Starting phenix.real_space_refine on Tue Mar 19 05:55:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sad_24949/03_2024/7sad_24949_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sad_24949/03_2024/7sad_24949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sad_24949/03_2024/7sad_24949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sad_24949/03_2024/7sad_24949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sad_24949/03_2024/7sad_24949_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sad_24949/03_2024/7sad_24949_updated.pdb" } resolution = 3.96 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= 0.004 sd= 0.493 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 298 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 14849 2.51 5 N 3799 2.21 5 O 4316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "D GLU 413": "OE1" <-> "OE2" Residue "D PHE 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23082 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5807 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 493 Unresolved non-hydrogen angles: 594 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 23, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 345 Chain: "B" Number of atoms: 5667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5667 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 556 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 482 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 17, 'TYR:plan': 6, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 33, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 394 Chain: "C" Number of atoms: 5751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 795, 5751 Classifications: {'peptide': 795} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 34, 'TRANS': 760} Chain breaks: 2 Unresolved non-hydrogen bonds: 550 Unresolved non-hydrogen angles: 659 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 4, 'GLU:plan': 28, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 387 Chain: "D" Number of atoms: 5634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5634 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 140} Link IDs: {'PTRANS': 27, 'TRANS': 757} Chain breaks: 2 Unresolved non-hydrogen bonds: 589 Unresolved non-hydrogen angles: 717 Unresolved non-hydrogen dihedrals: 508 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 35, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 412 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'377': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.70, per 1000 atoms: 0.55 Number of scatterers: 23082 At special positions: 0 Unit cell: (125.832, 154.936, 184.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 4316 8.00 N 3799 7.00 C 14849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 420 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS A 436 " - pdb=" SG CYS A 455 " distance=2.03 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 798 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 456 " distance=2.03 Simple disulfide: pdb=" SG CYS B 436 " - pdb=" SG CYS B 457 " distance=2.04 Simple disulfide: pdb=" SG CYS B 746 " - pdb=" SG CYS B 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 308 " distance=2.04 Simple disulfide: pdb=" SG CYS C 420 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 86 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 456 " distance=2.03 Simple disulfide: pdb=" SG CYS D 436 " - pdb=" SG CYS D 457 " distance=2.03 Simple disulfide: pdb=" SG CYS D 746 " - pdb=" SG CYS D 801 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 903 " - " ASN A 368 " " NAG D 901 " - " ASN D 491 " " NAG E 1 " - " ASN B 688 " " NAG F 1 " - " ASN C 368 " " NAG G 1 " - " ASN D 688 " Time building additional restraints: 9.20 Conformation dependent library (CDL) restraints added in 4.3 seconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 25 sheets defined 38.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.48 Creating SS restraints... Processing helix chain 'A' and resid 36 through 51 removed outlier: 4.607A pdb=" N LYS A 51 " --> pdb=" O ASN A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 103 through 113 Processing helix chain 'A' and resid 126 through 129 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 171 through 187 removed outlier: 4.020A pdb=" N ARG A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 removed outlier: 4.094A pdb=" N GLU A 213 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 removed outlier: 3.595A pdb=" N ALA A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR A 230 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 277 through 295 Processing helix chain 'A' and resid 319 through 326 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.585A pdb=" N LEU A 505 " --> pdb=" O MET A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 526 removed outlier: 4.068A pdb=" N TYR A 526 " --> pdb=" O GLU A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 583 removed outlier: 3.700A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 614 removed outlier: 3.860A pdb=" N MET A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP A 608 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 654 removed outlier: 3.948A pdb=" N GLY A 638 " --> pdb=" O MET A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 673 No H-bonds generated for 'chain 'A' and resid 670 through 673' Processing helix chain 'A' and resid 688 through 695 Processing helix chain 'A' and resid 698 through 706 removed outlier: 4.134A pdb=" N THR A 701 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET A 702 " --> pdb=" O LEU A 699 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG A 704 " --> pdb=" O THR A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 