Starting phenix.real_space_refine on Sat Sep 28 11:22:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/09_2024/7tnk_26012.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/09_2024/7tnk_26012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/09_2024/7tnk_26012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/09_2024/7tnk_26012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/09_2024/7tnk_26012.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tnk_26012/09_2024/7tnk_26012.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 136 5.16 5 Cl 4 4.86 5 C 12281 2.51 5 N 3064 2.21 5 O 3449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18934 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4783 Classifications: {'peptide': 615} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 598} Chain breaks: 3 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4688 Classifications: {'peptide': 602} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586} Chain breaks: 4 Chain: "C" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4669 Classifications: {'peptide': 599} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 583} Chain breaks: 4 Chain: "D" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4688 Classifications: {'peptide': 602} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 586} Chain breaks: 4 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'CYZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.75, per 1000 atoms: 0.62 Number of scatterers: 18934 At special positions: 0 Unit cell: (125.33, 114.54, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 4 17.00 S 136 16.00 O 3449 8.00 N 3064 7.00 C 12281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A1039 " - pdb=" SG CYS A1067 " distance=2.03 Simple disulfide: pdb=" SG CYS A1066 " - pdb=" SG CYS A1076 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 Simple disulfide: pdb=" SG CYS B1039 " - pdb=" SG CYS B1067 " distance=2.03 Simple disulfide: pdb=" SG CYS B1066 " - pdb=" SG CYS B1076 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C1039 " - pdb=" SG CYS C1067 " distance=2.03 Simple disulfide: pdb=" SG CYS C1066 " - pdb=" SG CYS C1076 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS D1039 " - pdb=" SG CYS D1067 " distance=2.03 Simple disulfide: pdb=" SG CYS D1066 " - pdb=" SG CYS D1076 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.48 Conformation dependent library (CDL) restraints added in 2.4 seconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 27 sheets defined 54.7% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 424 through 437 Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.850A pdb=" N GLU A 466 " --> pdb=" O GLY A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.672A pdb=" N TRP A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET A 527 " --> pdb=" O TYR A 523 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.712A pdb=" N THR A 568 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 569 " --> pdb=" O GLU A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 569' Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.583A pdb=" N SER A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 625 removed outlier: 3.766A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 Processing helix chain 'A' and resid 653 through 661 removed outlier: 4.012A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 removed outlier: 3.561A pdb=" N ASP A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.819A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 removed outlier: 3.886A pdb=" N ILE A 712 " --> pdb=" O MET A 708 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 713 " --> pdb=" O ASN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.528A pdb=" N LYS A 752 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 768 removed outlier: 3.866A pdb=" N LYS A 765 " --> pdb=" O LYS A 761 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 820 removed outlier: 4.015A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 813 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1029 removed outlier: 3.504A pdb=" N PHE A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1103 Processing helix chain 'A' and resid 1104 through 1126 removed outlier: 4.024A pdb=" N CYS A1120 " --> pdb=" O MET A1116 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE A1121 " --> pdb=" O GLY A1117 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1122 " --> pdb=" O GLY A1118 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLU A1125 " --> pdb=" O ILE A1121 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE A1126 " --> pdb=" O ALA A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1132 through 1158 removed outlier: 3.854A pdb=" N SER A1136 " --> pdb=" O ASN A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1206 removed outlier: 3.656A pdb=" N GLY A1182 " --> pdb=" O SER A1178 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A1187 " --> pdb=" O ALA A1183 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A1189 " --> pdb=" O SER A1185 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A1202 " --> pdb=" O HIS A1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 removed outlier: 3.971A pdb=" N GLU B 419 " --> pdb=" O GLU B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 416 through 419' Processing helix chain 'B' and resid 424 through 437 Processing helix chain 'B' and resid 461 through 470 removed outlier: 3.527A pdb=" N GLU B 466 " --> pdb=" O GLY B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.717A pdb=" N TRP B 526 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.520A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.842A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.864A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 675 removed outlier: 3.841A pdb=" N ARG B 675 " --> pdb=" O TRP B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 696 removed outlier: 3.956A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 694 " --> pdb=" O VAL B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.754A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.857A pdb=" N LEU B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA B 749 " --> pdb=" O PRO B 745 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 792 through 820 removed outlier: 3.600A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 805 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 817 " --> pdb=" O GLU B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1029 removed outlier: 3.918A pdb=" N SER B1021 " --> pdb=" O PHE B1017 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B1026 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B1028 " --> pdb=" O THR B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1089 removed outlier: 4.008A pdb=" N ASP B1087 " --> pdb=" O GLU B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1103 removed outlier: 3.689A pdb=" N ARG B1098 " --> pdb=" O GLU B1094 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B1099 " --> pdb=" O TYR B1095 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B1100 " --> pdb=" O PHE B1096 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1127 removed outlier: 3.745A pdb=" N LEU B1114 " --> pdb=" O SER B1110 " (cutoff:3.500A) Processing helix chain 'B' and resid 1132 through 1161 removed outlier: 3.554A pdb=" N PHE B1141 " --> pdb=" O ALA B1137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B1143 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B1144 " --> pdb=" O PHE B1140 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B1155 " --> pdb=" O GLY B1151 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN B1159 " --> pdb=" O TYR B1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1192 removed outlier: 3.517A pdb=" N PHE B1186 " --> pdb=" O GLY B1182 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA B1189 " --> pdb=" O SER B1185 " (cutoff:3.500A) Processing