Starting phenix.real_space_refine on Fri Feb 23 01:35:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4y_22044/02_2024/6x4y_22044_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4y_22044/02_2024/6x4y_22044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4y_22044/02_2024/6x4y_22044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4y_22044/02_2024/6x4y_22044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4y_22044/02_2024/6x4y_22044_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x4y_22044/02_2024/6x4y_22044_updated.pdb" } resolution = 3.6 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= 0.006 sd= 1.070 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 114 5.49 5 Mg 2 5.21 5 S 142 5.16 5 C 22317 2.51 5 N 6408 2.21 5 O 7103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 158": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A GLU 957": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 76": "OE1" <-> "OE2" Residue "G GLU 80": "OE1" <-> "OE2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "H GLU 204": "OE1" <-> "OE2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H GLU 214": "OE1" <-> "OE2" Residue "I GLU 40": "OE1" <-> "OE2" Residue "I GLU 84": "OE1" <-> "OE2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I GLU 256": "OE1" <-> "OE2" Residue "I ARG 268": "NH1" <-> "NH2" Residue "I GLU 290": "OE1" <-> "OE2" Residue "I GLU 304": "OE1" <-> "OE2" Residue "I ARG 332": "NH1" <-> "NH2" Residue "I GLU 365": "OE1" <-> "OE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "I GLU 626": "OE1" <-> "OE2" Residue "I GLU 631": "OE1" <-> "OE2" Residue "I GLU 738": "OE1" <-> "OE2" Residue "I GLU 778": "OE1" <-> "OE2" Residue "I GLU 813": "OE1" <-> "OE2" Residue "I GLU 859": "OE1" <-> "OE2" Residue "I ASP 942": "OD1" <-> "OD2" Residue "I GLU 950": "OE1" <-> "OE2" Residue "I GLU 987": "OE1" <-> "OE2" Residue "I GLU 1024": "OE1" <-> "OE2" Residue "I ASP 1064": "OD1" <-> "OD2" Residue "I GLU 1143": "OE1" <-> "OE2" Residue "I GLU 1174": "OE1" <-> "OE2" Residue "I GLU 1197": "OE1" <-> "OE2" Residue "I GLU 1316": "OE1" <-> "OE2" Residue "I GLU 1338": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J GLU 142": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J GLU 207": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J GLU 402": "OE1" <-> "OE2" Residue "J GLU 404": "OE1" <-> "OE2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J GLU 497": "OE1" <-> "OE2" Residue "J GLU 562": "OE1" <-> "OE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J GLU 652": "OE1" <-> "OE2" Residue "J GLU 714": "OE1" <-> "OE2" Residue "J GLU 811": "OE1" <-> "OE2" Residue "J GLU 846": "OE1" <-> "OE2" Residue "J GLU 913": "OE1" <-> "OE2" Residue "J GLU 981": "OE1" <-> "OE2" Residue "J GLU 1030": "OE1" <-> "OE2" Residue "J GLU 1066": "OE1" <-> "OE2" Residue "J GLU 1110": "OE1" <-> "OE2" Residue "J GLU 1146": "OE1" <-> "OE2" Residue "J GLU 1158": "OE1" <-> "OE2" Residue "J GLU 1187": "OE1" <-> "OE2" Residue "J GLU 1205": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K GLU 71": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36088 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1144, 8958 Classifications: {'peptide': 1144} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 55, 'TRANS': 1088} Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 129 Chain: "G" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1725 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 208} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "I" Number of atoms: 10373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1316, 10373 Classifications: {'peptide': 1316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1260} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "J" Number of atoms: 10383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10383 Classifications: {'peptide': 1336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1280} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 221 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "P" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1112 Classifications: {'DNA': 55} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 54} Chain: "Q" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 991 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" 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 23172 SG CYS J 70 25.047 95.205 100.651 1.00112.87 S ATOM 23186 SG CYS J 72 24.543 98.644 99.389 1.00118.54 S ATOM 23294 SG CYS J 85 22.368 95.538 98.439 1.00112.26 S ATOM 23318 SG CYS J 88 26.163 95.835 97.250 1.00111.11 S ATOM 28994 SG CYS J 814 52.409 34.517 103.893 1.00 80.10 S ATOM 29559 SG CYS J 888 53.415 38.006 103.635 1.00 70.16 S ATOM 29610 SG CYS J 895 51.934 36.475 107.150 1.00 70.25 S ATOM 29631 SG CYS J 898 55.384 35.597 105.566 1.00 66.00 S Time building chain proxies: 19.70, per 1000 atoms: 0.55 Number of scatterers: 36088 At special positions: 0 Unit cell: (140.4, 196.3, 192.4, 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 142 16.00 P 114 15.00 Mg 2 11.99 O 7103 8.00 N 6408 7.00 C 22317 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: 15.29 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " Number of angles added : 12 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 44 sheets defined 32.2% alpha, 11.6% beta 54 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 17.80 Creating SS restraints... Processing helix chain 'A' and resid 27 through 37 Processing helix chain 'A' and resid 49 through 62 removed outlier: 4.431A pdb=" N SER A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 3.832A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 221 through 234 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 288 through 306 removed outlier: 4.071A pdb=" N GLU A 293 " --> pdb=" O GLU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 320 No H-bonds generated for 'chain 'A' and resid 317 through 320' Processing helix chain 'A' and resid 324 through 333 removed outlier: 4.525A pdb=" N LYS A 332 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 removed outlier: 3.620A pdb=" N GLU A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 404 removed outlier: 3.573A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 446 through 448 No H-bonds generated for 'chain 'A' and resid 446 through 448' Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 514 through 516 No H-bonds generated for 'chain 'A' and resid 514 through 516' Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 568 through 577 Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.714A pdb=" N PHE A 593 " --> pdb=" O GLN A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 617 Processing helix chain 'A' and resid 635 through 648 removed outlier: 3.698A pdb=" N ASN A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 674 Processing helix chain 'A' and resid 689 through 701 removed outlier: 4.231A pdb=" N GLN A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.512A pdb=" N ARG A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 832 removed outlier: 3.860A pdb=" N GLU A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 859 removed outlier: 3.979A pdb=" N HIS A 859 " --> pdb=" O ASN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 872 Processing helix chain 'A' and resid 893 through 900 Processing helix chain 'A' and resid 924 through 935 Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.557A pdb=" N ALA A 946 " --> pdb=" O GLY A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 987 Processing helix chain 'A' and resid 994 through 1000 removed outlier: 3.624A pdb=" N SER A 999 " --> pdb=" O GLU A 995 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A1000 " --> pdb=" O ASP A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1032 Processing helix chain 'A' and resid 1036 through 1050 Processing helix chain 'A' and resid 1055 through 1073 removed outlier: 3.860A pdb=" N GLN