removed outlier: 4.627A pdb=" N GLN A 719 " --> pdb=" O ALA A 715 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG A 722 " --> pdb=" O ILE A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 767 through 781 removed outlier: 3.645A pdb=" N LEU A 777 " --> pdb=" O SER A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 792 Processing helix chain 'A' and resid 810 through 840 removed outlier: 4.303A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 4.310A pdb=" N GLU B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 107 through 118 removed outlier: 3.915A pdb=" N GLN B 118 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 131 Processing helix chain 'B' and resid 150 through 163 removed outlier: 3.895A pdb=" N MET B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.665A pdb=" N LYS B 222 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 247 removed outlier: 4.031A pdb=" N GLU B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 263 No H-bonds generated for 'chain 'B' and resid 260 through 263' Processing helix chain 'B' and resid 290 through 311 removed outlier: 3.554A pdb=" N HIS B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.888A pdb=" N ILE B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 496 through 502 Processing helix chain 'B' and resid 517 through 522 Processing helix chain 'B' and resid 549 through 552 No H-bonds generated for 'chain 'B' and resid 549 through 552' Processing helix chain 'B' and resid 559 through 578 Processing helix chain 'B' and resid 602 through 613 removed outlier: 3.640A pdb=" N TRP B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 655 removed outlier: 4.001A pdb=" N ILE B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TRP B 635 " --> pdb=" O MET B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 672 No H-bonds generated for 'chain 'B' and resid 669 through 672' Processing helix chain 'B' and resid 690 through 698 removed outlier: 3.680A pdb=" N ASN B 698 " --> pdb=" O ASN B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'B' and resid 706 through 708 No H-bonds generated for 'chain 'B' and resid 706 through 708' Processing helix chain 'B' and resid 714 through 723 Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.505A pdb=" N ALA B 740 " --> pdb=" O LEU B 736 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY B 741 " --> pdb=" O ASN B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 3.738A pdb=" N ARG B 774 " --> pdb=" O GLY B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 796 Processing helix chain 'B' and resid 815 through 844 removed outlier: 3.739A pdb=" N ALA B 819 " --> pdb=" O ASP B 816 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY B 820 " --> pdb=" O ASN B 817 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 821 " --> pdb=" O MET B 818 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR B 843 " --> pdb=" O HIS B 840 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 removed outlier: 4.200A pdb=" N LYS C 51 " --> pdb=" O ASN C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 85 removed outlier: 4.546A pdb=" N CYS C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 No H-bonds generated for 'chain 'C' and resid 105 through 108' Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.509A pdb=" N GLU C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 187 removed outlier: 3.765A pdb=" N ARG C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 212 removed outlier: 3.658A pdb=" N MET C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 236 removed outlier: 3.629A pdb=" N ALA C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 277 through 297 removed outlier: 3.538A pdb=" N GLU C 294 " --> pdb=" O GLN C 290 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 501 through 507 Processing helix chain 'C' and resid 523 through 525 No H-bonds generated for 'chain 'C' and resid 523 through 525' Processing helix chain 'C' and resid 560 through 583 Processing helix chain 'C' and resid 603 through 615 removed outlier: 4.654A pdb=" N MET C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TRP C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 656 removed outlier: 3.726A pdb=" N ALA C 640 " --> pdb=" O TRP C 636 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 654 " --> pdb=" O ASN C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 673 No H-bonds generated for 'chain 'C' and resid 670 through 673' Processing helix chain 'C' and resid 688 through 695 Processing helix chain 'C' and resid 700 through 708 Processing helix chain 'C' and resid 714 through 722 removed outlier: 3.600A pdb=" N GLN C 719 " --> pdb=" O ALA C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 742 Processing helix chain 'C' and resid 767 through 781 Processing helix chain 'C' and resid 784 through 792 removed outlier: 3.752A pdb=" N LEU C 788 " --> pdb=" O PHE C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 840 removed outlier: 3.970A pdb=" N GLY C 815 " --> pdb=" O GLU C 811 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE C 828 " --> pdb=" O ILE C 824 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 54 Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.918A pdb=" N ARG D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 117 Processing helix chain 'D' and resid 128 through 130 No H-bonds generated for 'chain 'D' and resid 128 through 130' Processing helix chain 'D' and resid 150 through 163 Processing helix chain 'D' and resid 182 through 189 Processing helix chain 'D' and resid 213 through 222 removed outlier: 4.007A pdb=" N LYS D 221 " --> pdb=" O GLN D 217 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LYS D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 247 Processing helix chain 'D' and resid 289 