helix chain 'B' and resid 1192 through 1204 removed outlier: 3.683A pdb=" N VAL B1197 " --> pdb=" O GLY B1193 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS B1198 " --> pdb=" O VAL B1194 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET B1199 " --> pdb=" O LEU B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1204 through 1209 removed outlier: 3.575A pdb=" N THR B1208 " --> pdb=" O HIS B1204 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 419 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.518A pdb=" N ASP C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 489 removed outlier: 3.805A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 544 removed outlier: 3.668A pdb=" N MET C 527 " --> pdb=" O TYR C 523 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL C 538 " --> pdb=" O ILE C 534 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 539 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 569 removed outlier: 3.857A pdb=" N THR C 568 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN C 569 " --> pdb=" O GLU C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 565 through 569' Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 596 through 630 removed outlier: 3.570A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG C 628 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 641 Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.869A pdb=" N GLU C 657 " --> pdb=" O GLY C 653 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 removed outlier: 4.103A pdb=" N MET C 670 " --> pdb=" O VAL C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 695 removed outlier: 3.510A pdb=" N ALA C 691 " --> pdb=" O ALA C 687 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 694 " --> pdb=" O VAL C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.746A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.903A pdb=" N LYS C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 820 removed outlier: 4.188A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS C 815 " --> pdb=" O LEU C 811 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1028 removed outlier: 3.617A pdb=" N LEU C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE C1017 " --> pdb=" O THR C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1093 through 1103 removed outlier: 3.610A pdb=" N ALA C1099 " --> pdb=" O TYR C1095 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C1102 " --> pdb=" O ARG C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1105 through 1123 removed outlier: 3.625A pdb=" N VAL C1111 " --> pdb=" O PRO C1107 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1158 removed outlier: 3.578A pdb=" N ILE C1139 " --> pdb=" O LEU C1135 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE C1140 " --> pdb=" O SER C1136 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C1150 " --> pdb=" O LEU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1208 removed outlier: 3.573A pdb=" N LEU C1195 " --> pdb=" O MET C1191 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 removed outlier: 3.736A pdb=" N GLU D 419 " --> pdb=" O GLU D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 416 through 419' Processing helix chain 'D' and resid 423 through 436 removed outlier: 3.550A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 522 through 545 removed outlier: 4.209A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 541 " --> pdb=" O SER D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.668A pdb=" N PHE D 584 " --> pdb=" O SER D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.874A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 640 Processing helix chain 'D' and resid 653 through 662 removed outlier: 4.016A pdb=" N ARG D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 662 " --> pdb=" O PHE D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 677 removed outlier: 3.830A pdb=" N THR D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 removed outlier: 3.764A pdb=" N GLY D 689 " --> pdb=" O THR D 685 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 694 " --> pdb=" O VAL D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 removed outlier: 3.522A pdb=" N TYR D 711 " --> pdb=" O THR D 707 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.633A pdb=" N LEU D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA D 749 " --> pdb=" O PRO D 745 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN D 756 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 768 Processing helix chain 'D' and resid 792 through 819 removed outlier: 4.021A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 810 " --> pdb=" O ALA D 806 " (cutoff:3.500A) Processing helix chain 'D' and resid 1006 through 1028 removed outlier: 3.746A pdb=" N THR D1024 " --> pdb=" O PHE D1020 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE D1025 " --> pdb=" O SER D1021 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY D1028 " --> pdb=" O THR D1024 " (cutoff:3.500A) Processing helix chain 'D' and resid 1084 through 1089 removed outlier: 3.746A pdb=" N TYR D1088 " --> pdb=" O ASP D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1093 through 1103 removed outlier: 3.643A pdb=" N VAL D1100 " --> pdb=" O PHE D1096 " (cutoff:3.500A) Processing helix chain 'D' and resid 1104 through 1123 removed outlier: 4.011A pdb=" N SER D1110 " --> pdb=" O PHE D1106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D1111 " --> pdb=" O PRO D1107 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS D1120 " --> pdb=" O MET D1116 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D1121 " --> pdb=" O GLY D1117 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA D1122 " --> pdb=" O GLY D1118 " (cutoff:3.500A) Processing helix chain 'D' and resid 1132 through 1161 removed outlier: 4.175A pdb=" N PHE D1141 " --> pdb=" O ALA D1137 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D1142 " --> pdb=" O GLY D1138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D1147 " --> pdb=" O SER D1143 " (cutoff:3.500A) Processing helix chain 'D' and resid 1176 through 1209 removed outlier: 3.677A pdb=" N TYR D1180 " --> pdb=" O GLY D1176 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D1186 " --> pdb=" O GLY D1182 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D1195 " --> pdb=" O MET D1191 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D1197 " --> pdb=" O GLY D1193 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D1209 " --> pdb=" O LYS D1205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 442 through 444 Processing sheet with id=AA2, first strand: chain 'A' and resid 406 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA4, first strand: chain 'A' and resid 496 through 498 removed outlier: 3.894A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 648 removed outlier: 6.265A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1033 through 1034 Processing sheet with id=AA7, first strand: chain 'A' and resid 1058 through 1059 removed outlier: 3.571A pdb=" N CYS A1066 " --> pdb=" O HIS A1059 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 442 through 444 removed outlier: 6.299A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 406 through 408 Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 496 through 498 removed outlier: 4.054A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 646 through 648 removed outlier: 6.543A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1057 through 1060 Processing sheet with id=AB5, first strand: chain 'B' and resid 1065 through 1066 Processing sheet with id=AB6, first strand: chain 'C' and resid 440 through 442 Processing sheet with id=AB7, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.745A pdb=" N ALA C 452 " --> pdb=" O ASN C 461 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP C 454 " --> pdb=" O ILE C 459 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE C 459 " --> pdb=" O ASP C 454 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 498 removed outlier: 3.662A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.527A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1058 through 1059 Processing sheet with id=AC3, first strand: chain 'D' and resid 441 through 444 Processing sheet with id=AC4, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC5, first strand: chain 'D' and resid 452 through 453 removed outlier: 3.540A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC7, first strand: chain 'D' and resid 496 through 498 removed outlier: 4.000A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 646 through 648 removed outlier: 6.429A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 1057 through 1060 removed outlier: 3.864A pdb=" N LEU D1033 " --> pdb=" O SER D1060 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.63 Time building geometry restraints manager: 5.