A1069 " --> pdb=" O ARG A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1128 through 1145 removed outlier: 4.216A pdb=" N GLU A1144 " --> pdb=" O ARG A1140 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 49 Processing helix chain 'G' and resid 78 through 85 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 213 through 230 removed outlier: 4.618A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.859A pdb=" N ASN H 41 " --> pdb=" O HIS H 37 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 86 Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 213 through 227 Processing helix chain 'I' and resid 29 through 38 Processing helix chain 'I' and resid 48 through 56 Processing helix chain 'I' and resid 82 through 88 Processing helix chain 'I' and resid 206 through 213 removed outlier: 3.518A pdb=" N LEU I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 224 Processing helix chain 'I' and resid 243 through 246 removed outlier: 3.715A pdb=" N LEU I 246 " --> pdb=" O PRO I 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 243 through 246' Processing helix chain 'I' and resid 271 through 279 Processing helix chain 'I' and resid 289 through 293 Processing helix chain 'I' and resid 319 through 328 Processing helix chain 'I' and resid 348 through 353 Processing helix chain 'I' and resid 359 through 370 Processing helix chain 'I' and resid 378 through 389 removed outlier: 3.794A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 399 through 408 Processing helix chain 'I' and resid 422 through 437 Processing helix chain 'I' and resid 456 through 480 removed outlier: 3.828A pdb=" N ARG I 470 " --> pdb=" O VAL I 466 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL I 471 " --> pdb=" O GLY I 467 " (cutoff:3.500A) Processing helix chain 'I' and resid 496 through 506 removed outlier: 4.392A pdb=" N PHE I 505 " --> pdb=" O ALA I 501 " (cutoff:3.500A) Processing helix chain 'I' and resid 521 through 526 Processing helix chain 'I' and resid 545 through 548 No H-bonds generated for 'chain 'I' and resid 545 through 548' Processing helix chain 'I' and resid 610 through 612 No H-bonds generated for 'chain 'I' and resid 610 through 612' Processing helix chain 'I' and resid 671 through 673 No H-bonds generated for 'chain 'I' and resid 671 through 673' Processing helix chain 'I' and resid 677 through 688 removed outlier: 4.266A pdb=" N GLN I 688 " --> pdb=" O ASN I 684 " (cutoff:3.500A) Processing helix chain 'I' and resid 705 through 711 Processing helix chain 'I' and resid 820 through 824 Processing helix chain 'I' and resid 943 through 978 Processing helix chain 'I' and resid 988 through 990 No H-bonds generated for 'chain 'I' and resid 988 through 990' Processing helix chain 'I' and resid 1006 through 1037 removed outlier: 4.451A pdb=" N GLU I1030 " --> pdb=" O GLU I1026 " (cutoff:3.500A) Processing helix chain 'I' and resid 1082 through 1084 No H-bonds generated for 'chain 'I' and resid 1082 through 1084' Processing helix chain 'I' and resid 1100 through 1105 Proline residue: I1104 - end of helix Processing helix chain 'I' and resid 1110 through 1133 Processing helix chain 'I' and resid 1138 through 1149 Processing helix chain 'I' and resid 1161 through 1163 No H-bonds generated for 'chain 'I' and resid 1161 through 1163' Processing helix chain 'I' and resid 1168 through 1178 removed outlier: 5.085A pdb=" N LYS I1178 " --> pdb=" O GLU I1174 " (cutoff:3.500A) Processing helix chain 'I' and resid 1192 through 1201 Processing helix chain 'I' and resid 1272 through 1279 Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1298 through 1309 removed outlier: 4.031A pdb=" N LYS I1303 " --> pdb=" O ASN I1299 " (cutoff:3.500A) Processing helix chain 'I' and resid 1321 through 1331 removed outlier: 3.745A pdb=" N LEU I1326 " --> pdb=" O SER I1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 123 through 127 Processing helix chain 'J' and resid 132 through 139 Processing helix chain 'J' and resid 162 through 171 Processing helix chain 'J' and resid 182 through 190 Processing helix chain 'J' and resid 194 through 206 Processing helix chain 'J' and resid 214 through 229 removed outlier: 4.329A pdb=" N LYS J 219 " --> pdb=" O LYS J 215 " (cutoff:3.500A) Processing helix chain 'J' and resid 234 through 237 Processing helix chain 'J' and resid 264 through 284 Processing helix chain 'J' and resid 289 through 307 Processing helix chain 'J' and resid 328 through 330 No H-bonds generated for 'chain 'J' and resid 328 through 330' Processing helix chain 'J' and resid 337 through 340 No H-bonds generated for 'chain 'J' and resid 337 through 340' Processing helix chain 'J' and resid 370 through 376 Processing helix chain 'J' and resid 378 through 387 Processing helix chain 'J' and resid 395 through 403 Processing helix chain 'J' and resid 408 through 415 Processing helix chain 'J' and resid 431 through 433 No H-bonds generated for 'chain 'J' and resid 431 through 433' Processing helix chain 'J' and resid 474 through 483 Processing helix chain 'J' and resid 505 through 513 Processing helix chain 'J' and resid 530 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.887A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 589 through 591 No H-bonds generated for 'chain 'J' and resid 589 through 591' Processing helix chain 'J' and resid 598 through 612 Processing helix chain 'J' and resid 615 through 635 Processing helix chain 'J' and resid 648 through 669 removed outlier: 3.957A pdb=" N HIS J 651 " --> pdb=" O GLU J 648 " (cutoff:3.500A) Processing helix chain 'J' and resid 675 through 702 Processing helix chain 'J' and resid 721 through 727 Processing helix chain 'J' and resid 734 through 741 Processing helix chain 'J' and resid 769 through 804 removed outlier: 4.058A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) Processing helix chain 'J' and resid 835 through 838 No H-bonds generated for 'chain 'J' and resid 835 through 838' Processing helix chain 'J' and resid 866 through 875 Processing helix chain 'J' and resid 915 through 924 Processing helix chain 'J' and resid 926 through 928 No H-bonds generated for 'chain 'J' and resid 926 through 928' Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1217 through 1224 Processing helix chain 'J' and resid 1226 through 1244 removed outlier: 3.849A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN J1235 " --> pdb=" O ARG J1231 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU J1243 " --> pdb=" O ASP J1239 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1251 through 1260 removed outlier: 4.080A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1294 removed outlier: 3.646A pdb=" N ILE J1287 " --> pdb=" O SER J1283 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU J1293 " --> pdb=" O ASN J1289 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1309 through 1314 Processing helix chain 'J' and resid 1319 through 1323 Processing helix chain 'J' and resid 1328 through 1337 Processing helix chain 'J' and resid 1349 through 1353 Processing helix chain 'J' and resid 1361 through 1372 removed outlier: 4.314A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 12 Processing helix chain 'K' and resid 18 through 31 Processing helix chain 'K' and resid 46 through 55 Processing helix chain 'K' and resid 61 through 78 Processing sheet with id= A, first strand: chain 'A' and resid 350 through 352 removed outlier: 8.263A pdb=" N ALA A 351 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 18 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ARG A 336 " --> pdb=" O ARG A 17 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N LEU A 19 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLN A 338 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THR A 285 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= C, first strand: chain 'A' and resid 162 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 355 through 357 Processing