdb=" N ASN N 513 " pdb=" CA ASN N 513 " ideal model delta harmonic sigma weight residual -180.00 -136.05 -43.95 0 5.00e+00 4.00e-02 7.73e+01 ... (remaining 18851 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4093 0.106 - 0.213: 825 0.213 - 0.319: 116 0.319 - 0.425: 19 0.425 - 0.531: 5 Chirality restraints: 5058 Sorted by residual: chirality pdb=" CB ILE L 530 " pdb=" CA ILE L 530 " pdb=" CG1 ILE L 530 " pdb=" CG2 ILE L 530 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CB VAL K 481 " pdb=" CA VAL K 481 " pdb=" CG1 VAL K 481 " pdb=" CG2 VAL K 481 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.51 2.00e-01 2.50e+01 6.62e+00 chirality pdb=" CB VAL L 518 " pdb=" CA VAL L 518 " pdb=" CG1 VAL L 518 " pdb=" CG2 VAL L 518 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.34e+00 ... (remaining 5055 not shown) Planarity restraints: 4730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 42 " 0.039 2.00e-02 2.50e+03 3.47e-02 2.71e+01 pdb=" N1 DC I 42 " -0.080 2.00e-02 2.50e+03 pdb=" C2 DC I 42 " 0.050 2.00e-02 2.50e+03 pdb=" O2 DC I 42 " -0.016 2.00e-02 2.50e+03 pdb=" N3 DC I 42 " -0.010 2.00e-02 2.50e+03 pdb=" C4 DC I 42 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 42 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC I 42 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 42 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.010 2.00e-02 2.50e+03 3.10e-02 2.64e+01 pdb=" N9 DA I -35 " -0.062 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.075 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.011 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.017 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -23 " -0.037 2.00e-02 2.50e+03 3.27e-02 2.41e+01 pdb=" N1 DC I -23 " 0.081 2.00e-02 2.50e+03 pdb=" C2 DC I -23 " -0.039 2.00e-02 2.50e+03 pdb=" O2 DC I -23 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC I -23 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DC I -23 " -0.000 2.00e-02 2.50e+03 pdb=" N4 DC I -23 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DC I -23 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC I -23 " -0.006 2.00e-02 2.50e+03 ... (remaining 4727 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3041 2.74 - 3.28: 28291 3.28 - 3.82: 60627 3.82 - 4.36: 70846 4.36 - 4.90: 105744 Nonbonded interactions: 268549 Sorted by model distance: nonbonded pdb=" OD1 ASP L 245 " pdb="ZN ZN L 801 " model vdw 2.197 2.230 nonbonded pdb=" OD2 ASP K 245 " pdb="ZN ZN K 801 " model vdw 2.216 2.230 nonbonded pdb=" OD2 ASP L 338 " pdb="ZN ZN L 801 " model vdw 2.227 2.230 nonbonded pdb=" O4 DT I 3 " pdb=" O6 DG J -4 " model vdw 2.268 2.432 nonbonded pdb=" O GLN N 121 " pdb=" OG SER N 125 " model vdw 2.278 2.440 ... (remaining 268544 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 40 through 515 or (resid 516 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 517 through 656 or resid 667 through 678 or resid 680 through 700 or resid 801) \ ) selection = (chain 'L' and (resid 40 through 439 or resid 445 through 700 or resid 801)) } 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=0.94 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: 12.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 33.700 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 96.050 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 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 : 0.010 0.098 32302 Z= 0.575 Angle : 1.617 17.750 44900 Z= 0.870 Chirality : 0.087 0.531 5058 Planarity : 0.011 0.090 4730 Dihedral : 23.433 155.755 12901 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.48 % Favored : 92.49 % Rotamer: Outliers : 1.29 % Allowed : 8.30 % Favored : 90.41 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 3.25 % Twisted General : 0.64 % 