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5633 1.34 - 1.46: 4459 1.46 - 1.58: 9039 1.58 - 1.70: 8 1.70 - 1.82: 220 Bond restraints: 19359 Sorted by residual: bond pdb=" CA ASP D1091 " pdb=" CB ASP D1091 " ideal model delta sigma weight residual 1.524 1.557 -0.034 1.30e-02 5.92e+03 6.72e+00 bond pdb=" C SER A 631 " pdb=" N PRO A 632 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.44e-02 4.82e+03 6.25e+00 bond pdb=" N ASN A1053 " pdb=" CA ASN A1053 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.02e+00 bond pdb=" C ASP B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.337 1.358 -0.021 9.80e-03 1.04e+04 4.64e+00 bond pdb=" N3 CYZ A1302 " pdb=" S2 CYZ A1302 " ideal model delta sigma weight residual 1.644 1.602 0.042 2.00e-02 2.50e+03 4.38e+00 ... (remaining 19354 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 25706 3.05 - 6.11: 382 6.11 - 9.16: 59 9.16 - 12.21: 5 12.21 - 15.27: 2 Bond angle restraints: 26154 Sorted by residual: angle pdb=" C VAL A1056 " pdb=" N MET A1057 " pdb=" CA MET A1057 " ideal model delta sigma weight residual 121.54 132.51 -10.97 1.91e+00 2.74e-01 3.30e+01 angle pdb=" C GLU B 772 " pdb=" N CYS B 773 " pdb=" CA CYS B 773 " ideal model delta sigma weight residual 121.54 132.22 -10.68 1.91e+00 2.74e-01 3.13e+01 angle pdb=" N ASN B1132 " pdb=" CA ASN B1132 " pdb=" C ASN B1132 " ideal model delta sigma weight residual 113.61 105.90 7.71 1.50e+00 4.44e-01 2.64e+01 angle pdb=" C GLU C1089 " pdb=" N ALA C1090 " pdb=" CA ALA C1090 " ideal model delta sigma weight residual 120.44 127.06 -6.62 1.30e+00 5.92e-01 2.60e+01 angle pdb=" C GLY C 771 " pdb=" N GLU C 772 " pdb=" CA GLU C 772 " ideal model delta sigma weight residual 121.54 131.07 -9.53 1.91e+00 2.74e-01 2.49e+01 ... (remaining 26149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.41: 11066 24.41 - 48.82: 352 48.82 - 73.23: 15 73.23 - 97.64: 9 97.64 - 122.05: 7 Dihedral angle restraints: 11449 sinusoidal: 4522 harmonic: 6927 Sorted by residual: dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 -179.42 -87.58 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CA ALA A 775 " pdb=" C ALA A 775 " pdb=" N LYS A 776 " pdb=" CA LYS A 776 " ideal model delta harmonic sigma weight residual 180.00 132.71 47.29 0 5.00e+00 4.00e-02 8.94e+01 dihedral pdb=" CA LYS B 509 " pdb=" C LYS B 509 " pdb=" N SER B 510 " pdb=" CA SER B 510 " ideal model delta harmonic sigma weight residual -180.00 -135.48 -44.52 0 5.00e+00 4.00e-02 7.93e+01 ... (remaining 11446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2185 0.052 - 0.105: 584 0.105 - 0.157: 129 0.157 - 0.209: 19 0.209 - 0.261: 8 Chirality restraints: 2925 Sorted by residual: chirality pdb=" C8 CYZ D1301 " pdb=" C1 CYZ D1301 " pdb=" N1 CYZ D1301 " pdb=" N2 CYZ D1301 " both_signs ideal model delta sigma weight residual False 2.20 2.46 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE B1079 " pdb=" CA ILE B1079 " pdb=" CG1 ILE B1079 " pdb=" CG2 ILE B1079 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C8 CYZ C1301 " pdb=" C1 CYZ C1301 " pdb=" N1 CYZ C1301 " pdb=" N2 CYZ C1301 " both_signs ideal model delta sigma weight residual False 2.20 2.45 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2922 not shown) Planarity restraints: 3209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 509 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.24e+01 pdb=" C LYS B 509 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS B 509 " 0.023 2.00e-02 2.50e+03 pdb=" N SER B 510 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D1106 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.16e+00 pdb=" N PRO D1107 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D1107 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D1107 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 744 " -0.050 5.00e-02 4.00e+02 7.41e-02 8.80e+00 pdb=" N PRO B 745 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " -0.042 5.00e-02 4.00e+02 ... (remaining 3206 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 4413 2.78 - 3.31: 17656 3.31 - 3.84: 30758 3.84 - 4.37: 36528 4.37 - 4.90: 60286 Nonbonded interactions: 149641 Sorted by model distance: nonbonded pdb=" O PHE D1106 " pdb=" OG SER D1147 " model vdw 2.244 3.040 nonbonded pdb=" OG1 THR C 643 " pdb=" OD1 ASP D 777 " model vdw 2.256 3.040 nonbonded pdb=" O GLU A 637 " pdb=" OG SER A 640 " model vdw 2.266 3.040 nonbonded pdb=" OG1 THR B1065 " pdb=" O LYS B1077 " model vdw 2.280 3.040 nonbonded pdb=" O ILE D1025 " pdb=" OG1 THR D1029 " model vdw 2.292 3.040 ... (remaining 149636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 394 through 564 or resid 566 through 1042 or resid 1056 th \ rough 1161 or resid 1169 through 1208 or resid 1302)) selection = (chain 'B' and (resid 394 through 549 or resid 564 or resid 566 through 1208 or \ resid 1301)) selection = chain 'C' selection = (chain 'D' and (resid 394 through 549 or resid 564 or resid 566 through 1208 or \ resid 1301)) } 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 41.980 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 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 : 0.005 0.079 19359 Z= 0.339 Angle : 1.011 15.267 26154 Z= 0.572 Chirality : 0.052 0.261 2925 Planarity : 0.006 0.076 3209 Dihedral : 11.811 122.047 6997 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.04 % Favored : 94.87 % Rotamer: Outliers : 0.40 % Allowed : 4.36 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.12), residues: 2380 helix: -3.73 (0.07), residues: 1242 sheet: -1.99 (0.38), residues: 162 loop : -2.69 (0.16), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A1177 HIS 0.006 0.001 HIS B1204 PHE 0.038 0.002 PHE C1082 TYR 0.042 0.003 TYR C1031 ARG 0.008 0.001 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 658 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 453 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7676 (ttp80) REVERT: A 573 ILE cc_start: 0.7831 (pt) cc_final: 0.7518 (mt) REVERT: A 610 LEU cc_start: 0.9201 (tp) cc_final: 0.8990 (tp) REVERT: A 644 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7622 (mp0) REVERT: A 670 MET cc_start: 0.8182 (mtp) cc_final: 0.7981 (mtt) REVERT: A 730 LYS cc_start: 0.8202 (mttt) cc_final: 0.7874 (mmmm) REVERT: A 800 VAL cc_start: 0.9121 (t) cc_final: 0.8892 (p) REVERT: A 1020 PHE cc_start: 0.7907 (t80) cc_final: 0.7352 (t80) REVERT: A 1025 ILE cc_start: 0.9065 (mm) cc_final: 0.8864 (mt) REVERT: A 1031 TYR cc_start: 0.6504 (p90) cc_final: 0.5637 (p90) REVERT: A 1155 TYR cc_start: 0.8062 (t80) cc_final: 0.7709 (t80) REVERT: A 1177 TRP cc_start: 0.5743 (p-90) cc_final: 0.4416 (m-10) REVERT: A 1190 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8612 (mm-30) REVERT: A 1191 MET cc_start: 0.7682 (tpt) cc_final: 0.7169 (mmt) REVERT: A 1205 LYS cc_start: 0.7558 (mtmt) cc_final: 0.6999 (tptp) REVERT: B 399 THR cc_start: 0.8625 (p) cc_final: 0.8388 (t) REVERT: B 425 CYS cc_start: 0.8636 (m) cc_final: 0.8075 (p) REVERT: B 428 LEU cc_start: 0.8694 (tp) cc_final: 0.8454 (tp) REVERT: B 434 