sheet with id= E, first strand: chain 'A' and resid 384 through 386 removed outlier: 5.914A pdb=" N GLY A 422 " --> pdb=" O VAL A 385 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 489 through 492 Processing sheet with id= G, first strand: chain 'A' and resid 496 through 500 removed outlier: 3.722A pdb=" N VAL A 521 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 652 through 655 removed outlier: 6.576A pdb=" N LEU A 725 " --> pdb=" O ALA A 653 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU A 655 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 727 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP A 750 " --> pdb=" O LEU A 726 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL A 728 " --> pdb=" O ASP A 750 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 752 " --> pdb=" O VAL A 728 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 680 through 683 removed outlier: 6.547A pdb=" N ILE A 706 " --> pdb=" O GLU A 681 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE A 683 " --> pdb=" O ILE A 706 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 708 " --> pdb=" O ILE A 683 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 787 through 792 removed outlier: 3.587A pdb=" N ARG A 791 " --> pdb=" O LEU A 914 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA A 839 " --> pdb=" O VAL A 866 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1003 through 1005 Processing sheet with id= L, first strand: chain 'A' and resid 193 through 195 removed outlier: 3.646A pdb=" N GLU A 204 " --> pdb=" O VAL A 194 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.867A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG G 182 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.685A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLY G 149 " --> pdb=" O CYS G 54 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N CYS G 54 " --> pdb=" O GLY G 149 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 151 through 153 Processing sheet with id= P, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.541A pdb=" N CYS G 131 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 13 through 18 Processing sheet with id= R, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= S, first strand: chain 'H' and resid 97 through 101 removed outlier: 3.664A pdb=" N GLU H 58 " --> pdb=" O LYS H 145 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLY H 149 " --> pdb=" O CYS H 54 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N CYS H 54 " --> pdb=" O GLY H 149 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 108 through 110 removed outlier: 3.510A pdb=" N CYS H 131 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.506A pdb=" N ILE I 127 " --> pdb=" O ALA I 94 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 116 through 123 removed outlier: 3.900A pdb=" N ASP I 116 " --> pdb=" O ILE I 104 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 143 through 145 Processing sheet with id= X, first strand: chain 'I' and resid 148 through 151 Processing sheet with id= Y, first strand: chain 'I' and resid 154 through 159 removed outlier: 6.569A pdb=" N TYR I 172 " --> pdb=" O PHE I 188 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE I 188 " --> pdb=" O TYR I 172 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN I 193 " --> pdb=" O ASP I 189 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 227 through 231 Processing sheet with id= AA, first strand: chain 'I' and resid 603 through 606 Processing sheet with id= AB, first strand: chain 'I' and resid 633 through 637 Processing sheet with id= AC, first strand: chain 'I' and resid 749 through 752 removed outlier: 3.679A pdb=" N TYR I 726 " --> pdb=" O VAL I 733 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 1226 through 1232 removed outlier: 4.306A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE I1096 " --> pdb=" O ALA I 803 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'I' and resid 830 through 839 removed outlier: 3.792A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.704A pdb=" N ALA I 257 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL I 261 " --> pdb=" O ALA I 257 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.413A pdb=" N VAL I 818 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE I1079 " --> pdb=" O VAL I 818 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 103 through 106 removed outlier: 3.650A pdb=" N GLY J 103 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL J 244 " --> pdb=" O GLY J 103 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'J' and resid 350 through 354 Processing sheet with id= AJ, first strand: chain 'J' and resid 547 through 556 Processing sheet with id= AK, first strand: chain 'J' and resid 820 through 823 Processing sheet with id= AL, first strand: chain 'J' and resid 957 through 961 Processing sheet with id= AM, first strand: chain 'J' and resid 965 through 967 Processing sheet with id= AN, first strand: chain 'J' and resid 1034 through 1038 Processing sheet with id= AO, first strand: chain 'J' and resid 1059 through 1061 removed outlier: 3.675A pdb=" N ALA J1105 " --> pdb=" O VAL J1061 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id= AQ, first strand: chain 'J' and resid 1279 through 1281 removed outlier: 4.181A pdb=" N LYS J1263 " --> pdb=" O ASP J1305 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR J1301 " --> pdb=" O VAL J1267 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'J' and resid 949 through 952 removed outlier: 3.578A pdb=" N ILE J 950 " --> pdb=" O ALA J1018 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA J1018 " --> pdb=" O ILE J 950 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL J 952 " --> pdb=" O THR J1016 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR J1016 " --> pdb=" O VAL J 952 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR 1097 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 278 hydrogen bond angles 0 basepair planarities 54 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 16.64 Time building geometry restraints manager: 16.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6061 1.31 - 1.44: 9473 1.44 - 1.57: 20900 1.57 - 1.69: 225 1.69 - 1.82: 249 Bond restraints: 36908 Sorted by residual: bond pdb=" C VAL A 786 " pdb=" O VAL A 786 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.12e-02 7.97e+03 1.76e+01 bond pdb=" N ARG A 783 " pdb=" CA ARG A 783 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" N MET I 488 " pdb=" CA MET I 488 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.04e-02 9.25e+03 1.05e+01 bond pdb=" N ILE A 465 " pdb=" CA ILE A 465 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N GLN I 490 " pdb=" CA GLN I 490 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.75e+00 ... (remaining 36903 not shown) Histogram of bond angle deviations from ideal: 94.62 - 102.94: 444 102.94 - 111.25: 15304 111.25 - 119.57: 16608 119.57 - 127.88: 17664 127.88 - 136.20: 380 Bond angle restraints: 50400 Sorted by residual: angle pdb=" N SER J 210 " pdb=" CA SER J 210 " pdb=" C SER J 210 " ideal model delta sigma weight residual 112.68 100.70 11.98 1.33e+00 5.65e-01 8.11e+01 angle pdb=" N ILE I 292 " pdb=" CA ILE I 292 " pdb=" C ILE I 292 " ideal model delta sigma weight residual 113.71 106.26 7.45 9.50e-01 1.11e+00 6.15e+01 angle pdb=" N THR J 212 " pdb=" CA THR J 212 " pdb=" C THR J 212 " ideal model delta sigma weight residual 114.64 104.51 10.13 1.52e+00 4.33e-01 4.44e+01 angle pdb=" N VAL J 839 " pdb=" CA VAL J 839 " pdb=" C VAL J 839 " ideal model delta sigma weight residual 111.88 105.29 6.59 1.06e+00 8.90e-01 3.87e+01 angle pdb=" CB MET A 639 " pdb=" CG MET A 639 " pdb=" SD MET A 639 " ideal model delta sigma weight residual 112.70 94.62 18.08 3.00e+00 1.11e-01 3.63e+01 ... (remaining 50395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.31: 20578 25.31 - 50.62: 1478 50.62 - 75.93: 255 