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: -4.87 (0.11), residues: 3088 helix: -3.37 (0.08), residues: 1567 sheet: -2.23 (0.32), residues: 222 loop : -3.06 (0.14), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP K 513 HIS 0.027 0.005 HIS K 507 PHE 0.035 0.005 PHE L 592 TYR 0.051 0.005 TYR D 80 ARG 0.013 0.002 ARG G 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 231 time to evaluate : 3.191 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: K 193 VAL cc_start: 0.6366 (m) cc_final: 0.6138 (m) REVERT: K 312 MET cc_start: 0.9455 (mmm) cc_final: 0.9029 (mmm) REVERT: L 60 LEU cc_start: 0.9715 (tt) cc_final: 0.9511 (pt) REVERT: L 149 MET cc_start: 0.5226 (mtt) cc_final: 0.5004 (mtp) REVERT: L 264 TYR cc_start: 0.9334 (t80) cc_final: 0.8628 (t80) REVERT: L 289 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8228 (tp30) REVERT: L 296 ASN cc_start: 0.9229 (t0) cc_final: 0.8711 (t0) REVERT: L 371 CYS cc_start: 0.9314 (p) cc_final: 0.8795 (t) REVERT: M 37 MET cc_start: 0.3530 (mtp) cc_final: 0.3039 (mtt) REVERT: N 251 TYR cc_start: 0.9125 (t80) cc_final: 0.8820 (p90) REVERT: N 260 MET cc_start: 0.9501 (ptm) cc_final: 0.9186 (ttp) REVERT: N 394 GLN cc_start: 0.9364 (mm110) cc_final: 0.9107 (pp30) REVERT: A 46 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.6990 (m) REVERT: B 84 MET cc_start: 0.9418 (mmm) cc_final: 0.9029 (tpp) REVERT: C 51 LEU cc_start: 0.8978 (tp) cc_final: 0.8666 (tp) REVERT: D 84 SER cc_start: 0.9379 (OUTLIER) cc_final: 0.8981 (p) REVERT: E 73 GLU cc_start: 0.8922 (tt0) cc_final: 0.8717 (tt0) REVERT: E 93 GLN cc_start: 0.9466 (tt0) cc_final: 0.9115 (tm-30) REVERT: E 94 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8701 (tp30) REVERT: E 100 LEU cc_start: 0.9519 (mt) cc_final: 0.9041 (pp) REVERT: F 84 MET cc_start: 0.9292 (mmm) cc_final: 0.8706 (tpp) REVERT: G 30 VAL cc_start: 0.9087 (t) cc_final: 0.8713 (p) outliers start: 36 outliers final: 4 residues processed: 263 average time/residue: 0.4482 time to fit residues: 186.2108 Evaluate side-chains 156 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 284 optimal weight: 1.9990 chunk 255 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 172 optimal weight: 30.0000 chunk 136 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 102 optimal weight: 0.0060 chunk 160 optimal weight: 6.9990 chunk 196 optimal weight: 8.9990 chunk 306 optimal weight: 1.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 464 GLN ** K 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 500 ASN ** K 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS L 135 HIS ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN L 286 GLN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 682 ASN M 47 GLN M 112 ASN M 124 ASN M 258 ASN M 316 GLN M 409 ASN ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 477 ASN M 572 ASN N 72 GLN N 80 ASN ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 347 ASN ** N 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 543 ASN ** N 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 620 ASN N 629 ASN N 634 ASN A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 31 HIS ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 92 GLN E 68 GLN E 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN H 64 ASN H 92 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32302 Z= 0.263 Angle : 0.764 11.005 44900 Z= 0.423 Chirality : 0.045 0.232 5058 Planarity : 0.006 0.090 4730 Dihedral : 26.671 160.962 6580 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.21 % Allowed : 4.15 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 1.63 % Twisted General : 0.10 % 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: -3.14 (0.13), residues: 3088 helix: -1.55 (0.11), residues: 1597 sheet: -2.33 (0.32), residues: 219 loop : -2.63 