Starting phenix.real_space_refine on Wed May 15 01:13:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8re4_19079/05_2024/8re4_19079.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8re4_19079/05_2024/8re4_19079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8re4_19079/05_2024/8re4_19079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8re4_19079/05_2024/8re4_19079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8re4_19079/05_2024/8re4_19079.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8re4_19079/05_2024/8re4_19079.pdb" } resolution = 2.8 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= 0.003 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 102 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 17981 2.51 5 N 5167 2.21 5 O 5810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 305": "OD1" <-> "OD2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 349": "OE1" <-> "OE2" Residue "C ASP 354": "OD1" <-> "OD2" Residue "C PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 413": "OE1" <-> "OE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 516": "OD1" <-> "OD2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 631": "OE1" <-> "OE2" Residue "C ASP 648": "OD1" <-> "OD2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C ASP 785": "OD1" <-> "OD2" Residue "C PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 814": "OD1" <-> "OD2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C GLU 835": "OE1" <-> "OE2" Residue "C ASP 842": "OD1" <-> "OD2" Residue "C GLU 848": "OE1" <-> "OE2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C GLU 859": "OE1" <-> "OE2" Residue "C GLU 898": "OE1" <-> "OE2" Residue "C ASP 930": "OD1" <-> "OD2" Residue "C GLU 949": "OE1" <-> "OE2" Residue "C GLU 963": "OE1" <-> "OE2" Residue "C GLU 1089": "OE1" <-> "OE2" Residue "C ASP 1095": "OD1" <-> "OD2" Residue "C ASP 1126": "OD1" <-> "OD2" Residue "C GLU 1137": "OE1" <-> "OE2" Residue "C ASP 1188": "OD1" <-> "OD2" Residue "C GLU 1192": "OE1" <-> "OE2" Residue "C TYR 1213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1240": "OD1" <-> "OD2" Residue "C ASP 1241": "OD1" <-> "OD2" Residue "C GLU 1329": "OE1" <-> "OE2" Residue "C GLU 1340": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 193": "OD1" <-> "OD2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ASP 284": "OD1" <-> "OD2" Residue "D GLU 301": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ASP 329": "OD1" <-> "OD2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D GLU 846": "OE1" <-> "OE2" Residue "D PHE 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1188": "OE1" <-> "OE2" Residue "D ASP 1219": "OD1" <-> "OD2" Residue "D GLU 1278": "OE1" <-> "OE2" Residue "D GLU 1349": "OE1" <-> "OE2" Residue "D TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 8": "OD1" <-> "OD2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M ASP 122": "OD1" <-> "OD2" Residue "M TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 160": "OD1" <-> "OD2" Residue "M ASP 163": "OD1" <-> "OD2" Residue "M ASP 167": "OD1" <-> "OD2" Residue "M ASP 275": "OD1" <-> "OD2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "M GLU 334": "OE1" <-> "OE2" Residue "M ASP 338": "OD1" <-> "OD2" Residue "M PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "M TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 410": "OE1" <-> "OE2" Residue "M GLU 414": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 29165 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1733 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9685 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 836 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 441 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2657 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 16, 'TRANS': 363} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 436 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 12, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 217 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 960 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain breaks: 1 Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain breaks: 1 Chain: "T" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1030 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14701 SG CYS D 70 103.972 112.746 93.290 1.00 58.66 S ATOM 14715 SG CYS D 72 102.253 116.852 95.537 1.00 47.22 S ATOM 14830 SG CYS D 88 102.041 113.314 96.978 1.00 51.38 S ATOM 20946 SG CYS D 898 93.575 45.025 89.115 1.00 44.84 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.58 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.58 Time building chain proxies: 15.79, per 1000 atoms: 0.54 Number of scatterers: 29165 At special positions: 0 Unit cell: (140.8, 169.4, 166.