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7876 (tttm) REVERT: B 444 ILE cc_start: 0.8093 (mm) cc_final: 0.7538 (mt) REVERT: B 474 ILE cc_start: 0.9096 (tt) cc_final: 0.8761 (mm) REVERT: B 498 LEU cc_start: 0.8975 (pt) cc_final: 0.8654 (pt) REVERT: B 527 MET cc_start: 0.7366 (ttt) cc_final: 0.6908 (tpt) REVERT: B 536 VAL cc_start: 0.8177 (t) cc_final: 0.5901 (p) REVERT: B 586 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7721 (mm-40) REVERT: B 600 ILE cc_start: 0.8871 (mt) cc_final: 0.8585 (mt) REVERT: B 605 TRP cc_start: 0.8307 (t-100) cc_final: 0.7487 (t-100) REVERT: B 609 THR cc_start: 0.9033 (p) cc_final: 0.8691 (t) REVERT: B 697 LYS cc_start: 0.6121 (mmtp) cc_final: 0.5609 (ptmt) REVERT: B 766 TRP cc_start: 0.5977 (t-100) cc_final: 0.4915 (t-100) REVERT: B 800 VAL cc_start: 0.9457 (t) cc_final: 0.9180 (p) REVERT: B 1003 PHE cc_start: 0.3351 (m-10) cc_final: 0.3129 (m-80) REVERT: B 1011 LEU cc_start: 0.8421 (tp) cc_final: 0.8118 (tt) REVERT: B 1181 PHE cc_start: 0.5888 (m-10) cc_final: 0.5527 (m-80) REVERT: B 1186 PHE cc_start: 0.7464 (t80) cc_final: 0.6942 (t80) REVERT: B 1191 MET cc_start: 0.8126 (mtp) cc_final: 0.7620 (mtm) REVERT: C 438 PHE cc_start: 0.7204 (p90) cc_final: 0.5703 (p90) REVERT: C 503 MET cc_start: 0.8424 (ttp) cc_final: 0.7850 (ttp) REVERT: C 511 LYS cc_start: 0.7518 (pmmt) cc_final: 0.6870 (mptt) REVERT: C 528 CYS cc_start: 0.8440 (m) cc_final: 0.7905 (m) REVERT: C 537 SER cc_start: 0.9190 (p) cc_final: 0.8673 (t) REVERT: C 585 MET cc_start: 0.8843 (mmt) cc_final: 0.8115 (mmt) REVERT: C 629 MET cc_start: 0.8386 (mtp) cc_final: 0.7629 (tmm) REVERT: C 702 TYR cc_start: 0.8041 (t80) cc_final: 0.7679 (t80) REVERT: C 764 ASN cc_start: 0.8181 (m-40) cc_final: 0.7872 (m-40) REVERT: C 1009 MET cc_start: 0.8701 (tpp) cc_final: 0.8473 (tpt) REVERT: C 1030 ASP cc_start: 0.6674 (p0) cc_final: 0.6424 (m-30) REVERT: C 1064 ARG cc_start: 0.7313 (mpp80) cc_final: 0.6554 (ttt180) REVERT: C 1141 PHE cc_start: 0.8818 (m-10) cc_final: 0.8550 (m-80) REVERT: C 1153 ILE cc_start: 0.9546 (mt) cc_final: 0.9205 (mm) REVERT: C 1180 TYR cc_start: 0.8577 (m-80) cc_final: 0.8124 (m-10) REVERT: D 431 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7738 (mm-30) REVERT: D 434 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8308 (mtpt) REVERT: D 489 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8192 (pp) REVERT: D 503 MET cc_start: 0.8169 (ttm) cc_final: 0.7543 (ptm) REVERT: D 505 LYS cc_start: 0.7491 (ttmt) cc_final: 0.7290 (pptt) REVERT: D 527 MET cc_start: 0.7993 (ptp) cc_final: 0.7694 (mtt) REVERT: D 537 SER cc_start: 0.8796 (p) cc_final: 0.8078 (t) REVERT: D 541 PHE cc_start: 0.8441 (t80) cc_final: 0.8156 (t80) REVERT: D 573 ILE cc_start: 0.9407 (tp) cc_final: 0.9177 (tt) REVERT: D 580 SER cc_start: 0.8574 (m) cc_final: 0.8138 (m) REVERT: D 601 VAL cc_start: 0.9504 (t) cc_final: 0.9297 (p) REVERT: D 629 MET cc_start: 0.5223 (pmt) cc_final: 0.4838 (mmm) REVERT: D 713 GLU cc_start: 0.7875 (tt0) cc_final: 0.7624 (tm-30) REVERT: D 714 GLN cc_start: 0.8376 (mm110) cc_final: 0.7865 (mm110) REVERT: D 752 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8675 (tptt) REVERT: D 1038 VAL cc_start: 0.7192 (t) cc_final: 0.6779 (m) REVERT: D 1062 LEU cc_start: 0.4783 (tp) cc_final: 0.4542 (tp) REVERT: D 1131 HIS cc_start: 0.6296 (m90) cc_final: 0.5989 (m90) REVERT: D 1134 ILE cc_start: 0.6307 (mp) cc_final: 0.6097 (mm) REVERT: D 1204 HIS cc_start: 0.7640 (m170) cc_final: 0.7152 (t-170) REVERT: D 1205 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7489 (mttm) outliers start: 8 outliers final: 0 residues processed: 662 average time/residue: 0.3076 time to fit residues: 303.7424 Evaluate side-chains 402 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 401 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 72 optimal weight: 0.4980 chunk 114 optimal weight: 7.9990 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 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 714 GLN B 575 ASN B 714 GLN B1204 HIS C 418 ASN C 586 GLN C 619 ASN C 791 ASN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1171 ASN C1204 HIS D 435 HIS D 587 GLN D 642 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1131 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19359 Z= 0.179 Angle : 0.625 8.095 26154 Z= 0.335 Chirality : 0.041 0.144 2925 Planarity : 0.005 0.084 3209 Dihedral : 8.505 103.850 2716 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.20 % Allowed : 3.27 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.48 (0.15), residues: 2380 helix: -1.18 (0.12), residues: 1282 sheet: -1.57 (0.40), residues: 155 loop : -2.17 (0.18), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1177 HIS 0.005 0.001 HIS B1059 PHE 0.024 0.001 PHE C 682 TYR 0.021 0.001 TYR A 673 ARG 0.011 0.001 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 545 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 SER cc_start: 0.9085 (m) cc_final: 0.8862 (t) REVERT: A 543 VAL cc_start: 0.9290 (t) cc_final: 0.9059 (p) REVERT: A 708 MET cc_start: 0.8453 (mmt) cc_final: 0.8245 (mmt) REVERT: A 728 ASP cc_start: 0.8333 (p0) cc_final: 0.7835 (p0) REVERT: A 808 LEU cc_start: 0.8876 (tp) cc_final: 0.8607 (mm) REVERT: A 1004 ASP cc_start: 0.7795 (t0) cc_final: 0.7309 (m-30) REVERT: A 1007 VAL cc_start: 0.8772 (t) cc_final: 0.8489 (t) REVERT: A 1020 PHE cc_start: 0.7623 (t80) cc_final: 0.7259 (t80) REVERT: A 1025 ILE cc_start: 0.9077 (mm) cc_final: 0.8856 (mt) REVERT: A 1177 TRP cc_start: 0.5753 (p-90) cc_final: 0.5511 (p-90) REVERT: A 1179 PHE cc_start: 0.8695 (t80) cc_final: 0.7917 (t80) REVERT: A 1191 MET cc_start: 0.7588 (tpt) cc_final: 0.7155 (mmt) REVERT: B 399 THR cc_start: 0.8656 (p) cc_final: 0.8415 (t) REVERT: B 428 LEU cc_start: 0.8702 (tp) cc_final: 0.8477 (tp) REVERT: B 434 LYS cc_start: 0.8274 (ptpt) cc_final: 0.7962 (tptp) REVERT: B 444 ILE cc_start: 0.8084 (mm) cc_final: 0.7676 (mt) REVERT: B 474 ILE cc_start: 0.9022 (tt) cc_final: 0.8818 (mm) REVERT: B 481 ILE cc_start: 0.6939 (mm) cc_final: 0.6699 (mm) REVERT: B 498 LEU cc_start: 0.8638 (pt) cc_final: 0.8290 (pt) REVERT: B 527 MET cc_start: 0.7258 (ttt) cc_final: 0.6720 (tpt) REVERT: B 540 LEU cc_start: 0.9221 (tt) cc_final: 0.8955 (tt) REVERT: B 586 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8215 (mm-40) REVERT: B 613 ILE cc_start: 0.9176 (mm) cc_final: 0.8913 (mm) REVERT: B 684 ARG cc_start: 0.6528 (ptp90) cc_final: 0.5969 (mmm160) REVERT: B 697 LYS cc_start: 0.6280 (mmtp) cc_final: 0.5658 (ptmm) REVERT: B 766 TRP cc_start: 0.5622 (t-100) cc_final: 0.5003 (t-100) REVERT: B 768 TYR cc_start: 0.7992 (m-10) cc_final: 0.7477 (m-80) REVERT: B 1003 PHE cc_start: 0.3494 (m-10) cc_final: 0.3263 (m-80) REVERT: B 1188 ILE cc_start: 0.8501 (mm) cc_final: 0.8185 (tt) REVERT: B 1191 MET cc_start: 0.7924 (mtp) cc_final: 0.7629 (tpp) REVERT: C 406 VAL cc_start: 0.9279 (t) cc_final: 0.8768 (m) REVERT: C 528 CYS cc_start: 0.7885 (m) cc_final: 0.7513 (m) REVERT: C 585 MET cc_start: 0.8903 (mmt) cc_final: 0.8315 (mmt) REVERT: C 606 TRP cc_start: 0.8306 (m-10) cc_final: 0.8081 (m-10) REVERT: C 629 MET cc_start: 0.8163 (mtp) cc_final: 0.7603 (tmm) REVERT: C 639 LEU cc_start: 0.8760 (tp) cc_final: 0.8428 (tp) REVERT: C 760 ASP cc_start: 0.8382 (t70) cc_final: 0.7912 (t0) REVERT: C 764 ASN cc_start: 0.8190 (m-40) cc_final: 0.7922 (t0) REVERT: C 1030 ASP cc_start: 0.6635 (p0) cc_final: 0.6262 (m-30) REVERT: C 1062 LEU cc_start: 0.7586 (tp) cc_final: 0.6721 (pt) REVERT: C 1064 ARG cc_start: 0.7137 (mpp80) cc_final: 0.6340 (ttt-90) REVERT: C 1153 ILE cc_start: 0.9340 (mt) cc_final: 0.9039 (mm) REVERT: C 1175 TYR cc_start: 0.6903 (m-80) cc_final: 0.6659 (m-80) REVERT: C 1180 TYR cc_start: 0.8311 (m-80) cc_final: 0.7997 (m-80) REVERT: C 1187 ILE cc_start: 0.9365 (mt) cc_final: 0.9067 (mt) REVERT: D 431 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7764 (mm-30) REVERT: D 434 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8212 (mtpt) REVERT: D 509 LYS cc_start: 0.6495 (ptpp) cc_final: 0.6054 (mmpt) REVERT: D 625 THR cc_start: 0.8639 (m) cc_final: 0.8245 (p) REVERT: D 713 GLU cc_start: 0.8189 (tt0) cc_final: 0.7908 (tm-30) REVERT: D 714 GLN cc_start: 0.8432 (mm110) cc_final: 0.7670 (mm-40) REVERT: D 752 LYS cc_start: 0.8991 (ttmt) cc_final: 0.7992 (tptt) REVERT: D 1062 LEU cc_start: 0.4941 (tp) cc_final: 0.4538 (tp) REVERT: D 1131 HIS cc_start: 0.6469 (m-70) cc_final: 0.6107 (m90) outliers start: 4 outliers final: 0 residues processed: 547 average time/residue: 0.2955 time to fit residues: 254.0447 Evaluate side-chains 377 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 235 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN A 619 ASN A 764 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19359 Z= 0.299 Angle : 0.676 7.798 26154 Z= 0.362 Chirality : 0.043 0.156 2925 Planarity : 0.005 0.071 3209 Dihedral : 8.291 104.276 2716 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.50 (0.16), residues: 2380 helix: -0.13 (0.14), residues: 1289 sheet: -1.55 (0.39), residues: 166 loop : -2.08 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A1032 HIS 0.009 0.002 HIS B1204 PHE 0.022 0.002 PHE B1179 TYR 0.031 0.002 TYR C1031 ARG 0.008 0.001 ARG B1098 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 444 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 LEU cc_start: 0.8874 (tp) cc_final: 0.8527 (tp) REVERT: A 503 MET cc_start: 0.7145 (tmm) cc_final: 0.6885 (tmm) REVERT: A 730 LYS cc_start: 0.8441 (mttt) cc_final: 0.8117 (mtpp) REVERT: A 1007 VAL cc_start: 0.8699 (t) cc_final: 0.8379 (t) REVERT: A 1025 ILE cc_start: 0.8942 (mm) cc_final: 0.8688 (mt) REVERT: A 1191 MET cc_start: 0.7587 (tpt) cc_final: 0.7191 (mmt) REVERT: B 408 MET cc_start: 0.7742 (mmm) cc_final: 0.7529 (mmm) REVERT: B 434 LYS cc_start: 0.8350 (ptpt) cc_final: 0.8003 (tttm) REVERT: B 444 ILE cc_start: 0.8231 (mm) cc_final: 0.7820 (mt) REVERT: B 474 ILE cc_start: 0.9131 (tt) cc_final: 0.8733 (mm) REVERT: B 498 LEU cc_start: 0.8744 (pt) cc_final: 0.8485 (pt) REVERT: B 527 MET cc_start: 0.7521 (ttt) cc_final: 0.6419 (tpt) REVERT: B 613 ILE cc_start: 0.9172 (mm) cc_final: 0.8901 (mm) REVERT: B 697 LYS cc_start: 0.6437 (mmtp) cc_final: 0.5959 (ptmm) REVERT: B 766 TRP cc_start: 0.5812 (t-100) cc_final: 0.5075 (t-100) REVERT: B 768 TYR cc_start: 0.7958 (m-10) cc_final: 0.7435 (m-80) REVERT: B 1005 ARG cc_start: 0.4637 (ptm160) cc_final: 0.4411 (ptm160) REVERT: B 1181 PHE cc_start: 0.6343 (m-10) cc_final: 0.6088 (m-80) REVERT: B 1188 ILE cc_start: 0.8309 (mm) cc_final: 0.8083 (tt) REVERT: C 406 VAL cc_start: 0.9327 (t) cc_final: 0.8830 (m) REVERT: C 503 MET cc_start: 0.8421 (ppp) cc_final: 0.7484 (ppp) REVERT: C 540 LEU cc_start: 0.9271 (tt) cc_final: 0.9030 (tt) REVERT: C 585 MET cc_start: 0.8974 (mmt) cc_final: 0.8375 (mmt) REVERT: C 591 ILE cc_start: 0.8893 (mp) cc_final: 0.8672 (mp) REVERT: C 629 MET cc_start: 0.8233 (mtp) cc_final: 0.7710 (tmm) REVERT: C 702 TYR cc_start: 0.8355 (t80) cc_final: 0.7583 (t80) REVERT: C 760 ASP cc_start: 0.8437 (t70) cc_final: 0.7951 (t0) REVERT: C 764 ASN cc_start: 0.8502 (m-40) cc_final: 0.8066 (t0) REVERT: C 1030 ASP cc_start: 0.6810 (p0) cc_final: 0.6234 (m-30) REVERT: C 1064 ARG cc_start: 0.6876 (mpp80) cc_final: 0.6605 (ttt180) REVERT: C 1153 ILE cc_start: 0.9308 (mt) cc_final: 0.9007 (mm) REVERT: C 1175 TYR cc_start: 0.7097 (m-80) cc_final: 0.6764 (m-80) REVERT: C 1180 TYR cc_start: 0.8185 (m-80) cc_final: 0.7769 (m-80) REVERT: D 580 SER cc_start: 0.8634 (m) cc_final: 0.8233 (m) REVERT: D 597 SER cc_start: 0.9224 (p) cc_final: 0.8970 (p) REVERT: D 670 MET cc_start: 0.7878 (mtt) cc_final: 0.7648 (mtt) REVERT: D 713 GLU cc_start: 0.8235 (tt0) cc_final: 0.8025 (tm-30) REVERT: D 714 GLN cc_start: 0.8209 (mm110) cc_final: 0.7725 (mm-40) REVERT: D 1023 MET cc_start: 0.6908 (ttp) cc_final: 0.6616 (ppp) REVERT: D 1101 ARG cc_start: 0.7268 (ppt170) cc_final: 0.6849 (ptm160) REVERT: D 1109 LEU cc_start: 0.8382 (tp) cc_final: 0.8138 (tp) REVERT: D 1131 HIS cc_start: 0.6617 (m-70) cc_final: 0.5781 (m-70) REVERT: D 1134 ILE cc_start: 0.6349 (mp) cc_final: 0.6063 (mm) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.2778 time to fit residues: 193.3202 Evaluate side-chains 331 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.9980 chunk 164 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 764 ASN C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 HIS D 587 GLN ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19359 Z= 0.201 Angle : 0.600 9.552 26154 Z= 0.317 Chirality : 0.042 0.178 2925 Planarity : 0.004 0.061 3209 Dihedral : 7.820 98.522 2716 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.17), residues: 2380 helix: 0.44 (0.14), residues: 1295 sheet: -1.16 (0.40), residues: 162 loop : -1.96 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A1177 HIS 0.007 0.001 HIS B1204 PHE 0.033 0.002 PHE D1020 TYR 0.026 0.001 TYR A 711 ARG 0.004 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 2.115 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 538 VAL cc_start: 0.9413 (p) cc_final: 0.9198 (p) REVERT: A 730 LYS cc_start: 0.8456 (mttt) cc_final: 0.8124 (mtpp) REVERT: A 1025 ILE cc_start: 0.8893 (mm) cc_final: 0.8626 (mt) REVERT: A 1177 TRP cc_start: 0.6064 (p-90) cc_final: 0.5560 (p-90) REVERT: A 1190 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8107 (mm-30) REVERT: A 1191 MET cc_start: 0.7563 (tpt) cc_final: 0.7136 (mmt) REVERT: B 408 MET cc_start: 0.7795 (mmm) cc_final: 0.7472 (mmm) REVERT: B 434 LYS cc_start: 0.8304 (ptpt) cc_final: 0.7970 (tttm) REVERT: B 444 ILE cc_start: 0.7993 (mm) cc_final: 0.7634 (mt) REVERT: B 474 ILE cc_start: 0.9118 (tt) cc_final: 0.8730 (mm) REVERT: B 481 ILE cc_start: 0.7082 (mm) cc_final: 0.6583 (mm) REVERT: B 527 MET cc_start: 0.7296 (ttt) cc_final: 0.6848 (tpp) REVERT: B 697 LYS cc_start: 0.6347 (mmtp) cc_final: 0.5932 (ptmm) REVERT: B 766 TRP cc_start: 0.5700 (t-100) cc_final: 0.5044 (t-100) REVERT: B 768 TYR cc_start: 0.7932 (m-10) cc_final: 0.7468 (m-80) REVERT: B 1181 PHE cc_start: 0.6159 (m-10) cc_final: 0.5913 (m-80) REVERT: B 1186 PHE cc_start: 0.7516 (t80) cc_final: 0.7131 (t80) REVERT: C 406 VAL cc_start: 0.9363 (t) cc_final: 0.8904 (m) REVERT: C 424 TYR cc_start: 0.6957 (t80) cc_final: 0.6627 (t80) REVERT: C 540 LEU cc_start: 0.9290 (tt) cc_final: 0.9082 (tt) REVERT: C 606 TRP cc_start: 0.8485 (m-10) cc_final: 0.8216 (m-10) REVERT: C 629 MET cc_start: 0.8132 (mtp) cc_final: 0.7647 (tmm) REVERT: C 668 ASP cc_start: 0.8978 (t70) cc_final: 0.8685 (t0) REVERT: C 704 LEU cc_start: 0.9153 (pt) cc_final: 0.8946 (pt) REVERT: C 760 ASP cc_start: 0.8298 (t70) cc_final: 0.7917 (t0) REVERT: C 764 ASN cc_start: 0.8410 (m-40) cc_final: 0.8026 (t0) REVERT: C 1030 ASP cc_start: 0.6637 (p0) cc_final: 0.6076 (m-30) REVERT: C 1064 ARG cc_start: 0.6834 (mpp80) cc_final: 0.6427 (ttt180) REVERT: C 1153 ILE cc_start: 0.9288 (mt) cc_final: 0.8966 (mm) REVERT: C 1175 TYR cc_start: 0.6986 (m-80) cc_final: 0.6580 (m-80) REVERT: C 1180 TYR cc_start: 0.8166 (m-80) cc_final: 0.7765 (m-80) REVERT: D 427 ASP cc_start: 0.8707 (m-30) cc_final: 0.8209 (m-30) REVERT: D 580 SER cc_start: 0.8622 (m) cc_final: 0.8180 (m) REVERT: D 670 MET cc_start: 0.8023 (mtt) cc_final: 0.7791 (mtt) REVERT: D 714 GLN cc_start: 0.8186 (mm110) cc_final: 0.7696 (mm-40) REVERT: D 772 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7211 (mp0) REVERT: D 1101 ARG cc_start: 0.7174 (ppt170) cc_final: 0.6912 (ptt180) REVERT: D 1131 HIS cc_start: 0.6705 (m-70) cc_final: 0.5859 (m-70) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.2789 time to fit residues: 193.7747 Evaluate side-chains 334 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 334 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 197 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 714 GLN D 791 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19359 Z= 0.342 Angle : 0.717 17.950 26154 Z= 0.375 Chirality : 0.045 0.153 2925 