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 577 HIS 0.008 0.001 HIS K 507 PHE 0.030 0.002 PHE E 67 TYR 0.031 0.002 TYR H 39 ARG 0.012 0.001 ARG L 671 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 177 time to evaluate : 3.092 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: K 242 LEU cc_start: 0.9749 (mt) cc_final: 0.9451 (pp) REVERT: K 312 MET cc_start: 0.9510 (mmm) cc_final: 0.9128 (mmm) REVERT: K 563 TYR cc_start: 0.9734 (t80) cc_final: 0.9473 (t80) REVERT: L 117 LEU cc_start: 0.9048 (tp) cc_final: 0.8808 (tp) REVERT: L 119 LEU cc_start: 0.9273 (tp) cc_final: 0.8979 (mp) REVERT: L 149 MET cc_start: 0.5217 (mtt) cc_final: 0.4951 (mtp) REVERT: L 264 TYR cc_start: 0.8896 (t80) cc_final: 0.8604 (t80) REVERT: L 296 ASN cc_start: 0.9143 (t0) cc_final: 0.8701 (t0) REVERT: L 358 MET cc_start: 0.9102 (mpp) cc_final: 0.8560 (mpp) REVERT: M 37 MET cc_start: 0.3656 (mtp) cc_final: 0.3239 (mtt) REVERT: M 298 TRP cc_start: 0.7905 (t60) cc_final: 0.7392 (t-100) REVERT: N 92 VAL cc_start: 0.4447 (OUTLIER) cc_final: 0.4230 (p) REVERT: N 128 PHE cc_start: 0.9006 (m-80) cc_final: 0.8762 (m-80) REVERT: N 260 MET cc_start: 0.9416 (ptm) cc_final: 0.9052 (ttp) REVERT: N 394 GLN cc_start: 0.9238 (mm110) cc_final: 0.8971 (pt0) REVERT: N 395 LEU cc_start: 0.3979 (tp) cc_final: 0.3617 (tp) REVERT: N 422 MET cc_start: 0.3857 (tpt) cc_final: 0.3568 (tpt) REVERT: N 592 MET cc_start: 0.2932 (tpt) cc_final: 0.2646 (tpt) REVERT: B 84 MET cc_start: 0.9338 (mmm) cc_final: 0.9067 (tpp) REVERT: E 73 GLU cc_start: 0.8729 (tt0) cc_final: 0.8277 (mt-10) REVERT: E 93 GLN cc_start: 0.9546 (tt0) cc_final: 0.9125 (tm-30) REVERT: E 100 LEU cc_start: 0.9576 (mt) cc_final: 0.9108 (pp) REVERT: F 84 MET cc_start: 0.9220 (mmm) cc_final: 0.8692 (tpp) outliers start: 6 outliers final: 1 residues processed: 182 average time/residue: 0.4293 time to fit residues: 125.9135 Evaluate side-chains 130 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 chunk 304 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 ASN K 247 HIS ** K 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 507 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 579 ASN ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 681 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 281 ASN ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 ASN ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 524 ASN ** N 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 600 ASN N 629 ASN N 634 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 106 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 32302 Z= 0.360 Angle : 0.798 9.231 44900 Z= 0.443 Chirality : 0.046 0.203 5058 Planarity : 0.006 0.091 4730 Dihedral : 26.598 165.279 6580 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 32.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.18 % Allowed : 5.44 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 1.63 % Twisted General : 0.03 % 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: -2.52 (0.14), residues: 3088 helix: -0.95 (0.12), residues: 1572 sheet: -2.28 (0.33), residues: 208 loop : -2.42 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP L 641 HIS 0.007 0.002 HIS D 46 PHE 0.034 0.003 PHE K 431 TYR 0.032 0.002 TYR K 276 ARG 0.012 0.001 ARG G 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 3.571 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: K 149 MET cc_start: 0.1476 (mtp) cc_final: 0.1218 (mtp) REVERT: K 240 MET cc_start: 0.3722 (mtt) cc_final: 0.3435 (mtt) REVERT: K 312 MET cc_start: 0.9370 (mmm) cc_final: 0.8925 (mmm) REVERT: K 322 MET cc_start: 0.8809 (mmm) cc_final: 0.8565 (tpp) REVERT: K 563 TYR cc_start: 0.9696 (t80) cc_final: 0.9477 (t80) REVERT: L 117 LEU cc_start: 0.9144 (tp) cc_final: 0.8868 (tp) REVERT: L 149 MET cc_start: 0.5245 (mtt) cc_final: 0.4943 (mtp) REVERT: L 495 ASN cc_start: 0.9341 (p0) cc_final: 0.9138 (t0) REVERT: M 37 MET cc_start: 0.3537 (mtp) cc_final: 0.3192 (mtt) REVERT: M 298 TRP cc_start: 0.7832 (t60) cc_final: 0.7544 (t-100) REVERT: N 128 PHE cc_start: 0.8987 (m-80) cc_final: 0.8766 (m-80) REVERT: N 422 MET cc_start: 0.5131 (tpt) cc_final: 0.4901 (tpt) REVERT: B 84 MET cc_start: 0.9305 (mmm) cc_final: 0.8980 (tpp) REVERT: E 73 GLU cc_start: 0.8694 (tt0) cc_final: 0.8192 (mt-10) REVERT: E 100 LEU cc_start: 0.9600 (mt) cc_final: 0.9135 (pp) REVERT: F 84 MET cc_start: 0.9233 (mmm) cc_final: 0.8851 (mmm) outliers start: 5 outliers final: 2 residues processed: 152 average time/residue: 0.4213 time to fit residues: 104.8989 Evaluate side-chains 119 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 302 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 205 optimal weight: 20.0000 chunk 307 optimal weight: 0.8980 chunk 325 optimal weight: 3.9990 chunk 160 optimal weight: 8.9990 chunk 291 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 GLN L 369 ASN ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 517 ASN ** L 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN N 634 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32302 Z= 0.261 Angle : 0.717 10.173 44900 Z= 0.396 Chirality : 0.044 0.231 5058 Planarity : 0.005 0.078 4730 Dihedral : 26.629 163.668 6580 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 27.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.03 % 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: -2.07 (0.14), residues: 3088 helix: -0.54 (0.12), residues: 1598 sheet: -2.11 (0.33), residues: 217 loop : -2.26 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 428 HIS 0.006 0.001 HIS N 114 PHE 0.028 0.002 PHE K 315 TYR 0.032 0.002 TYR K 276 ARG 0.006 0.001 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 3.239 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: K 128 SER cc_start: 0.9510 (p) cc_final: 0.9237 (p) REVERT: K 149 MET cc_start: 0.0701 (mtp) cc_final: -0.0023 (mtp) REVERT: K 312 MET cc_start: 0.9407 (mmm) cc_final: 0.8824 (mmm) REVERT: K 358 MET cc_start: 0.8583 (mtt) cc_final: 0.8263 (mtt) REVERT: K 394 LEU cc_start: 0.9224 (mt) cc_final: 0.8884 (mt) REVERT: K 563 TYR cc_start: 0.9656 (t80) cc_final: 0.9400 (t80) REVERT: L 117 LEU cc_start: 0.9116 (tp) cc_final: 0.8818 (tp) REVERT: L 149 MET cc_start: 0.5162 (mtt) cc_final: 0.4867 (mtp) REVERT: L 358 MET cc_start: 0.9275 (mpp) cc_final: 0.9061 (mpp) REVERT: L 495 ASN cc_start: 0.9358 (p0) cc_final: 0.9128 (t0) REVERT: M 37 MET cc_start: 0.3789 (mtp) cc_final: 0.3498 (mtt) REVERT: N 128 PHE cc_start: 0.8971 (m-80) cc_final: 0.8766 (m-80) REVERT: N 394 GLN cc_start: 0.9173 (mm110) cc_final: 0.8915 (pt0) REVERT: N 395 LEU cc_start: 0.3259 (tp) cc_final: 0.2911 (tp) REVERT: N 422 MET cc_start: 0.5212 (tpt) cc_final: 0.5000 (tpt) REVERT: N 592 MET cc_start: 0.3153 (tpt) cc_final: 0.2844 (tpt) REVERT: B 84 MET cc_start: 0.9353 (mmm) cc_final: 0.9045 (tpp) REVERT: E 73 GLU cc_start: 0.8690 (tt0) cc_final: 0.8169 (mt-10) REVERT: E 100 LEU cc_start: 0.9574 (mt) cc_final: 0.9135 (pp) REVERT: F 84 MET cc_start: 0.9213 (mmm) cc_final: 0.8851 (mmm) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.4118 time to fit residues: 100.7344 Evaluate side-chains 118 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 271 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 242 optimal weight: 0.9990 chunk 134 optimal weight: 40.0000 chunk 277 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 41 GLN ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 500 ASN N 629 ASN N 634 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32302 Z= 0.204 Angle : 0.669 13.221 44900 Z= 0.368 Chirality : 0.043 0.197 5058 Planarity : 0.004 0.078 4730 Dihedral : 26.386 161.091 6580 