75.93 - 101.23: 24 101.23 - 126.54: 2 Dihedral angle restraints: 22337 sinusoidal: 9908 harmonic: 12429 Sorted by residual: dihedral pdb=" O4' C R 11 " pdb=" C1' C R 11 " pdb=" N1 C R 11 " pdb=" C2 C R 11 " ideal model delta sinusoidal sigma weight residual 200.00 106.82 93.18 1 1.50e+01 4.44e-03 4.50e+01 dihedral pdb=" C5' ADP A2000 " pdb=" O5' ADP A2000 " pdb=" PA ADP A2000 " pdb=" O2A ADP A2000 " ideal model delta sinusoidal sigma weight residual -60.00 62.21 -122.21 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" CA ARG J 47 " pdb=" C ARG J 47 " pdb=" N THR J 48 " pdb=" CA THR J 48 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 22334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5254 0.094 - 0.189: 465 0.189 - 0.283: 21 0.283 - 0.378: 6 0.378 - 0.472: 1 Chirality restraints: 5747 Sorted by residual: chirality pdb=" CB ILE I 117 " pdb=" CA ILE I 117 " pdb=" CG1 ILE I 117 " pdb=" CG2 ILE I 117 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CB ILE A 444 " pdb=" CA ILE A 444 " pdb=" CG1 ILE A 444 " pdb=" CG2 ILE A 444 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR J 553 " pdb=" CA THR J 553 " pdb=" OG1 THR J 553 " pdb=" CG2 THR J 553 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 5744 not shown) Planarity restraints: 6199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 464 " -0.021 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C THR A 464 " 0.071 2.00e-02 2.50e+03 pdb=" O THR A 464 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE A 465 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU J 211 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C GLU J 211 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU J 211 " 0.020 2.00e-02 2.50e+03 pdb=" N THR J 212 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 98 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.68e+00 pdb=" N PRO A 99 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.041 5.00e-02 4.00e+02 ... (remaining 6196 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 257 2.51 - 3.11: 26093 3.11 - 3.71: 57424 3.71 - 4.30: 78672 4.30 - 4.90: 129409 Nonbonded interactions: 291855 Sorted by model distance: nonbonded pdb=" OD1 ASP H 15 " pdb=" OG1 THR H 27 " model vdw 1.919 2.440 nonbonded pdb=" O3' A R 20 " pdb="MG MG J1501 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP J 460 " pdb="MG MG J1501 " model vdw 2.008 2.170 nonbonded pdb=" OD1 ASP J 464 " pdb="MG MG J1501 " model vdw 2.042 2.170 nonbonded pdb=" O ARG H 45 " pdb=" OG SER H 49 " model vdw 2.184 2.440 ... (remaining 291850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 5 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 158 or resid 170 th \ rough 232)) selection = (chain 'H' and (resid 5 through 190 or (resid 191 and (name N or name CA or name \ C or name O or name CB )) or resid 192 through 232)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.980 Check model and map are aligned: 0.520 Set scattering table: 0.320 Process input model: 113.220 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 0.068 36908 Z= 0.415 Angle : 0.957 18.080 50400 Z= 0.535 Chirality : 0.055 0.472 5747 Planarity : 0.006 0.074 6199 Dihedral : 16.879 126.543 14325 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.06 % Favored : 91.59 % Rotamer: Outliers : 0.28 % Allowed : 0.52 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.60 (0.12), residues: 4294 helix: -0.97 (0.12), residues: 1507 sheet: -1.81 (0.20), residues: 618 loop : -2.25 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP J 115 HIS 0.013 0.001 HIS J 777 PHE 0.032 0.002 PHE I 186 TYR 0.037 0.002 TYR G 177 ARG 0.021 0.001 ARG G 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 474 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.7623 (tmm) cc_final: 0.7015 (tmm) REVERT: A 242 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 629 ASP cc_start: 0.6824 (t0) cc_final: 0.6364 (t0) REVERT: A 800 GLU cc_start: 0.7897 (pp20) cc_final: 0.7696 (pp20) REVERT: A 811 GLN cc_start: 0.8740 (mp10) cc_final: 0.8499 (mp10) REVERT: A 879 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7215 (p) REVERT: H 125 LYS cc_start: 0.7960 (tptm) cc_final: 0.7706 (tttp) REVERT: H 131 CYS cc_start: 0.8813 (m) cc_final: 0.8510 (m) REVERT: I 459 MET cc_start: 0.8915 (mtm) cc_final: 0.8696 (mtp) REVERT: I 488 MET cc_start: 0.8010 (mmm) cc_final: 0.6588 (mmm) REVERT: I 492 MET cc_start: 0.7697 (pmm) cc_final: 0.7411 (pmm) REVERT: I 955 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7207 (tp40) REVERT: I 959 ASP cc_start: 0.7962 (m-30) cc_final: 0.7645 (m-30) REVERT: I 1264 GLN cc_start: 0.8141 (mp-120) cc_final: 0.7905 (mp10) REVERT: J 117 LEU cc_start: 0.9071 (tp) cc_final: 0.8831 (tp) REVERT: J 129 ASP cc_start: 0.7682 (t70) cc_final: 0.7459 (t0) REVERT: J 133 ARG cc_start: 0.7533 (mtt180) cc_final: 0.7305 (mtt180) REVERT: J 698 MET cc_start: 0.9055 (tpt) cc_final: 0.8784 (mmt) REVERT: J 1334 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7331 (tm-30) outliers start: 10 outliers final: 5 residues processed: 480 average time/residue: 0.5172 time to fit residues: 404.4395 Evaluate side-chains 383 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 377 time to evaluate : 3.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain J residue 210 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 0.8980 chunk 331 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 343 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 208 optimal weight: 0.0970 chunk 255 optimal weight: 10.0000 chunk 397 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN I 273 HIS ** I 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN J 209 ASN J 232 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36908 Z= 0.171 Angle : 0.595 12.271 50400 Z= 0.309 Chirality : 0.042 0.250 5747 Planarity : 0.004 0.056 6199 Dihedral : 15.241 125.515 6006 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.29 % Favored : 93.60 % Rotamer: Outliers : 0.75 % Allowed : 8.23 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.12), residues: 4294 helix: -0.22 (0.13), residues: 1501 sheet: -1.40 (0.21), residues: 635 loop : -2.02 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 115 HIS 0.006 0.001 HIS A 84 PHE 0.019 0.001 PHE A 377 TYR 0.018 0.001 TYR H 185 ARG 0.005 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 447 time to evaluate : 4.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 ASP cc_start: 0.6882 (t0) cc_final: 0.6306 (t0) REVERT: A 800 GLU cc_start: 0.7943 (pp20) cc_final: 0.7577 (pp20) REVERT: A 811 GLN cc_start: 0.8638 (mp10) cc_final: 0.8436 (mp10) REVERT: A 879 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7588 (p) REVERT: G 33 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7576 (mmm160) REVERT: H 18 GLN cc_start: 0.8648 (tp-100) cc_final: 0.8345 (mm-40) REVERT: H 75 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8020 (tm-30) REVERT: H 125 LYS cc_start: 0.7816 (tptm) cc_final: 0.7541 (tttp) REVERT: H 131 CYS cc_start: 0.8619 (m) cc_final: 0.8265 (m) REVERT: H 206 GLU cc_start: 0.7919 (tt0) cc_final: 0.7659 (tt0) REVERT: I 185 ASP cc_start: 0.6641 (OUTLIER) cc_final: 0.6163 (p0) REVERT: I 200 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7517 (mtt-85) REVERT: I 396 ASP cc_start: 0.8529 (t0) cc_final: 0.7554 (p0) REVERT: I 488 MET cc_start: 0.7830 (mmm) cc_final: 0.6928 (mmm) REVERT: I 955 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7205 (tp40) REVERT: I 959 ASP cc_start: 0.7819 (m-30) cc_final: 0.7426 (m-30) REVERT: J 129 ASP cc_start: 0.7631 (t70) cc_final: 0.7295 (t0) REVERT: J 372 MET cc_start: 0.8835 (mtp) cc_final: 0.8572 (mtp) REVERT: J 402 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7755 (tm-30) REVERT: J 404 GLU cc_start: 0.7822 (mp0) cc_final: 0.7592 (mp0) REVERT: J 500 ILE cc_start: 0.9157 (mm) cc_final: 0.8789 (pt) REVERT: J 806 ASP cc_start: 0.8374 (p0) cc_final: 0.8125 (p0) REVERT: J 918 