Planarity : 0.005 0.058 3209 Dihedral : 8.172 106.284 2716 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % 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: -0.98 (0.17), residues: 2380 helix: 0.36 (0.14), residues: 1297 sheet: -1.10 (0.40), residues: 166 loop : -2.02 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 766 HIS 0.007 0.002 HIS C1204 PHE 0.024 0.002 PHE D1020 TYR 0.031 0.002 TYR C1031 ARG 0.006 0.001 ARG C 453 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 418 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 483 LEU cc_start: 0.8730 (tp) cc_final: 0.8496 (tp) REVERT: A 619 ASN cc_start: 0.7502 (t160) cc_final: 0.7210 (t0) REVERT: A 730 LYS cc_start: 0.8411 (mttt) cc_final: 0.8103 (mtpp) REVERT: A 1025 ILE cc_start: 0.8943 (mm) cc_final: 0.8696 (mt) REVERT: A 1057 MET cc_start: 0.7295 (mpp) cc_final: 0.6724 (mpp) REVERT: A 1190 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8241 (mm-30) REVERT: A 1191 MET cc_start: 0.7559 (tpt) cc_final: 0.7170 (mmt) REVERT: B 408 MET cc_start: 0.7646 (mmm) cc_final: 0.7409 (mmm) REVERT: B 434 LYS cc_start: 0.8314 (ptpt) cc_final: 0.7923 (tptp) REVERT: B 444 ILE cc_start: 0.8228 (mm) cc_final: 0.7885 (mt) REVERT: B 474 ILE cc_start: 0.9132 (tt) cc_final: 0.8714 (mm) REVERT: B 527 MET cc_start: 0.7193 (ttt) cc_final: 0.6968 (tpp) REVERT: B 613 ILE cc_start: 0.9177 (mm) cc_final: 0.8974 (mm) REVERT: B 697 LYS cc_start: 0.6628 (mmtp) cc_final: 0.6141 (ptmm) REVERT: B 707 THR cc_start: 0.9054 (p) cc_final: 0.8711 (t) REVERT: B 766 TRP cc_start: 0.5806 (t-100) cc_final: 0.5027 (t-100) REVERT: B 1065 THR cc_start: 0.5309 (p) cc_final: 0.4978 (t) REVERT: B 1181 PHE cc_start: 0.6132 (m-10) cc_final: 0.5729 (m-80) REVERT: B 1191 MET cc_start: 0.8011 (tpp) cc_final: 0.7008 (tpp) REVERT: B 1201 ILE cc_start: 0.8259 (pt) cc_final: 0.7889 (tp) REVERT: C 406 VAL cc_start: 0.9367 (t) cc_final: 0.8856 (m) REVERT: C 424 TYR cc_start: 0.7086 (t80) cc_final: 0.6675 (t80) REVERT: C 585 MET cc_start: 0.9010 (mmt) cc_final: 0.8505 (mmt) REVERT: C 590 ASP cc_start: 0.8620 (p0) cc_final: 0.8340 (p0) REVERT: C 629 MET cc_start: 0.8259 (mtp) cc_final: 0.7634 (tmm) REVERT: C 668 ASP cc_start: 0.9029 (t70) cc_final: 0.8675 (t0) REVERT: C 789 LEU cc_start: 0.9266 (mp) cc_final: 0.8440 (mp) REVERT: C 1030 ASP cc_start: 0.6716 (p0) cc_final: 0.6007 (m-30) REVERT: C 1064 ARG cc_start: 0.7097 (mpp80) cc_final: 0.6620 (ttt180) REVERT: C 1153 ILE cc_start: 0.9309 (mt) cc_final: 0.8992 (mm) REVERT: C 1175 TYR cc_start: 0.7089 (m-80) cc_final: 0.6643 (m-80) REVERT: C 1180 TYR cc_start: 0.8053 (m-80) cc_final: 0.7502 (m-80) REVERT: D 509 LYS cc_start: 0.6213 (ptpp) cc_final: 0.5938 (tttp) REVERT: D 581 LEU cc_start: 0.8803 (tt) cc_final: 0.8318 (tt) REVERT: D 597 SER cc_start: 0.9251 (p) cc_final: 0.9001 (p) REVERT: D 670 MET cc_start: 0.8201 (mtt) cc_final: 0.7913 (mtt) REVERT: D 674 MET cc_start: 0.8083 (mmm) cc_final: 0.7731 (mmt) REVERT: D 1005 ARG cc_start: 0.6609 (mtp180) cc_final: 0.5401 (ppt170) REVERT: D 1023 MET cc_start: 0.7115 (ppp) cc_final: 0.6691 (ppp) REVERT: D 1101 ARG cc_start: 0.7158 (ppt170) cc_final: 0.6957 (ptt180) REVERT: D 1131 HIS cc_start: 0.6764 (m-70) cc_final: 0.5850 (m-70) REVERT: D 1134 ILE cc_start: 0.6553 (mp) cc_final: 0.6123 (mm) REVERT: D 1191 MET cc_start: 0.8000 (ttt) cc_final: 0.7597 (ttm) outliers start: 1 outliers final: 0 residues processed: 419 average time/residue: 0.2717 time to fit residues: 180.9334 Evaluate side-chains 324 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 232 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 709 ASN C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS C1148 ASN C1204 HIS D 435 HIS D1204 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19359 Z= 0.231 Angle : 0.631 16.295 26154 Z= 0.329 Chirality : 0.042 0.160 2925 Planarity : 0.004 0.058 3209 Dihedral : 7.858 102.165 2716 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % 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: -0.64 (0.17), residues: 2380 helix: 0.67 (0.14), residues: 1306 sheet: -1.16 (0.39), residues: 171 loop : -1.90 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A1177 HIS 0.006 0.001 HIS B1204 PHE 0.020 0.002 PHE B1186 TYR 0.035 0.002 TYR C1031 ARG 0.005 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 2.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 TYR cc_start: 0.8098 (m-10) cc_final: 0.7781 (m-10) REVERT: A 619 ASN cc_start: 0.7142 (t0) cc_final: 0.6917 (t0) REVERT: A 728 ASP cc_start: 0.8537 (p0) cc_final: 0.8016 (p0) REVERT: A 730 LYS cc_start: 0.8472 (mttt) cc_final: 0.8112 (mttt) REVERT: A 796 PHE cc_start: 0.8437 (m-80) cc_final: 0.8178 (m-80) REVERT: A 1025 ILE cc_start: 0.8936 (mm) cc_final: 0.8680 (mt) REVERT: A 1064 ARG cc_start: 0.7147 (mpp-170) cc_final: 0.6481 (mtp180) REVERT: A 1177 TRP cc_start: 0.6045 (p-90) cc_final: 0.5537 (p-90) REVERT: A 1190 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8206 (mm-30) REVERT: A 1191 MET cc_start: 0.7631 (tpt) cc_final: 0.7187 (mmt) REVERT: A 1199 MET cc_start: 0.9035 (mtt) cc_final: 0.8712 (mtt) REVERT: B 434 LYS cc_start: 0.8241 (ptpt) cc_final: 0.8004 (tttm) REVERT: B 444 ILE cc_start: 0.8265 (mm) cc_final: 0.7846 (mt) REVERT: B 474 ILE cc_start: 0.9139 (tt) cc_final: 0.8761 (mm) REVERT: B 481 ILE cc_start: 0.7237 (mm) cc_final: 0.6583 (mm) REVERT: B 498 LEU cc_start: 0.8736 (pt) cc_final: 0.8530 (pt) REVERT: B 527 MET cc_start: 0.7183 (ttt) cc_final: 0.6825 (tpp) REVERT: B 638 ASP cc_start: 0.8906 (m-30) cc_final: 0.8697 (m-30) REVERT: B 642 GLN cc_start: 0.7905 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 697 LYS cc_start: 0.6618 (mmtp) cc_final: 0.6090 (ptmm) REVERT: B 707 THR cc_start: 0.9059 (p) cc_final: 0.8687 (t) REVERT: B 768 TYR cc_start: 0.7980 (m-10) cc_final: 0.7426 (m-80) REVERT: B 1065 THR cc_start: 0.5217 (p) cc_final: 0.4885 (t) REVERT: B 1181 PHE cc_start: 0.6036 (m-10) cc_final: 0.5646 (m-80) REVERT: C 406 VAL cc_start: 0.9393 (t) cc_final: 0.8929 (m) REVERT: C 424 TYR cc_start: 0.6997 (t80) cc_final: 0.6624 (t80) REVERT: C 590 ASP cc_start: 0.8700 (p0) cc_final: 0.8408 (p0) REVERT: C 629 MET cc_start: 0.8082 (mtp) cc_final: 0.7588 (tmm) REVERT: C 668 ASP cc_start: 0.9035 (t70) cc_final: 0.8827 (t0) REVERT: C 764 ASN cc_start: 0.8550 (m110) cc_final: 0.8258 (m110) REVERT: C 1030 ASP cc_start: 0.6685 (p0) cc_final: 0.6052 (m-30) REVERT: C 1064 ARG cc_start: 0.6995 (mpp80) cc_final: 0.6411 (ttt180) REVERT: C 1153 ILE cc_start: 0.9317 (mt) cc_final: 0.9021 (mm) REVERT: C 1180 TYR cc_start: 0.8041 (m-80) cc_final: 0.7601 (m-80) REVERT: D 509 LYS cc_start: 0.6207 (ptpp) cc_final: 0.5901 (tttp) REVERT: D 549 TYR cc_start: 0.6179 (p90) cc_final: 0.5320 (t80) REVERT: D 597 SER cc_start: 0.9216 (p) cc_final: 0.8889 (p) REVERT: D 1042 LYS cc_start: 0.6948 (pttp) cc_final: 0.6683 (mmtm) REVERT: D 1101 ARG cc_start: 0.7070 (ppt170) cc_final: 0.6720 (ptm160) REVERT: D 1131 HIS cc_start: 0.6574 (m-70) cc_final: 0.5730 (m-70) REVERT: D 1191 MET cc_start: 0.8096 (ttt) cc_final: 0.7715 (ttm) outliers start: 0 outliers final: 0 residues processed: 415 average time/residue: 0.2868 time to fit residues: 186.9428 Evaluate side-chains 329 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 169 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 141 optimal weight: 0.9980 chunk 106 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 586 GLN A 619 ASN A 709 ASN B1131 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19359 Z= 0.348 Angle : 0.716 8.673 26154 Z= 0.377 Chirality : 0.045 0.180 2925 Planarity : 0.005 0.058 3209 Dihedral : 8.126 106.357 2716 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % 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: -0.81 (0.17), residues: 2380 helix: 0.51 (0.14), residues: 1305 sheet: -1.10 (0.40), residues: 168 loop : -1.97 (0.19), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1177 HIS 0.008 0.002 HIS D1204 PHE 0.043 0.002 PHE B 546 TYR 