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 102 16.00 P 102 15.00 Mg 1 11.99 O 5810 8.00 N 5167 7.00 C 17981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.01 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6802 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 45 sheets defined 41.4% alpha, 14.0% beta 38 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 10.46 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.842A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.760A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.363A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.573A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.985A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.526A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.721A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.515A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.695A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.752A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.079A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.712A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.771A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.612A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.844A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.681A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.340A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.743A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.602A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.547A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.528A pdb=" N SER C 863 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.554A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.658A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.834A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.626A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.563A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.298A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.638A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.765A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.846A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.768A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 removed outlier: 3.747A pdb=" N THR D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 4.003A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.984A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.442A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.647A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.737A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.515A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 removed outlier: 3.922A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.651A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.672A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.538A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.067A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.857A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.591A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.556A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.507A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.757A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.157A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.561A pdb=" N GLY D1299 " --> pdb=" O GLY D1296 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1314 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.728A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.563A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.792A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.623A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 130 Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.732A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.597A pdb=" N ALA M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 removed outlier: 3.903A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 4.348A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 256 removed outlier: 3.544A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 311 removed outlier: 3.883A pdb=" N GLY M 307 " --> pdb=" O TYR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 322 through 351 removed outlier: 3.658A pdb=" N ARG M 327 " --> pdb=" O LEU M 323 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TRP M 328 " --> pdb=" O GLN M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 356 removed outlier: 3.628A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.757A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.550A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 404 removed outlier: 3.710A pdb=" N SER M 404 " --> pdb=" O TYR M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 466 removed outlier: 3.526A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 8.794A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.534A pdb=" N VAL A 98 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.729A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.386A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 7.133A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.224A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.779A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.779A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.663A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.102A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.213A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.606A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 723 through 727 removed outlier: 6.685A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC4, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.222A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.713A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.713A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.798A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1243 through 