ILE cc_start: 0.8757 (pt) cc_final: 0.8465 (mt) REVERT: J 1334 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7295 (tm-30) REVERT: K 71 GLU cc_start: 0.7921 (tt0) cc_final: 0.7333 (tm-30) outliers start: 27 outliers final: 17 residues processed: 457 average time/residue: 0.4858 time to fit residues: 361.8624 Evaluate side-chains 407 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 388 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 879 THR Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 506 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 331 optimal weight: 3.9990 chunk 270 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 398 optimal weight: 0.5980 chunk 430 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 395 optimal weight: 20.0000 chunk 135 optimal weight: 0.0970 chunk 319 optimal weight: 7.9990 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 863 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 ASN H 227 GLN I 273 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN J 716 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 36908 Z= 0.415 Angle : 0.679 12.511 50400 Z= 0.350 Chirality : 0.045 0.235 5747 Planarity : 0.005 0.053 6199 Dihedral : 15.246 127.171 6001 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.57 % Favored : 91.31 % Rotamer: Outliers : 1.88 % Allowed : 13.25 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.12), residues: 4294 helix: -0.11 (0.13), residues: 1503 sheet: -1.59 (0.20), residues: 647 loop : -1.95 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J1193 HIS 0.011 0.001 HIS J 777 PHE 0.020 0.002 PHE A 377 TYR 0.022 0.002 TYR J 772 ARG 0.007 0.000 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 380 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 629 ASP cc_start: 0.6723 (t0) cc_final: 0.6211 (t0) REVERT: A 800 GLU cc_start: 0.8125 (pp20) cc_final: 0.7811 (pp20) REVERT: G 62 ASP cc_start: 0.7603 (p0) cc_final: 0.7337 (p0) REVERT: H 18 GLN cc_start: 0.8852 (tp-100) cc_final: 0.8527 (mm-40) REVERT: H 75 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8038 (tm-30) REVERT: H 125 LYS cc_start: 0.7828 (tptm) cc_final: 0.7569 (tttp) REVERT: I 200 ARG cc_start: 0.7856 (mtt-85) cc_final: 0.7496 (mtt-85) REVERT: I 370 MET cc_start: 0.8881 (mmm) cc_final: 0.8555 (mmm) REVERT: I 396 ASP cc_start: 0.8667 (t0) cc_final: 0.8318 (t0) REVERT: I 492 MET cc_start: 0.7745 (pmm) cc_final: 0.7534 (pmm) REVERT: I 955 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7176 (tp40) REVERT: I 959 ASP cc_start: 0.7875 (m-30) cc_final: 0.7440 (m-30) REVERT: I 1066 MET cc_start: 0.8844 (ptp) cc_final: 0.8420 (ptm) REVERT: J 42 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: J 129 ASP cc_start: 0.7578 (t70) cc_final: 0.7277 (t0) REVERT: J 289 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7614 (t0) REVERT: J 500 ILE cc_start: 0.9135 (mm) cc_final: 0.8809 (pt) REVERT: J 1334 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7526 (tm-30) outliers start: 68 outliers final: 45 residues processed: 427 average time/residue: 0.4572 time to fit residues: 325.0578 Evaluate side-chains 397 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 350 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1096 ASN Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 877 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1352 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 72 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 20.0000 chunk 299 optimal weight: 10.0000 chunk 206 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 267 optimal weight: 0.8980 chunk 399 optimal weight: 0.8980 chunk 423 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 chunk 379 optimal weight: 3.9990 chunk 114 optimal weight: 8.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN I 273 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 761 GLN J 716 GLN J 865 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36908 Z= 0.232 Angle : 0.589 11.851 50400 Z= 0.303 Chirality : 0.042 0.214 5747 Planarity : 0.004 0.051 6199 Dihedral : 15.108 125.279 6000 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.20 % Favored : 92.71 % Rotamer: Outliers : 1.90 % Allowed : 15.84 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 4294 helix: 0.10 (0.13), residues: 1513 sheet: -1.43 (0.21), residues: 635 loop : -1.88 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J1193 HIS 0.009 0.001 HIS J 777 PHE 0.022 0.001 PHE A 377 TYR 0.017 0.001 TYR J 679 ARG 0.004 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 387 time to evaluate : 4.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8884 (tp) REVERT: A 66 MET cc_start: 0.8247 (tpp) cc_final: 0.8019 (tpp) REVERT: A 68 MET cc_start: 0.7755 (pmm) cc_final: 0.7080 (pmm) REVERT: A 629 ASP cc_start: 0.6869 (t0) cc_final: 0.6281 (t0) REVERT: A 710 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9161 (m) REVERT: A 800 GLU cc_start: 0.8116 (pp20) cc_final: 0.7746 (pp20) REVERT: A 811 GLN cc_start: 0.8679 (mp10) cc_final: 0.8160 (mp10) REVERT: G 62 ASP cc_start: 0.7728 (p0) cc_final: 0.7450 (p0) REVERT: H 75 GLN cc_start: 0.8427 (tm-30) cc_final: 0.7991 (tm-30) REVERT: H 125 LYS cc_start: 0.7835 (tptm) cc_final: 0.7581 (tttp) REVERT: H 227 GLN cc_start: 0.9021 (mm110) cc_final: 0.8746 (mm110) REVERT: I 200 ARG cc_start: 0.7749 (mtt-85) cc_final: 0.7486 (mtt-85) REVERT: I 396 ASP cc_start: 0.8570 (t0) cc_final: 0.7561 (p0) REVERT: I 492 MET cc_start: 0.7686 (pmm) cc_final: 0.7193 (pmm) REVERT: I 496 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8568 (tptt) REVERT: I 515 MET cc_start: 0.8840 (ttp) cc_final: 0.8595 (ttp) REVERT: I 955 GLN cc_start: 0.8061 (tp-100) cc_final: 0.7386 (tp40) REVERT: I 959 ASP cc_start: 0.7871 (m-30) cc_final: 0.7518 (m-30) REVERT: J 117 LEU cc_start: 0.8914 (tp) cc_final: 0.8590 (tp) REVERT: J 129 ASP cc_start: 0.7615 (t70) cc_final: 0.7292 (t0) REVERT: J 225 GLU cc_start: 0.8775 (tp30) cc_final: 0.8415 (tp30) REVERT: J 229 GLN cc_start: 0.8236 (mm110) cc_final: 0.7960 (mm110) REVERT: J 311 ARG cc_start: 0.7633 (tpp80) cc_final: 0.7357 (tpp80) REVERT: J 372 MET cc_start: 0.8815 (mtp) cc_final: 0.8560 (mtp) REVERT: J 500 ILE cc_start: 0.9095 (mm) cc_final: 0.8815 (pt) REVERT: J 1101 LEU cc_start: 0.7849 (mp) cc_final: 0.7641 (mp) REVERT: J 1334 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7439 (tm-30) outliers start: 69 outliers final: 48 residues processed: 436 average time/residue: 0.4612 time to fit residues: 336.1936 Evaluate side-chains 409 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 359 time to evaluate : 3.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 315 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 361 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 216 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 716 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 36908 Z= 0.498 Angle : 0.708 14.607 50400 Z= 0.364 Chirality : 0.046 0.218 5747 Planarity : 0.005 0.056 6199 Dihedral : 15.257 127.951 5997 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.39 % Favored : 90.52 % Rotamer: Outliers : 3.12 % Allowed : 17.06 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.12), residues: 4294 helix: -0.04 (0.13), residues: 1513 sheet: -1.55 (0.21), residues: 616 loop : -2.01 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J1193 HIS 0.009 0.001 HIS J 545 PHE 0.026 0.002 PHE A 184 TYR 0.022 0.002 TYR J 772 ARG 0.005 0.000 ARG A 737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 358 time to evaluate : 4.