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.03 % 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: -1.66 (0.15), residues: 3088 helix: -0.16 (0.12), residues: 1613 sheet: -1.94 (0.33), residues: 226 loop : -2.16 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 391 HIS 0.006 0.001 HIS K 247 PHE 0.017 0.002 PHE L 326 TYR 0.030 0.002 TYR C 50 ARG 0.006 0.000 ARG L 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 146 time to evaluate : 3.093 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: K 152 GLU cc_start: 0.9826 (tp30) cc_final: 0.9596 (pm20) REVERT: K 312 MET cc_start: 0.9398 (mmm) cc_final: 0.8825 (mmm) REVERT: K 358 MET cc_start: 0.8427 (mtt) cc_final: 0.7918 (mtt) REVERT: K 563 TYR cc_start: 0.9724 (t80) cc_final: 0.9474 (t80) REVERT: L 117 LEU cc_start: 0.9148 (tp) cc_final: 0.8836 (tp) REVERT: L 370 LEU cc_start: 0.9648 (mm) cc_final: 0.9437 (mm) REVERT: L 483 MET cc_start: 0.7814 (tpt) cc_final: 0.7606 (tpp) REVERT: L 495 ASN cc_start: 0.9362 (p0) cc_final: 0.9130 (t0) REVERT: L 566 MET cc_start: 0.8819 (ptp) cc_final: 0.8579 (pmm) REVERT: M 37 MET cc_start: 0.3808 (mtp) cc_final: 0.3538 (mtt) REVERT: N 128 PHE cc_start: 0.8969 (m-80) cc_final: 0.8752 (m-80) REVERT: N 260 MET cc_start: 0.9348 (ptm) cc_final: 0.8839 (ttm) REVERT: N 394 GLN cc_start: 0.9218 (mm110) cc_final: 0.8939 (pt0) REVERT: N 395 LEU cc_start: 0.2967 (tp) cc_final: 0.2687 (tp) REVERT: N 592 MET cc_start: 0.3294 (tpt) cc_final: 0.2995 (tpt) REVERT: E 73 GLU cc_start: 0.8785 (tt0) cc_final: 0.8254 (mt-10) REVERT: E 100 LEU cc_start: 0.9534 (mt) cc_final: 0.9116 (pp) REVERT: F 84 MET cc_start: 0.9165 (mmm) cc_final: 0.8613 (mmm) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.3942 time to fit residues: 97.9925 Evaluate side-chains 123 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 109 optimal weight: 6.9990 chunk 293 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 326 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 171 optimal weight: 50.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 369 ASN ** L 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 20 GLN ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 455 ASN N 629 ASN N 634 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32302 Z= 0.279 Angle : 0.704 11.295 44900 Z= 0.389 Chirality : 0.043 0.198 5058 Planarity : 0.005 0.074 4730 Dihedral : 26.196 168.036 6580 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 28.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.03 % 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: -1.65 (0.15), residues: 3088 helix: -0.15 (0.12), residues: 1619 sheet: -1.99 (0.33), residues: 226 loop : -2.14 (0.17), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 391 HIS 0.005 0.001 HIS K 206 PHE 0.027 0.002 PHE K 315 TYR 0.048 0.002 TYR N 571 ARG 0.007 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 144 time to evaluate : 2.889 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: K 312 MET cc_start: 0.9447 (mmm) cc_final: 0.8813 (mmm) REVERT: K 358 MET cc_start: 0.8652 (mtt) cc_final: 0.8214 (mtt) REVERT: K 563 TYR cc_start: 0.9647 (t80) cc_final: 0.9378 (t80) REVERT: L 117 LEU cc_start: 0.9194 (tp) cc_final: 0.8884 (tp) REVERT: L 358 MET cc_start: 0.9259 (mpp) cc_final: 0.8991 (mmt) REVERT: L 370 LEU cc_start: 0.9618 (mm) cc_final: 0.9386 (mm) REVERT: L 483 MET cc_start: 0.7873 (tpt) cc_final: 0.7626 (tpp) REVERT: L 495 ASN cc_start: 0.9357 (p0) cc_final: 0.9076 (t0) REVERT: M 37 MET cc_start: 0.3538 (mtp) cc_final: 0.3301 (mtt) REVERT: N 128 PHE cc_start: 0.8964 (m-80) cc_final: 0.8748 (m-80) REVERT: N 394 GLN cc_start: 0.9199 (mm110) cc_final: 0.8924 (pt0) REVERT: N 395 LEU cc_start: 0.2927 (tp) cc_final: 0.2654 (tp) REVERT: N 422 MET cc_start: 0.3126 (tpt) cc_final: 0.2885 (tpt) REVERT: N 592 MET cc_start: 