through 307 Processing helix chain 'D' and resid 325 through 328 removed outlier: 3.783A pdb=" N ARG D 328 " --> pdb=" O HIS D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 335 through 338 No H-bonds generated for 'chain 'D' and resid 335 through 338' Processing helix chain 'D' and resid 460 through 472 Processing helix chain 'D' and resid 496 through 502 removed outlier: 3.694A pdb=" N VAL D 502 " --> pdb=" O ILE D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 520 No H-bonds generated for 'chain 'D' and resid 517 through 520' Processing helix chain 'D' and resid 549 through 552 No H-bonds generated for 'chain 'D' and resid 549 through 552' Processing helix chain 'D' and resid 556 through 578 Processing helix chain 'D' and resid 602 through 613 Processing helix chain 'D' and resid 626 through 655 Processing helix chain 'D' and resid 669 through 672 No H-bonds generated for 'chain 'D' and resid 669 through 672' Processing helix chain 'D' and resid 690 through 698 removed outlier: 3.749A pdb=" N ASN D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN D 698 " --> pdb=" O ASN D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 700 through 708 removed outlier: 4.756A pdb=" N LYS D 708 " --> pdb=" O ALA D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 722 removed outlier: 3.951A pdb=" N LYS D 722 " --> pdb=" O LEU D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.631A pdb=" N TYR D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY D 741 " --> pdb=" O ASN D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 786 removed outlier: 3.593A pdb=" N GLN D 782 " --> pdb=" O LEU D 778 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D 783 " --> pdb=" O ALA D 779 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE D 784 " --> pdb=" O ILE D 780 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 797 Processing helix chain 'D' and resid 815 through 844 removed outlier: 4.200A pdb=" N ALA D 819 " --> pdb=" O ASP D 816 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLY D 820 " --> pdb=" O ASN D 817 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL D 821 " --> pdb=" O MET D 818 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 59 through 65 Processing sheet with id= B, first strand: chain 'A' and resid 194 through 197 removed outlier: 6.839A pdb=" N LEU A 165 " --> pdb=" O LEU A 195 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N PHE A 197 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL A 167 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER A 168 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 246 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LEU A 221 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU A 248 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 267 through 271 removed outlier: 3.551A pdb=" N GLN A 270 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TYR A 351 " --> pdb=" O TYR A 367 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 365 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASN A 355 " --> pdb=" O GLN A 363 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLN A 363 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLN A 357 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 366 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 397 through 402 removed outlier: 6.847A pdb=" N THR A 473 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE A 400 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLU A 475 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N THR A 402 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS A 477 " --> pdb=" O THR A 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 410 through 412 removed outlier: 3.635A pdb=" N TYR A 456 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS A 412 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS A 454 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 729 through 732 removed outlier: 3.723A pdb=" N TRP A 731 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 540 " --> pdb=" O THR A 749 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 747 " --> pdb=" O VAL A 542 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 67 through 73 removed outlier: 3.579A pdb=" N GLU B 69 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ALA B 38 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 97 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE B 40 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE B 99 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N VAL B 42 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE B 99 " --> pdb=" O PRO B 122 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 124 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 170 through 173 removed outlier: 6.695A pdb=" N THR B 255 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU B 230 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 257 " --> pdb=" O LEU B 230 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 278 through 282 removed outlier: 3.608A pdb=" N LEU B 362 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 377 " --> pdb=" O ILE B 364 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU B 366 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ARG B 375 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 405 through 410 removed outlier: 6.484A pdb=" N THR B 475 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE B 408 " --> pdb=" O THR B 475 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ASP B 477 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N THR B 410 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TYR B 479 " --> pdb=" O THR B 410 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 417 through 420 removed outlier: 3.910A