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8887 (tp) REVERT: A 66 MET cc_start: 0.8346 (tpp) cc_final: 0.8133 (tpp) REVERT: A 68 MET cc_start: 0.7633 (pmm) cc_final: 0.7126 (pmm) REVERT: A 629 ASP cc_start: 0.6774 (t0) cc_final: 0.6284 (t70) REVERT: A 800 GLU cc_start: 0.8167 (pp20) cc_final: 0.7765 (pp20) REVERT: A 827 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: G 62 ASP cc_start: 0.7810 (p0) cc_final: 0.7438 (p0) REVERT: H 75 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7929 (tm-30) REVERT: H 125 LYS cc_start: 0.7831 (tptm) cc_final: 0.7593 (tttp) REVERT: H 227 GLN cc_start: 0.9029 (mm110) cc_final: 0.8749 (mm110) REVERT: I 183 TRP cc_start: 0.8381 (m-10) cc_final: 0.7726 (m-10) REVERT: I 488 MET cc_start: 0.8037 (mmm) cc_final: 0.7741 (tpp) REVERT: I 492 MET cc_start: 0.7896 (pmm) cc_final: 0.7370 (pmm) REVERT: I 496 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8561 (tptt) REVERT: I 955 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7266 (tp40) REVERT: I 959 ASP cc_start: 0.7887 (m-30) cc_final: 0.7456 (m-30) REVERT: I 1066 MET cc_start: 0.8880 (ptp) cc_final: 0.8427 (ptm) REVERT: J 42 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6999 (pm20) REVERT: J 129 ASP cc_start: 0.7549 (t70) cc_final: 0.7175 (t0) REVERT: J 229 GLN cc_start: 0.8194 (mm110) cc_final: 0.7962 (mm110) REVERT: J 289 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7575 (t0) REVERT: J 500 ILE cc_start: 0.9108 (mm) cc_final: 0.8731 (pt) REVERT: J 788 LEU cc_start: 0.8616 (mp) cc_final: 0.8315 (mp) REVERT: J 1284 ARG cc_start: 0.8274 (mmt180) cc_final: 0.8045 (mmt180) outliers start: 113 outliers final: 83 residues processed: 443 average time/residue: 0.4574 time to fit residues: 341.4910 Evaluate side-chains 430 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 343 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 56 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 335 THR Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 434 ILE Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1073 ASP Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 9.9990 chunk 381 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 104 optimal weight: 0.6980 chunk 423 optimal weight: 4.9990 chunk 351 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 222 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 574 GLN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN H 103 ASN H 132 HIS I 31 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 824 GLN J 716 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36908 Z= 0.201 Angle : 0.580 12.496 50400 Z= 0.298 Chirality : 0.042 0.211 5747 Planarity : 0.004 0.050 6199 Dihedral : 15.038 125.336 5995 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.36 % Favored : 93.57 % Rotamer: Outliers : 2.48 % Allowed : 18.49 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 4294 helix: 0.30 (0.14), residues: 1501 sheet: -1.40 (0.21), residues: 621 loop : -1.83 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J1193 HIS 0.004 0.001 HIS J 777 PHE 0.028 0.001 PHE A 184 TYR 0.016 0.001 TYR J 679 ARG 0.005 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 390 time to evaluate : 4.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7463 (pmm) cc_final: 0.7102 (pmm) REVERT: A 629 ASP cc_start: 0.6633 (t0) cc_final: 0.5974 (t0) REVERT: A 708 ILE cc_start: 0.9005 (mp) cc_final: 0.8782 (mt) REVERT: A 710 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.9095 (m) REVERT: A 800 GLU cc_start: 0.8074 (pp20) cc_final: 0.7679 (pp20) REVERT: A 811 GLN cc_start: 0.8745 (mp10) cc_final: 0.8117 (mp10) REVERT: A 827 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: G 62 ASP cc_start: 0.7790 (p0) cc_final: 0.7554 (p0) REVERT: H 66 HIS cc_start: 0.7807 (t-90) cc_final: 0.7267 (t-90) REVERT: H 75 GLN cc_start: 0.8395 (tm-30) cc_final: 0.7912 (tm-30) REVERT: H 132 HIS cc_start: 0.8522 (m-70) cc_final: 0.8225 (m90) REVERT: H 227 GLN cc_start: 0.8984 (mm110) cc_final: 0.8698 (mm110) REVERT: I 183 TRP cc_start: 0.8373 (m-10) cc_final: 0.7756 (m-10) REVERT: I 200 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.7413 (mtt-85) REVERT: I 396 ASP cc_start: 0.8680 (t0) cc_final: 0.7650 (p0) REVERT: I 492 MET cc_start: 0.7674 (pmm) cc_final: 0.7116 (pmm) REVERT: I 496 LYS cc_start: 0.8773 (tmtt) cc_final: 0.8563 (tptt) REVERT: I 781 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7996 (t70) REVERT: I 955 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7342 (tp40) REVERT: I 959 ASP cc_start: 0.7881 (m-30) cc_final: 0.7411 (m-30) REVERT: I 1085 MET cc_start: 0.9549 (mmm) cc_final: 0.9252 (mmm) REVERT: J 42 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: J 129 ASP cc_start: 0.7584 (t70) cc_final: 0.7194 (t0) REVERT: J 311 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7552 (tpp80) REVERT: J 500 ILE cc_start: 0.9091 (mm) cc_final: 0.8779 (pt) REVERT: J 625 MET cc_start: 0.8585 (ttp) cc_final: 0.8221 (ttp) REVERT: J 777 HIS cc_start: 0.6768 (t-90) cc_final: 0.6313 (t70) REVERT: J 785 ASP cc_start: 0.8666 (t70) cc_final: 0.8030 (t70) REVERT: J 918 ILE cc_start: 0.8812 (pt) cc_final: 0.8437 (mt) REVERT: J 1284 ARG cc_start: 0.8212 (mmt180) cc_final: 0.7932 (mmt180) REVERT: J 1334 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7473 (tm-30) REVERT: K 3 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.6621 (tpm170) REVERT: K 61 ASN cc_start: 0.8229 (t0) cc_final: 0.7958 (t0) outliers start: 90 outliers final: 66 residues processed: 452 average time/residue: 0.4550 time to fit residues: 345.8226 Evaluate side-chains 430 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 360 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 0.4980 chunk 47 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 309 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 356 optimal weight: 7.9990 chunk 236 optimal weight: 0.6980 chunk 422 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 194 optimal weight: 0.0670 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN I 36 GLN ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1289 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 36908 Z= 0.194 Angle : 0.577 11.909 50400 Z= 0.294 Chirality : 0.042 0.207 5747 Planarity : 0.004 0.051 6199 Dihedral : 14.905 126.125 5995 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.03 % Favored : 92.90 % Rotamer: Outliers : 2.59 % Allowed : 19.16 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 4294 helix: 0.44 (0.14), residues: 1505 sheet: -1.27 (0.21), residues: 612 loop : -1.76 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J1193 HIS 0.004 0.001 HIS I 165 PHE 0.023 0.001 PHE A 377 TYR 0.017 0.001 TYR J 679 ARG 0.006 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 393 time to evaluate : 4.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7657 (t70) cc_final: 0.7186 (t0) REVERT: A 194 VAL cc_start: 0.6671 (OUTLIER) cc_final: 0.6466 (p) REVERT: A 204 GLU cc_start: 0.6604 (pp20) cc_final: 0.6339 (pp20) REVERT: A 509 LEU cc_start: 0.9031 (mt) cc_final: 0.8815 (mt) REVERT: A 583 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.5292 (m-10) REVERT: A 629 ASP cc_start: 0.6798 (t0) cc_final: 0.6280 (t0) REVERT: A 708 ILE cc_start: 0.8996 (mp) cc_final: 0.8785 (mt) REVERT: A 710 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9101 (m) REVERT: A 800 GLU cc_start: 0.8048 (pp20) cc_final: 0.7626 (pp20) REVERT: A 811 GLN cc_start: 0.8722 (mp10) cc_final: 0.8168 (mp10) REVERT: A 827 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7604 (pm20) REVERT: H 66 HIS cc_start: 0.7744 (t-90) cc_final: 0.7235 (t-90) REVERT: H 75 GLN cc_start: 0.8387 (tm-30) cc_final: 0.7925 (tm-30) REVERT: H 132 HIS cc_start: 0.8602 (m-70) cc_final: 0.8175 (m90) REVERT: H 227 GLN cc_start: 0.8976 (mm110) cc_final: 0.8594 (mm110) REVERT: I 183 TRP cc_start: 0.8373 (m-10) cc_final: 0.7706 (m-10) REVERT: I 200 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7419 (mtt-85) REVERT: I 396 ASP cc_start: 0.8601 (t0) cc_final: 0.7957 (p0) REVERT: I 492 MET cc_start: 0.7679 (pmm) cc_final: 0.7395 (pmm) REVERT: I 496 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8305 (tptp) REVERT: I 949 GLU cc_start: 0.8288 (mp0) cc_final: 0.7995 (pm20) REVERT: I 955 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7280 (tp40) REVERT: I 959 ASP cc_start: 0.7845 (m-30) cc_final: 0.7312 (m-30) REVERT: I 1076 ILE cc_start: 0.8775 (pt) cc_final: 0.8563 (pt) REVERT: I 1085 MET cc_start: 0.9550 (mmm) cc_final: 0.9208 (mmm) REVERT: J 42 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7157 (pm20) REVERT: J 117 LEU cc_start: 0.8824 (tp) cc_final: 0.8610 (tp) REVERT: J 129 ASP cc_start: 0.7595 (t70) cc_final: 0.7190 (t0) REVERT: J 500 ILE cc_start: 0.9097 (mm) cc_final: 0.8811 (pt) REVERT: J 625 MET cc_start: 0.8562 (ttp) cc_final: 0.8182 (ttp) REVERT: J 777 HIS cc_start: 0.6783 (t-90) cc_final: 0.6391 (t70) REVERT: J 785 ASP cc_start: 0.8609 (t70) cc_final: 0.8035 (t70) REVERT: J 1284 ARG cc_start: 0.8156 (mmt180) cc_final: 0.7875 (mmt180) REVERT: J 1334 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7389 (tm-30) REVERT: K 61 ASN cc_start: 0.8249 (t0) cc_final: 0.7935 (t0) outliers start: 94 outliers final: 71 residues processed: 462 average time/residue: 0.4546 time to fit residues: 353.8994 Evaluate side-chains 447 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 371 time to evaluate : 4.