0.041 0.002 TYR C1031 ARG 0.007 0.001 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8642 (t) cc_final: 0.8432 (t) REVERT: A 469 TYR cc_start: 0.8279 (m-10) cc_final: 0.7975 (m-10) REVERT: A 483 LEU cc_start: 0.8718 (tp) cc_final: 0.8469 (tp) REVERT: A 730 LYS cc_start: 0.8430 (mttt) cc_final: 0.7972 (mtpp) REVERT: A 796 PHE cc_start: 0.8487 (m-80) cc_final: 0.8234 (m-80) REVERT: A 1025 ILE cc_start: 0.8939 (mm) cc_final: 0.8676 (mt) REVERT: A 1064 ARG cc_start: 0.6735 (mpp-170) cc_final: 0.6283 (mmm-85) REVERT: A 1177 TRP cc_start: 0.6045 (p-90) cc_final: 0.5792 (p-90) REVERT: A 1190 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 1191 MET cc_start: 0.7611 (tpt) cc_final: 0.7221 (mmt) REVERT: B 434 LYS cc_start: 0.8342 (ptpt) cc_final: 0.8013 (tttm) REVERT: B 474 ILE cc_start: 0.9140 (tt) cc_final: 0.8777 (mm) REVERT: B 481 ILE cc_start: 0.7295 (mm) cc_final: 0.6698 (mm) REVERT: B 502 ILE cc_start: 0.7418 (mt) cc_final: 0.7215 (mt) REVERT: B 527 MET cc_start: 0.7180 (ttt) cc_final: 0.6806 (tpp) REVERT: B 540 LEU cc_start: 0.9189 (tt) cc_final: 0.8978 (tt) REVERT: B 642 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7272 (pp30) REVERT: B 697 LYS cc_start: 0.6888 (mmtp) cc_final: 0.6294 (ptmm) REVERT: B 707 THR cc_start: 0.9073 (p) cc_final: 0.8738 (t) REVERT: B 1181 PHE cc_start: 0.6163 (m-10) cc_final: 0.5725 (m-80) REVERT: B 1201 ILE cc_start: 0.8343 (pt) cc_final: 0.7947 (tp) REVERT: C 406 VAL cc_start: 0.9407 (t) cc_final: 0.8980 (m) REVERT: C 424 TYR cc_start: 0.7136 (t80) cc_final: 0.6778 (t80) REVERT: C 585 MET cc_start: 0.9060 (mmt) cc_final: 0.8519 (mmt) REVERT: C 590 ASP cc_start: 0.8700 (p0) cc_final: 0.8438 (p0) REVERT: C 629 MET cc_start: 0.8152 (mtp) cc_final: 0.7604 (tmm) REVERT: C 668 ASP cc_start: 0.9067 (t70) cc_final: 0.8748 (t0) REVERT: C 764 ASN cc_start: 0.8610 (m110) cc_final: 0.8318 (m110) REVERT: C 1064 ARG cc_start: 0.7288 (mpp80) cc_final: 0.6572 (ttt180) REVERT: C 1153 ILE cc_start: 0.9294 (mt) cc_final: 0.9018 (mm) REVERT: C 1180 TYR cc_start: 0.7978 (m-80) cc_final: 0.7476 (m-80) REVERT: D 405 TYR cc_start: 0.7647 (m-80) cc_final: 0.7413 (m-80) REVERT: D 407 MET cc_start: 0.7930 (mmt) cc_final: 0.7617 (mmt) REVERT: D 415 LEU cc_start: 0.7624 (mt) cc_final: 0.7422 (mp) REVERT: D 509 LYS cc_start: 0.6171 (ptpp) cc_final: 0.5757 (tttp) REVERT: D 549 TYR cc_start: 0.6274 (p90) cc_final: 0.5470 (t80) REVERT: D 597 SER cc_start: 0.9220 (p) cc_final: 0.8937 (p) REVERT: D 674 MET cc_start: 0.8116 (mmm) cc_final: 0.7755 (mmt) REVERT: D 1005 ARG cc_start: 0.6606 (mtp180) cc_final: 0.5610 (ppt170) REVERT: D 1023 MET cc_start: 0.7184 (ppp) cc_final: 0.6852 (ppp) REVERT: D 1042 LYS cc_start: 0.7128 (pttp) cc_final: 0.6924 (mmtp) REVERT: D 1057 MET cc_start: 0.4799 (ttp) cc_final: 0.4488 (ttp) REVERT: D 1131 HIS cc_start: 0.6771 (m-70) cc_final: 0.5898 (m-70) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2697 time to fit residues: 171.4284 Evaluate side-chains 314 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 4.9990 chunk 92 optimal weight: 0.0770 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 0.0000 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 709 ASN B 619 ASN B1131 HIS C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19359 Z= 0.201 Angle : 0.618 8.592 26154 Z= 0.323 Chirality : 0.042 0.179 2925 Planarity : 0.004 0.058 3209 Dihedral : 7.719 99.224 2716 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % 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: -0.48 (0.17), residues: 2380 helix: 0.87 (0.14), residues: 1302 sheet: -1.13 (0.40), residues: 170 loop : -1.94 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1177 HIS 0.006 0.001 HIS B1204 PHE 0.030 0.002 PHE B 682 TYR 0.030 0.001 TYR C1031 ARG 0.006 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8560 (t) cc_final: 0.8346 (t) REVERT: A 466 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7171 (mm-30) REVERT: A 469 TYR cc_start: 0.8175 (m-10) cc_final: 0.7844 (m-10) REVERT: A 619 ASN cc_start: 0.7033 (t160) cc_final: 0.6832 (t0) REVERT: A 705 GLU cc_start: 0.8170 (mp0) cc_final: 0.7879 (mp0) REVERT: A 730 LYS cc_start: 0.8480 (mttt) cc_final: 0.8079 (mtpp) REVERT: A 1025 ILE cc_start: 0.8904 (mm) cc_final: 0.8629 (mt) REVERT: A 1064 ARG cc_start: 0.6619 (mpp-170) cc_final: 0.6239 (mmm-85) REVERT: A 1177 TRP cc_start: 0.6027 (p-90) cc_final: 0.5711 (p-90) REVERT: A 1190 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8497 (mm-30) REVERT: A 1191 MET cc_start: 0.7636 (tpt) cc_final: 0.7189 (mmt) REVERT: B 434 LYS cc_start: 0.8296 (ptpt) cc_final: 0.8019 (tttm) REVERT: B 474 ILE cc_start: 0.9163 (tt) cc_final: 0.8818 (mm) REVERT: B 481 ILE cc_start: 0.7001 (mm) cc_final: 0.6517 (mm) REVERT: B 527 MET cc_start: 0.7257 (ttt) cc_final: 0.6951 (tpp) REVERT: B 540 LEU cc_start: 0.9141 (tt) cc_final: 0.8904 (tt) REVERT: B 642 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7466 (pp30) REVERT: B 697 LYS cc_start: 0.6810 (mmtp) cc_final: 0.6198 (ptmm) REVERT: B 766 TRP cc_start: 0.5745 (t-100) cc_final: 0.5326 (t-100) REVERT: B 768 TYR cc_start: 0.8182 (m-80) cc_final: 0.7933 (m-80) REVERT: B 1023 MET cc_start: 0.6916 (tpt) cc_final: 0.6698 (tpp) REVERT: B 1181 PHE cc_start: 0.6063 (m-10) cc_final: 0.5660 (m-80) REVERT: C 406 VAL cc_start: 0.9435 (t) cc_final: 0.9032 (m) REVERT: C 424 TYR cc_start: 0.7005 (t80) cc_final: 0.6504 (t80) REVERT: C 585 MET cc_start: 0.8751 (mmt) cc_final: 0.8520 (mmt) REVERT: C 590 ASP cc_start: 0.8651 (p0) cc_final: 0.8421 (p0) REVERT: C 629 MET cc_start: 0.8010 (mtp) cc_final: 0.7592 (tmm) REVERT: C 764 ASN cc_start: 0.8497 (m110) cc_final: 0.8212 (m110) REVERT: C 1030 ASP cc_start: 0.6249 (p0) cc_final: 0.5900 (m-30) REVERT: C 1064 ARG cc_start: 0.7193 (mpp80) cc_final: 0.6383 (ttt180) REVERT: C 1153 ILE cc_start: 0.9270 (mt) cc_final: 0.9007 (mm) REVERT: C 1180 TYR cc_start: 0.8019 (m-80) cc_final: 0.7531 (m-80) REVERT: C 1188 ILE cc_start: 0.8104 (tt) cc_final: 0.7894 (mt) REVERT: D 407 MET cc_start: 0.7948 (mmt) cc_final: 0.7532 (mmt) REVERT: D 414 MET cc_start: 0.8582 (mpp) cc_final: 0.8186 (mpp) REVERT: D 509 LYS cc_start: 0.6252 (ptpp) cc_final: 0.5904 (tttp) REVERT: D 549 TYR cc_start: 0.6099 (p90) cc_final: 0.5430 (t80) REVERT: D 1005 ARG cc_start: 0.6509 (mtp180) cc_final: 0.5575 (ppt170) REVERT: D 1057 MET cc_start: 0.4763 (ttp) cc_final: 0.4507 (ttp) REVERT: D 1131 HIS cc_start: 0.6535 (m-70) cc_final: 0.5766 (m90) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.2694 time to fit residues: 175.7501 Evaluate side-chains 325 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.1980 chunk 221 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 194 optimal weight: 0.4980 chunk 203 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 709 ASN B 619 ASN B1131 HIS ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS D1159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19359 Z= 0.155 Angle : 0.595 8.546 26154 Z= 0.305 Chirality : 0.041 0.191 2925 Planarity : 0.004 0.059 3209 Dihedral : 7.211 92.386 2716 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % 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: -0.20 (0.17), residues: 2380 helix: 1.13 (0.15), residues: 1305 sheet: -0.78 (0.42), residues: 161 loop : -1.92 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1177 HIS 0.004 0.001 HIS A1059 PHE 0.023 0.001 PHE B1186 TYR 0.025 0.001 TYR D1127 ARG 0.004 0.000 ARG B 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 2.193 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 406 VAL cc_start: 0.8479 (t) cc_final: 0.8249 (t) REVERT: A 466 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7117 (mm-30) REVERT: A 469 TYR cc_start: 0.8032 (m-10) cc_final: 0.7697 (m-10) REVERT: A 728 ASP cc_start: 0.8184 (p0) cc_final: 0.7569 (p0) REVERT: A 730 LYS cc_start: 0.8526 (mttt) cc_final: 0.8155 (mttt) REVERT: A 1025 ILE cc_start: 0.8880 (mm) cc_final: 0.8588 (mt) REVERT: A 1032 TRP cc_start: 0.8150 (m100) cc_final: 0.7625 (m100) REVERT: A 1064 ARG cc_start: 0.6642 (mpp-170) cc_final: 0.6167 (mmm-85) REVERT: A 1177 TRP cc_start: 0.6086 (p-90) cc_final: 0.4249 (m-10) REVERT: A 1190 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 1191 MET cc_start: 0.7703 (tpt) cc_final: 0.7279 (mmt) REVERT: A 1199 MET cc_start: 0.9028 (mtt) cc_final: 0.8740 (mtt) REVERT: B 434 LYS cc_start: 0.8225 (ptpt) cc_final: 0.7988 (tttm) REVERT: B 474 ILE cc_start: 0.9135 (tt) cc_final: 0.8768 (mm) REVERT: B 481 ILE cc_start: 0.6994 (mm) cc_final: 0.6498 (mm) REVERT: B 527 MET cc_start: 0.7271 (ttt) cc_final: 0.6677 (tpp) REVERT: B 540 LEU cc_start: 0.9141 (tt) cc_final: 0.8910 (tt) REVERT: B 585 MET cc_start: 0.8913 (mmm) cc_final: 0.8626 (mmp) REVERT: B 642 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7548 (pp30) REVERT: B 697 LYS cc_start: 0.6804 (mmtp) cc_final: 0.6180 (ptmm) REVERT: B 766 TRP cc_start: 0.5667 (t-100) cc_final: 0.5362 (t-100) REVERT: B 768 TYR cc_start: 0.8161 (m-80) cc_final: 0.7934 (m-80) REVERT: B 1181 PHE cc_start: 0.5966 (m-10) cc_final: 0.5623 (m-80) REVERT: C 424 TYR cc_start: 0.6961 (t80) cc_final: 0.6539 (t80) REVERT: C 585 MET cc_start: 0.9010 (mmt) cc_final: 0.8478 (mmt) REVERT: C 590 ASP cc_start: 0.8603 (p0) cc_final: 0.8372 (p0) REVERT: C 606 TRP cc_start: 0.8430 (m-10) cc_final: 0.8151 (m-10) REVERT: C 624 LEU cc_start: 0.8916 (mt) cc_final: 0.8615 (mt) REVERT: C 629 MET cc_start: 0.7919 (mtp) cc_final: 0.7627 (tmm) REVERT: C 760 ASP cc_start: 0.8297 (t70) cc_final: 0.8078 (t0) REVERT: C 764 ASN cc_start: 0.8326 (m110) cc_final: 0.7916 (t0) REVERT: C 1023 MET cc_start: 0.8433 (mmt) cc_final: 0.8158 (tpp) REVERT: C 1030 ASP cc_start: 0.6198 (p0) cc_final: 0.5915 (m-30) REVERT: C 1064 ARG cc_start: 0.7216 (mpp80) cc_final: 0.6394 (ttt180) REVERT: C 1153 ILE cc_start: 0.9230 (mt) cc_final: 0.8975 (mm) REVERT: C 1180 TYR cc_start: 0.8058 (m-80) cc_final: 0.7771 (m-80) REVERT: D 407 MET cc_start: 0.7953 (mmt) cc_final: 0.7438 (mmt) REVERT: D 414 MET cc_start: 0.8547 (mpp) cc_final: 0.8223 (mpp) REVERT: D 422 GLU cc_start: 0.7352 (tp30) cc_final: 0.7125 (tp30) REVERT: D 581 LEU cc_start: 0.8596 (tt) cc_final: 0.8331 (tt) REVERT: D 597 SER cc_start: 0.9097 (p) cc_final: 0.8895 (p) REVERT: D 607 PHE cc_start: 0.8128 (t80) cc_final: 0.7730 (t80) REVERT: D 674 MET cc_start: 0.8192 (mmm) cc_final: 0.7877 (mmt) REVERT: D 685 THR cc_start: 0.8252 (t) cc_final: 0.7217 (m) REVERT: D 1005 ARG cc_start: 0.6415 (mtp180) cc_final: 0.5667 (ppt170) REVERT: D 1057 MET cc_start: 0.4828 (ttp) cc_final: 0.4526 (ttp) REVERT: D 1131 HIS cc_start: 0.6323 (m-70) cc_final: 0.5634 (m90) REVERT: D 1159 ASN cc_start: 0.6965 (OUTLIER) cc_final: 0.6341 (t0) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.2741 time to fit residues: 185.3178 Evaluate side-chains 333 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 332 time to evaluate : 2.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 108 optimal weight: 0.0050 chunk 158 optimal weight: 0.4980 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 756 GLN B 619 ASN B1131 HIS ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 586 GLN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS D1159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19359 Z= 0.154 Angle : 0.594 9.032 26154 Z= 0.303 Chirality : 0.041 0.192 2925 Planarity : 0.004 0.059 3209 Dihedral : 6.966 88.544 2716 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % 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: -0.04 (0.17), residues: 2380 helix: 1.26 (0.15), residues: 1303 sheet: -0.72 (0.43), residues: 157 loop : -1.83 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1177 HIS 0.004 0.001 HIS A1059 PHE 0.021 0.001 PHE B1186 TYR 0.026 0.001 TYR C1031 ARG 0.004 0.000 ARG B 453 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 VAL cc_start: 0.8429 (t) cc_final: 0.8200 (t) REVERT: A 469 TYR cc_start: 0.7982 (m-10) cc_final: 0.7654 (m-10) REVERT: A 728 ASP cc_start: 0.8076 (p0) cc_final: 0.7842 (t70) REVERT: A 730 LYS cc_start: 0.8514 (mttt) cc_final: 0.8160 (mmmm) REVERT: A 1025 ILE cc_start: 0.8816 (mm) cc_final: 0.8520 (mt) REVERT: A 1032 TRP cc_start: 0.8129 (m100) cc_final: 0.7605 (m100) REVERT: A 1064 ARG cc_start: 0.6666 (mpp-170) cc_final: 0.6136 (mmm-85) REVERT: A 1177 TRP cc_start: 0.6139 (p-90) cc_final: 0.4327 (m-10) REVERT: A 1190 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8198 (mm-30) REVERT: A 1191 MET cc_start: 0.7697 (tpt) cc_final: 0.7280 (mmt) REVERT: A 1199 MET cc_start: 0.9016 (mtt) cc_final: 0.8744 (mtt) REVERT: B 434 LYS cc_start: 0.8223 (ptpt) cc_final: 0.7998 (tttm) REVERT: B 474 ILE cc_start: 0.9135 (tt) cc_final: 0.8750 (mm) REVERT: B 527 MET cc_start: 0.7287 (ttt) cc_final: 0.6782 (tpp) REVERT: B 540 LEU cc_start: 0.9071 (tt) cc_final: 0.8794 (tt) REVERT: B 585 MET cc_start: 0.8800 (mmm) cc_final: 0.8501 (mmp) REVERT: B 642 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7535 (pp30) REVERT: B 670 MET cc_start: 0.7383 (mmt) cc_final: 0.7055 (mmt) REVERT: B 697 LYS cc_start: 0.6751 (mmtp) cc_final: 0.6152 (ptmm) REVERT: B 766 TRP cc_start: 0.5585 (t-100) cc_final: 0.5323 (t-100) REVERT: B 768 TYR cc_start: 0.8184 (m-80) cc_final: 0.7947 (m-80) REVERT: B 1023 MET cc_start: 0.6877 (tpt) cc_final: 0.6670 (tpp) REVERT: B 1181 PHE cc_start: 0.5984 (m-10) cc_final: 0.5627 (m-80) REVERT: C 424 TYR cc_start: 0.6865 (t80) cc_final: 0.6237 (t80) REVERT: C 585 MET cc_start: 0.9008 (mmt) cc_final: 0.8534 (mmt) REVERT: C 590 ASP cc_start: 0.8604 (p0) cc_final: 0.8347 (p0) REVERT: C 624 LEU cc_start: 0.8881 (mt) cc_final: 0.8608 (mt) REVERT: C 629 MET cc_start: 0.8000 (mtp) cc_final: 0.7670 (tmm) REVERT: C 760 ASP cc_start: 0.8359 (t70) cc_final: 0.8101 (t0) REVERT: C 764 ASN cc_start: 0.8316 (m110) cc_final: 0.7895 (t0) REVERT: C 1064 ARG cc_start: 0.7161 (mpp80) cc_final: 0.6395 (ttt180) REVERT: C 1153 ILE cc_start: 0.9222 (mt) cc_final: 0.8948 (mm) REVERT: C 1180 TYR cc_start: 0.8114 (m-80) cc_final: 0.7850 (m-80) REVERT: D 407 MET cc_start: 0.7972 (mmt) cc_final: 0.7444 (mmt) REVERT: D 414 MET cc_start: 0.8555 (mpp) cc_final: 0.8189 (mpp) REVERT: D 422 GLU cc_start: 0.7381 (tp30) cc_final: 0.7146 (tp30) REVERT: D 607 PHE cc_start: 0.8038 (t80) cc_final: 0.7653 (t80) REVERT: D 674 MET cc_start: 0.8088 (mmm) cc_final: 0.7882 (mmt) REVERT: D 1005 ARG cc_start: 0.6354 (mtp180) cc_final: 0.5771 (ppt170) REVERT: D 1057 MET cc_start: 0.4789 (ttp) cc_final: 0.4496 (ttp) REVERT: D 1131 HIS cc_start: 0.6412 (m-70) cc_final: 0.5786 (m90) outliers start: 0 outliers final: 0 residues processed: 419 average time/residue: 0.2727 time to fit residues: 182.8706 Evaluate side-chains 330 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 0.0670 chunk 35 optimal weight: 3.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN B 619 ASN ** B1204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1131 HIS ** C1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1204 HIS D 586 GLN D1159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081999 restraints weight = 64414.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.084296 restraints weight = 39634.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.085693 restraints weight = 27685.938| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19359 Z= 0.193 Angle : 0.607 8.749 26154 Z= 0.312 Chirality : 0.042 0.229 2925 Planarity : 0.004 0.057 3209 Dihedral : 6.996 91.885 2716 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.03 % 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: -0.07 (0.17), residues: 2380 helix: 1.22 (0.15), residues: 1308 sheet: -0.72 (0.43), residues: 157 loop : -1.83 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 671 HIS 0.007 0.001 HIS D1204 PHE 0.046 0.002 PHE B 682 TYR 0.027 0.001 TYR C1031 ARG 0.004 0.000 ARG B 453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4279.65 seconds wall clock time: 80 minutes 13.25 seconds (4813.25 seconds total)