1246 Processing sheet with id=AD1, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.731A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD3, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.760A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 111 removed outlier: 10.330A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.774A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.097A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 572 " --> pdb=" O VAL D 548 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.654A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 848 through 849 removed outlier: 7.181A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 958 Processing sheet with id=AE5, first strand: chain 'D' and resid 974 through 975 removed outlier: 4.071A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.801A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 4.306A pdb=" N VAL D1176 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU D1188 " --> pdb=" O VAL D1176 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE9, first strand: chain 'M' and resid 277 through 278 removed outlier: 7.023A pdb=" N LEU M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 1181 hydrogen bonds defined for protein. 3285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 15.36 Time building geometry restraints manager: 13.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8484 1.34 - 1.46: 4728 1.46 - 1.58: 16210 1.58 - 1.70: 199 1.70 - 1.82: 177 Bond restraints: 29798 Sorted by residual: bond pdb=" N GLU C1316 " pdb=" CA GLU C1316 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 2.05e+01 bond pdb=" N GLY D 742 " pdb=" CA GLY D 742 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.99e+01 bond pdb=" CE1 HIS C1237 " pdb=" NE2 HIS C1237 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" CE1 HIS C 628 " pdb=" NE2 HIS C 628 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" CE1 HIS D 430 " pdb=" NE2 HIS D 430 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.76e+01 ... (remaining 29793 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.69: 1020 105.69 - 112.82: 16320 112.82 - 119.94: 10348 119.94 - 127.07: 12796 127.07 - 134.19: 421 Bond angle restraints: 40905 Sorted by residual: angle pdb=" C3' DT N 2 " pdb=" O3' DT N 2 " pdb=" P DA N 3 " ideal model delta sigma weight residual 120.20 108.30 11.90 1.50e+00 4.44e-01 6.29e+01 angle pdb=" C3' DA N 3 " pdb=" O3' DA N 3 " pdb=" P DG N 4 " ideal model delta sigma weight residual 120.20 111.82 8.38 1.50e+00 4.44e-01 3.12e+01 angle pdb=" CA GLY C 48 " pdb=" C GLY C 48 " pdb=" O GLY C 48 " ideal model delta sigma weight residual 122.29 118.08 4.21 8.10e-01 1.52e+00 2.71e+01 angle pdb=" C ARG A 235 " pdb=" CA ARG A 235 " pdb=" CB ARG A 235 " ideal model delta sigma weight residual 116.54 110.77 5.77 1.15e+00 7.56e-01 2.52e+01 angle pdb=" CA GLY D 103 " pdb=" C GLY D 103 " pdb=" O GLY D 103 " ideal model delta sigma weight residual 122.24 117.98 4.26 8.70e-01 1.32e+00 2.40e+01 ... (remaining 40900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 16902 34.30 - 68.60: 977 68.60 - 102.90: 36 102.90 - 137.20: 0 137.20 - 171.50: 3 Dihedral angle restraints: 17918 sinusoidal: 7374 harmonic: 10544 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 137.49 42.51 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CD ARG A 235 " pdb=" NE ARG A 235 " pdb=" CZ ARG A 235 " pdb=" NH1 ARG A 235 " ideal model delta sinusoidal sigma weight residual 0.00 -57.78 57.78 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CA PHE C 15 " pdb=" C PHE C 15 " pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 17915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4338 0.096 - 0.193: 500 0.193 - 0.289: 11 0.289 - 0.386: 0 0.386 - 0.482: 2 Chirality restraints: 4851 Sorted by residual: chirality pdb=" P DT N 2 " pdb=" OP1 DT N 2 " pdb=" OP2 DT N 2 " pdb=" O5' DT N 2 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" P DA N 3 " pdb=" OP1 DA N 3 " pdb=" OP2 DA N 3 " pdb=" O5' DA N 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CA ILE D 856 " pdb=" N ILE D 856 " pdb=" C ILE D 856 " pdb=" CB ILE D 856 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 4848 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 235 " -0.920 9.50e-02 1.11e+02 4.13e-01 1.03e+02 pdb=" NE ARG A 235 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 235 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 235 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 235 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1330 " 0.544 9.50e-02 1.11e+02 2.44e-01 3.64e+01 pdb=" NE ARG D1330 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D1330 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D1330 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D1330 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 535 " -0.420 9.50e-02 1.11e+02 1.88e-01 2.17e+01 pdb=" NE ARG D 535 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 535 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 535 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 535 " -0.014 2.00e-02 2.50e+03 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 113 2.52 - 3.12: 22072 3.12 - 3.71: 46098 3.71 - 4.31: 62752 4.31 - 4.90: 103319 Nonbonded interactions: 234354 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 1.931 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR D 980 " pdb=" O VAL D 997 " model vdw 2.188 2.440 nonbonded pdb=" OH TYR C 179 " pdb=" OE2 GLU C 458 " model vdw 2.202 2.440 nonbonded pdb=" O TYR C 810 " pdb=" OG SER C1077 " model vdw 2.206 2.440 ... (remaining 234349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.350 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: 0.020 Extract box with map and model: 3.440 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 93.120 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 0.006 0.057 29798 Z= 0.404 Angle : 0.838 14.383 40905 Z= 0.573 Chirality : 0.057 0.482 4851 Planarity : 0.010 0.413 5004 Dihedral : 18.842 171.503 11116 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.09 % Favored : 93.66 % Rotamer: Outliers : 1.66 % Allowed : 24.96 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.49 (0.14), residues: 3643 helix: 0.92 (0.15), residues: 1323 sheet: 0.30 (0.27), residues: 396 loop : -1.39 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 115 HIS 0.005 0.001 HIS C1116 PHE 0.023 0.001 PHE M 354 TYR 0.021 0.001 TYR A 177 ARG 0.010 0.001 ARG M 279 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 3.325 Fit side-chains revert: symmetry clash REVERT: C 1240 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6552 (m-30) outliers start: 45 outliers final: 12 residues processed: 220 average time/residue: 1.4407 time to fit residues: 374.9012 Evaluate side-chains 135 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 3.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 4.9990 chunk 283 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 339 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 294 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 518 ASN C1061 GLN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 300 GLN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN D1249 ASN D1259 GLN M 406 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29798 Z= 0.352 Angle : 0.623 9.552 40905 Z= 0.327 Chirality : 0.043 0.161 4851 Planarity : 0.005 0.066 5004 Dihedral : 16.366 169.763 5113 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer: Outliers : 4.47 % Allowed : 22.78 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.23 (0.14), residues: 3643 helix: 1.23 (0.14), residues: 1361 sheet: 0.56 (0.27), residues: 374 loop : -1.39 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 115 HIS 0.008 0.001 HIS C 832 PHE 0.015 0.001 PHE A 231 TYR 0.017 0.001 TYR D 631 ARG 0.009 0.001 ARG C 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 127 time to evaluate : 3.297 Fit side-chains revert: symmetry clash REVERT: C 1069 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7881 (ptt-90) REVERT: C 1319 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7316 (tpp) REVERT: D 115 TRP cc_start: 0.7988 (OUTLIER) cc_final: 0.6277 (m-90) REVERT: D 1222 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7959 (ttm-80) outliers start: 121 outliers final: 34 residues processed: 236 average time/residue: 1.2356 time to fit residues: 353.4286 Evaluate side-chains 160 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 3.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 282 optimal weight: 30.0000 chunk 231 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 340 optimal weight: 40.0000 chunk 367 optimal weight: 40.0000 chunk 303 optimal weight: 20.0000 chunk 337 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN C1061 GLN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1289 ASN ** M 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29798 Z= 0.289 Angle : 0.582 10.691 40905 Z= 0.303 Chirality : 0.042 0.157 4851 Planarity : 0.004 0.062 5004 Dihedral : 16.208 171.715 5104 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.71 % Rotamer: Outliers : 4.14 % Allowed : 23.26 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.03 (0.14), residues: 3643 helix: 1.49 (0.15), residues: 1355 sheet: 0.36 (0.26), residues: 396 loop : -1.29 (0.14), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 285 HIS 0.007 0.001 HIS M 406 PHE 0.011 0.001 PHE D 49 TYR 0.015 0.001 TYR D 140 ARG 0.005 0.000 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 123 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1069 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7929 (ptt-90) REVERT: C 1240 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7344 (m-30) REVERT: D 1222 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8121 (ttm-80) outliers start: 112 outliers final: 42 residues processed: 221 average time/residue: 1.2530 time to fit residues: 335.2093 Evaluate side-chains 164 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 119 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain C residue 1341 ASP Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 0.9980 chunk 255 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 228 optimal weight: 1.9990 chunk 341 optimal weight: 40.0000 chunk 361 optimal weight: 50.0000 chunk 178 optimal weight: 9.9990 chunk 323 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29798 Z= 0.264 Angle : 0.565 9.034 40905 Z= 0.293 Chirality : 0.041 0.196 4851 Planarity : 0.004 0.060 5004 Dihedral : 16.129 172.631 5104 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 3.73 % Allowed : 24.22 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.07 (0.14), residues: 3643 helix: 1.56 (0.15), residues: 1367 sheet: 0.56 (0.27), residues: 385 loop : -1.26 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.007 0.001 HIS M 377 PHE 0.010 0.001 PHE D 49 TYR 0.013 0.001 TYR D 140 ARG 0.005 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 124 time to evaluate : 3.247 Fit side-chains revert: symmetry clash REVERT: C 1069 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8010 (ptt-90) REVERT: D 1222 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8058 (ttm-80) outliers start: 101 outliers final: 46 residues processed: 215 average time/residue: 1.2784 time to fit residues: 333.8049 Evaluate side-chains 167 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 119 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 149 optimal weight: 7.9990 chunk 308 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 184 optimal weight: 2.9990 chunk 324 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29798 Z= 0.230 Angle : 0.552 11.237 40905 Z= 0.285 Chirality : 0.041 0.206 4851 Planarity : 0.004 0.058 5004 Dihedral : 16.094 173.673 5102 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 3.66 % Allowed : 24.96 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.16 (0.14), residues: 3643 helix: 1.70 (0.15), residues: 1359 sheet: 0.58 (0.27), residues: 383 loop : -1.25 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 126 HIS 0.003 0.001 HIS M 377 PHE 0.009 0.001 PHE D 116 TYR 0.015 0.001 TYR C 105 ARG 0.004 0.000 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 123 time to evaluate : 3.272 Fit side-chains revert: symmetry clash REVERT: C 1069 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7971 (ptt-90) REVERT: D 1222 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8043 (ttm-80) outliers start: 99 outliers final: 47 residues processed: 209 average time/residue: 1.2744 time to fit residues: 327.5825 Evaluate side-chains 169 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 120 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 212 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 361 optimal weight: 50.0000 chunk 300 optimal weight: 0.0970 chunk 167 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1220 GLN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29798 Z= 0.318 Angle : 0.581 10.283 40905 Z= 0.301 Chirality : 0.042 0.208 4851 Planarity : 0.004 0.059 5004 Dihedral : 16.127 174.557 5100 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.45 % Favored : 93.52 % Rotamer: Outliers : 3.80 % Allowed : 25.00 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.14 (0.14), residues: 3643 helix: 1.70 (0.15), residues: 1359 sheet: 0.53 (0.27), residues: 383 loop : -1.26 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 321 HIS 0.006 0.001 HIS M 377 PHE 0.012 0.001 PHE D 49 TYR 0.015 0.001 TYR D 631 ARG 0.004 0.000 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 121 time to evaluate : 3.242 Fit side-chains revert: symmetry clash REVERT: C 741 MET cc_start: 0.7537 (mtp) cc_final: 0.7268 (ttt) REVERT: C 1069 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8006 (ptt-90) REVERT: D 1003 LEU cc_start: 0.7124 (pp) cc_final: 0.6790 (pt) REVERT: D 1222 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.8048 (ttm-80) outliers start: 103 outliers final: 50 residues processed: 214 average time/residue: 1.2323 time to fit residues: 323.0971 Evaluate side-chains 172 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 120 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 264 optimal weight: 7.9990 chunk 204 optimal weight: 40.0000 chunk 304 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 360 optimal weight: 30.0000 chunk 225 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29798 Z= 0.314 Angle : 0.591 10.378 40905 Z= 0.305 Chirality : 0.042 0.205 4851 Planarity : 0.004 0.059 5004 Dihedral : 16.142 175.946 5100 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.67 % Favored : 93.30 % Rotamer: Outliers : 3.21 % Allowed : 25.74 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.18 (0.14), residues: 3643 helix: 1.75 (0.15), residues: 1350 sheet: 0.55 (0.27), residues: 383 loop : -1.24 (0.14), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 126 HIS 0.003 0.001 HIS D1252 PHE 0.011 0.001 PHE D 49 TYR 0.015 0.001 TYR M 401 ARG 0.004 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 122 time to evaluate : 3.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 741 MET cc_start: 0.7594 (mtp) cc_final: 0.7335 (ttt) REVERT: C 1069 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8050 (ptt-90) outliers start: 87 outliers final: 56 residues processed: 199 average time/residue: 1.2527 time to fit residues: 303.4055 Evaluate side-chains 175 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 118 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1356 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 357 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 0.6980 chunk 143 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 229 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 391 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29798 Z= 0.222 Angle : 0.566 12.142 40905 Z= 0.290 Chirality : 0.041 0.199 4851 Planarity : 0.004 0.058 5004 Dihedral : 16.070 176.838 5100 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.71 % Rotamer: Outliers : 3.06 % Allowed : 26.11 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.24 (0.14), residues: 3643 helix: 1.82 (0.15), residues: 1351 sheet: 0.66 (0.28), residues: 372 loop : -1.23 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.003 0.001 HIS A 66 PHE 0.008 0.001 PHE C 906 TYR 0.016 0.001 TYR M 401 ARG 0.007 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 121 time to evaluate : 3.448 Fit side-chains revert: symmetry clash REVERT: C 1069 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8098 (ptt-90) outliers start: 83 outliers final: 47 residues processed: 194 average time/residue: 1.2854 time to fit residues: 303.0385 Evaluate side-chains 164 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 116 time to evaluate : 3.