0.3291 (tpt) cc_final: 0.2981 (tpt) REVERT: B 84 MET cc_start: 0.9402 (mmm) cc_final: 0.8958 (tpt) REVERT: E 73 GLU cc_start: 0.8831 (tt0) cc_final: 0.8341 (mt-10) REVERT: E 100 LEU cc_start: 0.9552 (mt) cc_final: 0.9160 (pp) REVERT: F 84 MET cc_start: 0.9131 (mmm) cc_final: 0.8720 (mmm) outliers start: 2 outliers final: 0 residues processed: 145 average time/residue: 0.3799 time to fit residues: 93.4923 Evaluate side-chains 119 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 314 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 185 optimal weight: 30.0000 chunk 238 optimal weight: 1.9990 chunk 184 optimal weight: 0.5980 chunk 274 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 324 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 198 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 349 HIS ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 464 GLN ** L 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 629 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 32302 Z= 0.269 Angle : 0.700 10.092 44900 Z= 0.387 Chirality : 0.044 0.250 5058 Planarity : 0.005 0.075 4730 Dihedral : 26.288 178.565 6580 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 29.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.03 % 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: -1.62 (0.15), residues: 3088 helix: -0.12 (0.12), residues: 1619 sheet: -1.99 (0.33), residues: 225 loop : -2.13 (0.18), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP N 391 HIS 0.006 0.001 HIS K 247 PHE 0.031 0.002 PHE N 37 TYR 0.034 0.002 TYR K 276 ARG 0.027 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 3.112 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: K 138 GLU cc_start: 0.9743 (mm-30) cc_final: 0.9481 (pm20) REVERT: K 312 MET cc_start: 0.9479 (mmm) cc_final: 0.8839 (mmm) REVERT: K 358 MET cc_start: 0.8710 (mtt) cc_final: 0.8018 (mtt) REVERT: K 563 TYR cc_start: 0.9741 (t80) cc_final: 0.9485 (t80) REVERT: L 117 LEU cc_start: 0.9181 (tp) cc_final: 0.8881 (tp) REVERT: L 358 MET cc_start: 0.9354 (mpp) cc_final: 0.8468 (mpp) REVERT: L 370 LEU cc_start: 0.9651 (mm) cc_final: 0.9445 (mm) REVERT: L 483 MET cc_start: 0.7881 (tpt) cc_final: 0.7595 (tpp) REVERT: M 37 MET cc_start: 0.3492 (mtp) cc_final: 0.3277 (mtt) REVERT: N 128 PHE cc_start: 0.8922 (m-80) cc_final: 0.8709 (m-80) REVERT: N 592 MET cc_start: 0.3383 (tpt) cc_final: 0.3048 (tpt) REVERT: B 84 MET cc_start: 0.9404 (mmm) cc_final: 0.9030 (tpp) REVERT: E 73 GLU cc_start: 0.8860 (tt0) cc_final: 0.8377 (mt-10) REVERT: E 100 LEU cc_start: 0.9547 (mt) cc_final: 0.9149 (pp) REVERT: F 84 MET cc_start: 0.9181 (mmm) cc_final: 0.8744 (mmm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.4007 time to fit residues: 100.6509 Evaluate side-chains 119 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 200 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 63 optimal weight: 0.1980 chunk 62 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 369 ASN ** L 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 495 ASN ** L 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 HIS M 293 HIS ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 497 ASN N 629 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32302 Z= 0.236 Angle : 0.674 9.429 44900 Z= 0.372 Chirality : 0.043 0.246 5058 Planarity : 0.004 0.073 4730 Dihedral : 26.214 167.417 6580 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.04 % Allowed : 1.25 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.00 % 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: -1.43 (0.15), residues: 3088 helix: 0.01 (0.13), residues: 1619 sheet: -1.94 (0.33), residues: 237 loop : -2.00 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 391 HIS 0.006 0.001 HIS K 247 PHE 0.027 0.002 PHE L 475 TYR 0.033 0.002 TYR K 276 ARG 