pdb=" N GLU B 420 " --> pdb=" O CYS B 456 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N CYS B 456 " --> pdb=" O GLU B 420 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 434 " --> pdb=" O CYS B 457 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 729 through 732 removed outlier: 3.600A pdb=" N VAL B 538 " --> pdb=" O VAL B 749 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 59 through 65 removed outlier: 3.540A pdb=" N THR C 63 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 65 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 92 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.702A pdb=" N PHE C 197 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 168 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL C 246 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU C 248 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 267 through 271 removed outlier: 6.173A pdb=" N ASN C 355 " --> pdb=" O GLN C 363 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLN C 363 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 397 through 402 removed outlier: 7.163A pdb=" N THR C 473 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE C 400 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU C 475 " --> pdb=" O ILE C 400 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR C 402 " --> pdb=" O GLU C 475 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N HIS C 477 " --> pdb=" O THR C 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 409 through 412 removed outlier: 3.668A pdb=" N TYR C 456 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS C 455 " --> pdb=" O VAL C 434 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 512 through 514 Processing sheet with id= S, first strand: chain 'C' and resid 729 through 732 removed outlier: 3.619A pdb=" N TRP C 731 " --> pdb=" O THR C 539 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 539 " --> pdb=" O TRP C 731 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 540 " --> pdb=" O THR C 749 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 749 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 542 " --> pdb=" O VAL C 747 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 747 " --> pdb=" O VAL C 542 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 67 through 73 removed outlier: 3.636A pdb=" N LEU D 41 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET D 73 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA D 38 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 97 " --> pdb=" O ALA D 38 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE D 40 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N PHE D 99 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL D 42 " --> pdb=" O PHE D 99 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 202 through 205 removed outlier: 6.807A pdb=" N ILE D 171 " --> pdb=" O LEU D 203 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N LEU D 205 " --> pdb=" O ILE D 171 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR D 173 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR D 231 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR D 174 " --> pdb=" O TYR D 231 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR D 255 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU D 230 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE D 257 " --> pdb=" O LEU D 230 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 278 through 282 removed outlier: 3.857A pdb=" N LEU D 362 " --> pdb=" O TRP D 379 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 364 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLY D 377 " --> pdb=" O ILE D 364 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 366 " --> pdb=" O ARG D 375 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG D 375 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 405 through 410 removed outlier: 6.820A pdb=" N THR D 475 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ILE D 408 " --> pdb=" O THR D 475 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP D 477 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR D 410 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR D 479 " --> pdb=" O THR D 410 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'D' and resid 417 through 420 removed outlier: 4.037A pdb=" N GLU D 420 " --> pdb=" O CYS D 456 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS D 456 " --> pdb=" O GLU D 420 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS D 455 " --> pdb=" O CYS D 436 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 434 " --> pdb=" O CYS D 457 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 748 through 750 removed outlier: 3.820A pdb=" N VAL D 749 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL D 538 " --> pdb=" O VAL D 749 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY D 684 " --> pdb=" O ALA D 728 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE D 730 " --> pdb=" O GLY D 684 " (cutoff:3.500A) 853 hydrogen bonds defined for protein. 2283 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: 7.96 Time building geometry restraints manager: 9.