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 30.0000 chunk 345 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 chunk 335 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 263 optimal weight: 9.9990 chunk 103 optimal weight: 9.9990 chunk 303 optimal weight: 20.0000 chunk 317 optimal weight: 8.9990 chunk 334 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 450 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29798 Z= 0.327 Angle : 0.609 14.415 40905 Z= 0.312 Chirality : 0.042 0.311 4851 Planarity : 0.004 0.058 5004 Dihedral : 16.120 177.148 5098 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.70 % Favored : 93.27 % Rotamer: Outliers : 2.81 % Allowed : 26.40 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.22 (0.14), residues: 3643 helix: 1.80 (0.15), residues: 1351 sheet: 0.59 (0.27), residues: 374 loop : -1.23 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 126 HIS 0.005 0.001 HIS M 406 PHE 0.012 0.001 PHE D 49 TYR 0.021 0.001 TYR M 361 ARG 0.008 0.000 ARG D 388 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 119 time to evaluate : 3.503 Fit side-chains revert: symmetry clash REVERT: C 1069 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8060 (ptt-90) REVERT: D 130 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7308 (ptm) REVERT: D 901 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7241 (ptp-170) outliers start: 76 outliers final: 54 residues processed: 186 average time/residue: 1.2928 time to fit residues: 290.5218 Evaluate side-chains 174 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 117 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 6.9990 chunk 355 optimal weight: 7.9990 chunk 216 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 246 optimal weight: 10.0000 chunk 372 optimal weight: 20.0000 chunk 342 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 229 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 29798 Z= 0.361 Angle : 0.625 13.575 40905 Z= 0.320 Chirality : 0.043 0.340 4851 Planarity : 0.004 0.059 5004 Dihedral : 16.187 177.812 5098 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.36 % Rotamer: Outliers : 2.51 % Allowed : 26.51 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.16 (0.14), residues: 3643 helix: 1.75 (0.14), residues: 1358 sheet: 0.46 (0.27), residues: 380 loop : -1.25 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 126 HIS 0.004 0.001 HIS M 406 PHE 0.019 0.001 PHE M 403 TYR 0.019 0.001 TYR M 401 ARG 0.007 0.000 ARG D 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 119 time to evaluate : 3.414 Fit side-chains revert: symmetry clash REVERT: C 436 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7651 (ttm-80) REVERT: C 1066 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7610 (mtp) REVERT: C 1069 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8048 (ptt-90) REVERT: D 115 TRP cc_start: 0.8365 (OUTLIER) cc_final: 0.7198 (m-90) REVERT: D 130 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7153 (ptt) REVERT: D 901 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7240 (ptp-170) outliers start: 68 outliers final: 52 residues processed: 179 average time/residue: 1.3496 time to fit residues: 292.7223 Evaluate side-chains 176 residues out of total 3136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 118 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 130 MET Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 235 optimal weight: 5.9990 chunk 316 optimal weight: 8.9990 chunk 90 optimal weight: 0.0870 chunk 273 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 297 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D1244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.065957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.041097 restraints weight = 107332.695| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.31 r_work: 0.2648 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2646 r_free = 0.2646 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29798 Z= 0.267 Angle : 0.596 13.431 40905 Z= 0.304 Chirality : 0.042 0.232 4851 Planarity : 0.004 0.059 5004 Dihedral : 16.154 178.407 5098 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.71 % Rotamer: Outliers : 2.62 % Allowed : 26.44 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.21 (0.14), residues: 3643 helix: 1.80 (0.14), residues: 1354 sheet: 0.47 (0.27), residues: 383 loop : -1.22 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 212 HIS 0.004 0.001 HIS M 406 PHE 0.015 0.001 PHE M 403 TYR 0.020 0.001 TYR M 401 ARG 0.007 0.000 ARG D 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7579.86 seconds wall clock time: 138 minutes 3.77 seconds (8283.77 seconds total)