0.006 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 3.317 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: K 138 GLU cc_start: 0.9752 (mm-30) cc_final: 0.9484 (pm20) REVERT: K 272 MET cc_start: 0.8600 (tpt) cc_final: 0.8304 (tpt) REVERT: K 312 MET cc_start: 0.9485 (mmm) cc_final: 0.8872 (mmm) REVERT: K 358 MET cc_start: 0.8664 (mtt) cc_final: 0.8082 (mtt) REVERT: K 563 TYR cc_start: 0.9654 (t80) cc_final: 0.9452 (t80) REVERT: L 66 MET cc_start: 0.7891 (ttt) cc_final: 0.7310 (tmm) REVERT: L 117 LEU cc_start: 0.9177 (tp) cc_final: 0.8885 (tp) REVERT: L 358 MET cc_start: 0.9326 (mpp) cc_final: 0.8434 (mpp) REVERT: L 483 MET cc_start: 0.7828 (tpt) cc_final: 0.7512 (tpp) REVERT: N 128 PHE cc_start: 0.8903 (m-80) cc_final: 0.8683 (m-80) REVERT: N 592 MET cc_start: 0.3464 (tpt) cc_final: 0.3162 (tpt) REVERT: B 84 MET cc_start: 0.9395 (mmm) cc_final: 0.9023 (tpp) REVERT: E 73 GLU cc_start: 0.8887 (tt0) cc_final: 0.8445 (mt-10) REVERT: E 100 LEU cc_start: 0.9538 (mt) cc_final: 0.9161 (pp) REVERT: F 84 MET cc_start: 0.9192 (mmm) cc_final: 0.8742 (mmm) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.3972 time to fit residues: 100.7713 Evaluate side-chains 125 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 295 optimal weight: 1.9990 chunk 311 optimal weight: 10.0000 chunk 283 optimal weight: 3.9990 chunk 302 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 131 optimal weight: 0.0670 chunk 237 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 301 optimal weight: 1.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 369 ASN ** L 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 579 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 293 HIS ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32302 Z= 0.198 Angle : 0.654 9.282 44900 Z= 0.358 Chirality : 0.042 0.234 5058 Planarity : 0.004 0.074 4730 Dihedral : 26.038 147.723 6580 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.00 % 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: -1.17 (0.15), residues: 3088 helix: 0.25 (0.13), residues: 1623 sheet: -1.84 (0.33), residues: 236 loop : -1.92 (0.18), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 391 HIS 0.006 0.001 HIS F 75 PHE 0.041 0.002 PHE E 104 TYR 0.029 0.002 TYR K 276 ARG 0.005 0.000 ARG N 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 3.124 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: K 138 GLU cc_start: 0.9737 (mm-30) cc_final: 0.9453 (pm20) REVERT: K 272 MET cc_start: 0.8491 (tpt) cc_final: 0.8262 (tpt) REVERT: K 312 MET cc_start: 0.9480 (mmm) cc_final: 0.8888 (mmm) REVERT: K 358 MET cc_start: 0.8583 (mtt) cc_final: 0.7919 (mtt) REVERT: K 416 MET cc_start: 0.6365 (ttt) cc_final: 0.5887 (ttt) REVERT: K 563 TYR cc_start: 0.9638 (t80) cc_final: 0.9258 (t80) REVERT: L 66 MET cc_start: 0.8019 (ttt) cc_final: 0.7498 (tmm) REVERT: L 117 LEU cc_start: 0.9163 (tp) cc_final: 0.8861 (tp) REVERT: L 483 MET cc_start: 0.7686 (tpt) cc_final: 0.7414 (tpp) REVERT: L 495 ASN cc_start: 0.9348 (p0) cc_final: 0.9060 (t0) REVERT: N 103 MET cc_start: 0.5082 (mmp) cc_final: 0.4335 (mtp) REVERT: N 124 ASN cc_start: 0.9800 (m-40) cc_final: 0.9389 (p0) REVERT: N 592 MET cc_start: 0.3867 (tpt) cc_final: 0.3591 (tpt) REVERT: B 84 MET cc_start: 0.9424 (mmm) cc_final: 0.9040 (tpp) REVERT: E 73 GLU cc_start: 0.8901 (tt0) cc_final: 0.8439 (mt-10) REVERT: E 100 LEU cc_start: 0.9548 (mt) cc_final: 0.9244 (pp) REVERT: F 84 MET cc_start: 0.9202 (mmm) cc_final: 0.8768 (mmm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.4067 time to fit residues: 108.2638 Evaluate side-chains 130 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 3.