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 252 optimal weight: 0.0970 chunk 127 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 268 optimal weight: 5.9990 chunk 287 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36908 Z= 0.216 Angle : 0.580 11.807 50400 Z= 0.296 Chirality : 0.042 0.221 5747 Planarity : 0.004 0.051 6199 Dihedral : 14.841 125.923 5995 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 2.95 % Allowed : 18.91 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4294 helix: 0.48 (0.14), residues: 1508 sheet: -1.19 (0.21), residues: 616 loop : -1.74 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP J1193 HIS 0.005 0.001 HIS I 165 PHE 0.022 0.001 PHE A 377 TYR 0.017 0.001 TYR J 679 ARG 0.005 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 388 time to evaluate : 3.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8682 (mm) REVERT: A 72 ASP cc_start: 0.7638 (t70) cc_final: 0.7220 (t0) REVERT: A 204 GLU cc_start: 0.6806 (pp20) cc_final: 0.6527 (pp20) REVERT: A 311 MET cc_start: 0.7664 (tpp) cc_final: 0.7446 (tpp) REVERT: A 583 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.5266 (m-10) REVERT: A 629 ASP cc_start: 0.6809 (t0) cc_final: 0.6300 (t0) REVERT: A 708 ILE cc_start: 0.9019 (mp) cc_final: 0.8814 (mt) REVERT: A 710 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9092 (m) REVERT: A 786 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9179 (p) REVERT: A 800 GLU cc_start: 0.8067 (pp20) cc_final: 0.7657 (pp20) REVERT: A 827 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: A 967 MET cc_start: 0.6751 (mpp) cc_final: 0.6529 (mpp) REVERT: A 1040 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7574 (mp0) REVERT: H 66 HIS cc_start: 0.7763 (t-90) cc_final: 0.7249 (t-90) REVERT: H 75 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7914 (tm-30) REVERT: H 132 HIS cc_start: 0.8614 (m-70) cc_final: 0.8170 (m90) REVERT: H 227 GLN cc_start: 0.8972 (mm110) cc_final: 0.8588 (mm110) REVERT: I 132 ASP cc_start: 0.7791 (t0) cc_final: 0.7587 (t0) REVERT: I 183 TRP cc_start: 0.8416 (m-10) cc_final: 0.7785 (m-10) REVERT: I 200 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7353 (mtt-85) REVERT: I 396 ASP cc_start: 0.8519 (t0) cc_final: 0.7932 (p0) REVERT: I 492 MET cc_start: 0.7693 (pmm) cc_final: 0.7438 (pmm) REVERT: I 496 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8264 (tptp) REVERT: I 781 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8016 (t70) REVERT: I 949 GLU cc_start: 0.8204 (mp0) cc_final: 0.7750 (pm20) REVERT: I 955 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7306 (tp40) REVERT: I 959 ASP cc_start: 0.7894 (m-30) cc_final: 0.7415 (m-30) REVERT: I 1085 MET cc_start: 0.9553 (mmm) cc_final: 0.9163 (mmm) REVERT: J 42 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7120 (pm20) REVERT: J 117 LEU cc_start: 0.8808 (tp) cc_final: 0.8584 (tp) REVERT: J 129 ASP cc_start: 0.7622 (t70) cc_final: 0.7196 (t0) REVERT: J 500 ILE cc_start: 0.9092 (mm) cc_final: 0.8808 (pt) REVERT: J 625 MET cc_start: 0.8566 (ttp) cc_final: 0.8175 (ttp) REVERT: J 777 HIS cc_start: 0.6464 (t-90) cc_final: 0.6215 (t70) REVERT: J 785 ASP cc_start: 0.8675 (t70) cc_final: 0.8101 (t70) REVERT: J 1284 ARG cc_start: 0.8148 (mmt180) cc_final: 0.7874 (mmt180) REVERT: J 1334 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7392 (tm-30) REVERT: K 11 GLU cc_start: 0.8111 (pt0) cc_final: 0.7878 (pt0) REVERT: K 61 ASN cc_start: 0.8260 (t0) cc_final: 0.7946 (t0) outliers start: 107 outliers final: 83 residues processed: 464 average time/residue: 0.4693 time to fit residues: 365.1548 Evaluate side-chains 465 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 374 time to evaluate : 4.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 627 CYS Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 786 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1073 ASP Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 3.9990 chunk 404 optimal weight: 6.9990 chunk 368 optimal weight: 0.9980 chunk 393 optimal weight: 20.0000 chunk 236 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 308 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 355 optimal weight: 7.9990 chunk 372 optimal weight: 7.9990 chunk 392 optimal weight: 30.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 824 GLN J 158 GLN J 716 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 36908 Z= 0.350 Angle : 0.634 12.356 50400 Z= 0.323 Chirality : 0.044 0.209 5747 Planarity : 0.004 0.051 6199 Dihedral : 14.893 126.965 5995 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.99 % Favored : 91.92 % Rotamer: Outliers : 2.93 % Allowed : 19.18 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4294 helix: 0.40 (0.14), residues: 1507 sheet: -1.17 (0.21), residues: 620 loop : -1.82 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP J1193 HIS 0.006 0.001 HIS J 545 PHE 0.022 0.002 PHE A 377 TYR 0.019 0.001 TYR J 679 ARG 0.005 0.000 ARG J 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 366 time to evaluate : 4.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8673 (mm) REVERT: A 72 ASP cc_start: 0.7739 (t70) cc_final: 0.7201 (t0) REVERT: A 204 GLU cc_start: 0.6895 (pp20) cc_final: 0.6635 (pp20) REVERT: A 583 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.5291 (m-10) REVERT: A 629 ASP cc_start: 0.6604 (t0) cc_final: 0.5871 (t0) REVERT: A 800 GLU cc_start: 0.8130 (pp20) cc_final: 0.7713 (pp20) REVERT: A 827 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: H 66 HIS cc_start: 0.7820 (t-90) cc_final: 0.7278 (t-90) REVERT: H 75 GLN cc_start: 0.8483 (tm-30) cc_final: 0.7944 (tm-30) REVERT: H 132 HIS cc_start: 0.8697 (m-70) cc_final: 0.8248 (m90) REVERT: H 227 GLN cc_start: 0.8995 (mm110) cc_final: 0.8643 (mm-40) REVERT: I 183 TRP cc_start: 0.8468 (m-10) cc_final: 0.7653 (m-10) REVERT: I 200 ARG cc_start: 0.7545 (mtt-85) cc_final: 0.7225 (mtt-85) REVERT: I 396 ASP cc_start: 0.8626 (t0) cc_final: 0.7964 (p0) REVERT: I 492 MET cc_start: 0.7808 (pmm) cc_final: 0.7478 (pmm) REVERT: I 496 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8320 (tptp) REVERT: I 781 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8013 (t70) REVERT: I 955 GLN cc_start: 0.8079 (tp-100) cc_final: 0.7569 (tp40) REVERT: J 42 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7155 (pm20) REVERT: J 117 LEU cc_start: 0.8886 (tp) cc_final: 0.8650 (tp) REVERT: J 129 ASP cc_start: 0.7519 (t70) cc_final: 0.7070 (t0) REVERT: J 484 MET cc_start: 0.9174 (mtp) cc_final: 0.8951 (mtm) REVERT: J 500 ILE cc_start: 0.9136 (mm) cc_final: 0.8835 (pt) REVERT: J 785 ASP cc_start: 0.8698 (t70) cc_final: 0.8166 (t70) REVERT: J 821 MET cc_start: 0.8494 (mmm) cc_final: 0.8141 (tpt) REVERT: J 1284 ARG cc_start: 0.8171 (mmt180) cc_final: 0.7908 (mmt180) REVERT: K 11 GLU cc_start: 0.8172 (pt0) cc_final: 0.7952 (pt0) REVERT: K 61 ASN cc_start: 0.8261 (t0) cc_final: 0.7965 (t0) outliers start: 106 outliers final: 89 residues processed: 446 average time/residue: 0.4403 time to fit residues: 330.7297 Evaluate side-chains 449 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 355 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1073 ASP Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 20.0000 chunk 415 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 289 optimal weight: 0.5980 chunk 436 optimal weight: 4.9990 chunk 401 optimal weight: 8.9990 chunk 347 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 213 optimal weight: 0.1980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 824 GLN J 716 GLN J 777 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 36908 Z= 0.231 Angle : 0.598 11.999 50400 Z= 0.304 Chirality : 0.042 0.218 5747 Planarity : 0.004 0.050 6199 Dihedral : 14.787 125.841 5995 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.66 % Favored : 93.27 % Rotamer: Outliers : 2.93 % Allowed : 19.24 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 4294 helix: 0.45 (0.14), residues: 1514 sheet: -1.04 (0.21), residues: 621 loop : -1.78 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J1193 HIS 0.006 0.001 HIS A 711 PHE 0.023 0.001 PHE A 377 TYR 0.017 0.001 TYR J 679 ARG 0.005 0.000 ARG J 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8588 Ramachandran restraints generated. 4294 Oldfield, 0 Emsley, 4294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 378 time to evaluate : 4.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8657 (mm) REVERT: A 72 ASP cc_start: 0.7639 (t70) cc_final: 0.7193 (t0) REVERT: A 204 GLU cc_start: 0.6909 (pp20) cc_final: 0.6672 (pp20) REVERT: A 583 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.5172 (m-10) REVERT: A 629 ASP cc_start: 0.7037 (t0) cc_final: 0.6538 (t0) REVERT: A 800 GLU cc_start: 0.8096 (pp20) cc_final: 0.7685 (pp20) REVERT: A 827 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: A 855 ASN cc_start: 0.8271 (t0) cc_final: 0.8027 (t0) REVERT: A 1040 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: H 66 HIS cc_start: 0.7793 (t-90) cc_final: 0.7261 (t-90) REVERT: H 75 GLN cc_start: 0.8456 (tm-30) cc_final: 0.7894 (tm-30) REVERT: H 132 HIS cc_start: 0.8664 (m-70) cc_final: 0.8229 (m90) REVERT: H 227 GLN cc_start: 0.8980 (mm110) cc_final: 0.8629 (mm-40) REVERT: I 5 TYR cc_start: 0.7722 (t80) cc_final: 0.7440 (t80) REVERT: I 183 TRP cc_start: 0.8429 (m-10) cc_final: 0.7663 (m-10) REVERT: I 200 ARG cc_start: 0.7534 (mtt-85) cc_final: 0.7219 (mtt-85) REVERT: I 396 ASP cc_start: 0.8559 (t0) cc_final: 0.7945 (p0) REVERT: I 488 MET cc_start: 0.7592 (tpp) cc_final: 0.6974 (tpp) REVERT: I 492 MET cc_start: 0.7749 (pmm) cc_final: 0.7491 (pmm) REVERT: I 496 LYS cc_start: 0.8673 (tmtt) cc_final: 0.8237 (tptp) REVERT: I 781 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8002 (t70) REVERT: I 949 GLU cc_start: 0.8331 (mp0) cc_final: 0.7974 (pm20) REVERT: I 955 GLN cc_start: 0.8094 (tp-100) cc_final: 0.7614 (tp40) REVERT: J 42 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7117 (pm20) REVERT: J 86 GLU cc_start: 0.8308 (mp0) cc_final: 0.7926 (mp0) REVERT: J 117 LEU cc_start: 0.8845 (tp) cc_final: 0.8598 (tp) REVERT: J 129 ASP cc_start: 0.7471 (t70) cc_final: 0.7022 (t0) REVERT: J 484 MET cc_start: 0.9152 (mtp) cc_final: 0.8901 (mtm) REVERT: J 500 ILE cc_start: 0.9096 (mm) cc_final: 0.8807 (pt) REVERT: J 625 MET cc_start: 0.8607 (ttp) cc_final: 0.8251 (ttp) REVERT: J 785 ASP cc_start: 0.8768 (t70) cc_final: 0.8254 (t70) REVERT: J 821 MET cc_start: 0.8472 (mmm) cc_final: 0.8121 (tpt) REVERT: J 1259 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8843 (mm-40) REVERT: J 1284 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7885 (mmt180) REVERT: K 3 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.6553 (tpm170) REVERT: K 11 GLU cc_start: 0.8135 (pt0) cc_final: 0.7904 (pt0) REVERT: K 61 ASN cc_start: 0.8215 (t0) cc_final: 0.7921 (t0) outliers start: 106 outliers final: 90 residues processed: 456 average time/residue: 0.4584 time to fit residues: 348.8479 Evaluate side-chains 463 residues out of total 3671 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 367 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 583 PHE Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 1011 LEU Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1139 MET Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 118 ASP Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 205 MET Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 81 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 117 HIS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 185 ASP Chi-restraints excluded: chain I residue 236 LYS Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 446 ASP Chi-restraints excluded: chain I residue 448 LEU Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 GLN Chi-restraints excluded: chain I residue 516 ASP Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 569 ILE Chi-restraints excluded: chain I residue 736 VAL Chi-restraints excluded: chain I residue 754 THR Chi-restraints excluded: chain I residue 781 ASP Chi-restraints excluded: chain I residue 814 ASP Chi-restraints excluded: chain I residue 933 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1056 VAL Chi-restraints excluded: chain I residue 1066 MET Chi-restraints excluded: chain I residue 1075 VAL Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1290 MET Chi-restraints excluded: chain I residue 1298 VAL Chi-restraints excluded: chain J residue 42 GLU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 256 ASP Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 453 VAL Chi-restraints excluded: chain J residue 506 VAL Chi-restraints excluded: chain J residue 525 MET Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 708 ASN Chi-restraints excluded: chain J residue 803 VAL Chi-restraints excluded: chain J residue 823 THR Chi-restraints excluded: chain J residue 825 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1073 ASP Chi-restraints excluded: chain J residue 1165 PHE Chi-restraints excluded: chain J residue 1169 THR Chi-restraints excluded: chain J residue 1178 THR Chi-restraints excluded: chain J residue 1180 VAL Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1309 ILE Chi-restraints excluded: chain J residue 1332 LEU Chi-restraints excluded: chain J residue 1351 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 4.9990 chunk 370 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 320 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 348 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 357 optimal weight: 0.0030 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 0.0070 overall best weight: 0.7612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 447 HIS ** I 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 ASN J 777 HIS ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.095079 restraints weight = 70181.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096632 restraints weight = 41618.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.096800 restraints weight = 28897.568| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36908 Z= 0.175 Angle : 0.579 11.278 50400 Z= 0.293 Chirality : 0.041 0.219 5747 Planarity : 0.004 0.050 6199 Dihedral : 14.645 125.467 5995 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.48 % Rotamer: Outliers : 2.54 % Allowed : 19.82 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 4294 helix: 0.64 (0.14), residues: 1499 sheet: -0.98 (0.22), residues: 607 loop : -1.71 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP J1193 HIS 0.004 0.001 HIS A 890 PHE 0.023 0.001 PHE A 377 TYR 0.016 0.001 TYR J 679 ARG 0.006 0.000 ARG J 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7175.90 seconds wall clock time: 131 minutes 35.27 seconds (7895.27 seconds total)