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 198 optimal weight: 0.9980 chunk 320 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 335 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 267 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 206 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 HIS L 369 ASN ** L 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 449 ASN ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 32302 Z= 0.322 Angle : 0.732 9.867 44900 Z= 0.404 Chirality : 0.044 0.215 5058 Planarity : 0.005 0.087 4730 Dihedral : 26.096 137.017 6580 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 34.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.00 % 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: -1.52 (0.15), residues: 3088 helix: -0.07 (0.12), residues: 1618 sheet: -1.98 (0.33), residues: 227 loop : -2.03 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP N 391 HIS 0.017 0.002 HIS M 419 PHE 0.033 0.003 PHE E 104 TYR 0.032 0.002 TYR K 276 ARG 0.008 0.001 ARG K 385 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6176 Ramachandran restraints generated. 3088 Oldfield, 0 Emsley, 3088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 3.188 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: K 138 GLU cc_start: 0.9745 (mm-30) cc_final: 0.9469 (pm20) REVERT: K 312 MET cc_start: 0.9463 (mmm) cc_final: 0.8801 (mmm) REVERT: K 322 MET cc_start: 0.7322 (tpt) cc_final: 0.6823 (tpt) REVERT: K 358 MET cc_start: 0.8691 (mtt) cc_final: 0.7877 (mtt) REVERT: K 416 MET cc_start: 0.6581 (ttt) cc_final: 0.6296 (ttt) REVERT: K 563 TYR cc_start: 0.9646 (t80) cc_final: 0.9394 (t80) REVERT: L 66 MET cc_start: 0.8038 (ttt) cc_final: 0.7518 (tmm) REVERT: L 117 LEU cc_start: 0.9192 (tp) cc_final: 0.8905 (tp) REVERT: L 149 MET cc_start: 0.4192 (ttp) cc_final: 0.3347 (tmm) REVERT: L 358 MET cc_start: 0.9285 (mpp) cc_final: 0.8624 (mpp) REVERT: L 370 LEU cc_start: 0.9666 (mm) cc_final: 0.9463 (mm) REVERT: L 483 MET cc_start: 0.7824 (tpt) cc_final: 0.7523 (tpp) REVERT: N 103 MET cc_start: 0.5190 (mmp) cc_final: 0.4633 (mtm) REVERT: B 84 MET cc_start: 0.9401 (mmm) cc_final: 0.9029 (tpp) REVERT: E 73 GLU cc_start: 0.8910 (tt0) cc_final: 0.8443 (mt-10) REVERT: F 84 MET cc_start: 0.9194 (mmm) cc_final: 0.8698 (mmm) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.4039 time to fit residues: 102.8023 Evaluate side-chains 116 residues out of total 2794 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 212 optimal weight: 4.9990 chunk 284 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 274 optimal weight: 20.0000 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 369 ASN ** L 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN ** M 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 629 ASN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.052187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.033506 restraints weight = 371916.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.034014 restraints weight = 298043.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.034331 restraints weight = 254242.140| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32302 Z= 0.260 Angle : 0.701 9.249 44900 Z= 0.386 Chirality : 0.044 0.302 5058 Planarity : 0.005 0.084 4730 Dihedral : 26.278 138.491 6580 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 30.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.25 % Cis-general : 0.03 % Twisted Proline : 0.81 % Twisted General : 0.00 % 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: -1.45 (0.15), residues: 3088 helix: -0.01 (0.13), residues: 1621 sheet: -1.99 (0.33), residues: 234 loop : -2.00 (0.18), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP N 391 HIS 0.007 0.001 HIS K 206 PHE 0.034 0.002 PHE N 547 TYR 0.032 0.002 TYR K 276 ARG 0.008 0.001 ARG K 385 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5782.84 seconds wall clock time: 107 minutes 37.92 seconds (6457.92 seconds total)