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3756 1.30 - 1.43: 6047 1.43 - 1.56: 13568 1.56 - 1.70: 2 1.70 - 1.83: 198 Bond restraints: 23571 Sorted by residual: bond pdb=" CA ALA B 648 " pdb=" C ALA B 648 " ideal model delta sigma weight residual 1.524 1.423 0.101 1.27e-02 6.20e+03 6.32e+01 bond pdb=" CG PRO C 142 " pdb=" CD PRO C 142 " ideal model delta sigma weight residual 1.503 1.264 0.239 3.40e-02 8.65e+02 4.93e+01 bond pdb=" N PHE D 642 " pdb=" CA PHE D 642 " ideal model delta sigma weight residual 1.459 1.379 0.080 1.20e-02 6.94e+03 4.48e+01 bond pdb=" C ALA C 649 " pdb=" O ALA C 649 " ideal model delta sigma weight residual 1.237 1.163 0.074 1.17e-02 7.31e+03 3.96e+01 bond pdb=" CA PRO A 557 " pdb=" C PRO A 557 " ideal model delta sigma weight residual 1.524 1.458 0.066 1.06e-02 8.90e+03 3.84e+01 ... (remaining 23566 not shown) Histogram of bond angle deviations from ideal: 87.33 - 98.02: 6 98.02 - 108.70: 1314 108.70 - 119.39: 18655 119.39 - 130.07: 12123 130.07 - 140.76: 149 Bond angle restraints: 32247 Sorted by residual: angle pdb=" C THR D 647 " pdb=" CA THR D 647 " pdb=" CB THR D 647 " ideal model delta sigma weight residual 110.88 90.92 19.96 1.57e+00 4.06e-01 1.62e+02 angle pdb=" C GLN A 556 " pdb=" N PRO A 557 " pdb=" CA PRO A 557 " ideal model delta sigma weight residual 121.04 106.91 14.13 1.21e+00 6.83e-01 1.36e+02 angle pdb=" N PRO C 142 " pdb=" CD PRO C 142 " pdb=" CG PRO C 142 " ideal model delta sigma weight residual 103.20 87.33 15.87 1.50e+00 4.44e-01 1.12e+02 angle pdb=" CA LEU A 819 " pdb=" CB LEU A 819 " pdb=" CG LEU A 819 " ideal model delta sigma weight residual 116.30 89.55 26.75 3.50e+00 8.16e-02 5.84e+01 angle pdb=" N VAL C 656 " pdb=" CA VAL C 656 " pdb=" C VAL C 656 " ideal model delta sigma weight residual 113.10 120.24 -7.14 9.70e-01 1.06e+00 5.42e+01 ... (remaining 32242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.69: 13399 24.69 - 49.37: 599 49.37 - 74.06: 54 74.06 - 98.75: 10 98.75 - 123.43: 3 Dihedral angle restraints: 14065 sinusoidal: 4917 harmonic: 9148 Sorted by residual: dihedral pdb=" C THR D 647 " pdb=" N THR D 647 " pdb=" CA THR D 647 " pdb=" CB THR D 647 " ideal model delta harmonic sigma weight residual -122.00 -99.45 -22.55 0 2.50e+00 1.60e-01 8.13e+01 dihedral pdb=" CB CYS C 744 " pdb=" SG CYS C 744 " pdb=" SG CYS C 798 " pdb=" CB CYS C 798 " ideal model delta sinusoidal sigma weight residual -86.00 -12.16 -73.84 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CB CYS A 436 " pdb=" SG CYS A 436 " pdb=" SG CYS A 455 " pdb=" CB CYS A 455 " ideal model delta sinusoidal sigma weight residual -86.00 -153.67 67.67 1 1.00e+01 1.00e-02 5.95e+01 ... (remaining 14062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 3892 0.145 - 0.290: 21 0.290 - 0.435: 7 0.435 - 0.580: 2 0.580 - 0.725: 2 Chirality restraints: 3924 Sorted by residual: chirality pdb=" CG LEU A 819 " pdb=" CB LEU A 819 " pdb=" CD1 LEU A 819 " pdb=" CD2 LEU A 819 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ASN C 650 " pdb=" N ASN C 650 " pdb=" C ASN C 650 " pdb=" CB ASN C 650 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ILE B 655 " pdb=" N ILE B 655 " pdb=" C ILE B 655 " pdb=" CB ILE B 655 " both_signs ideal model delta sigma weight residual False 2.43 1.90 0.54 2.00e-01 2.50e+01 7.20e+00 ... (remaining 3921 not shown) Planarity restraints: 4070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 141 " -0.079 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO C 142 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO C 142 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 142 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 641 " 0.021 2.00e-02 2.50e+03 4.43e-02 1.97e+01 pdb=" C ILE D 641 " -0.077 2.00e-02 2.50e+03 pdb=" O ILE D 641 " 0.029 2.00e-02 2.50e+03 pdb=" N PHE D 642 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 559 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLN A 559 " -0.070 2.00e-02 2.50e+03 pdb=" O GLN A 559 " 0.026 2.00e-02 2.50e+03 pdb=" N SER A 560 " 0.024 2.00e-02 2.50e+03 ... (remaining 4067 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.19: 4 2.19 - 2.87: 8617 2.87 - 3.55: 32118 3.55 - 4.22: 45082 4.22 - 4.90: 77676 Nonbonded interactions: 163497 Sorted by model distance: nonbonded pdb=" O LEU A 562 " pdb=" N LEU A 564 " model vdw 1.515 2.520 nonbonded pdb=" N GLN A 559 " pdb=" OE1 GLN A 559 " model vdw 2.120 2.520 nonbonded pdb=" OG SER D 149 " pdb=" OE1 GLN D 152 " model vdw 2.172 2.440 nonbonded pdb=" OG1 THR C 550 " pdb=" OE1 GLU C 811 " model vdw 2.187 2.440 nonbonded pdb=" O ASP B 77 " pdb=" OG SER B 80 " model vdw 2.235 2.440 ... (remaining 163492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 41 or (resid 42 through 45 and (name N or name \ CA or name C or name O or name CB )) or resid 46 or (resid 47 through 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 72 or (res \ id 73 and (name N or name CA or name C or name O or name CB )) or resid 74 throu \ gh 130 or (resid 131 and (name N or name CA or name C or name O or name CB )) or \ resid 132 through 171 or (resid 172 and (name N or name CA or name C or name O \ or name CB )) or resid 173 or (resid 174 through 176 and (name N or name CA or n \ ame C or name O or name CB )) or resid 177 through 180 or (resid 181 and (name N \ or name CA or name C or name O or name CB )) or resid 182 through 186 or (resid \ 187 through 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 or (resid 190 through 192 and (name N or name CA or name C or name O or n \ ame CB )) or resid 193 through 197 or (resid 198 and (name N or name CA or name \ C or name O or name CB )) or resid 199 through 214 or (resid 215 through 216 and \ (name N or name CA or name C or name O or name CB )) or resid 217 through 251 o \ r (resid 252 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 53 through 259 or (resid 260 and (name N or name CA or name C or name O or name \ CB )) or resid 261 through 274 or (resid 275 and (name N or name CA or name C or \ name O or name CB )) or resid 276 through 289 or (resid 290 through 291 and (na \ me N or name CA or name C or name O or name CB )) or resid 292 or (resid 293 thr \ ough 299 and (name N or name CA or name C or name O or name CB )) or resid 300 t \ hrough 336 or (resid 337 and (name N or name CA or name C or name O or name CB ) \ ) or resid 338 or (resid 339 and (name N or name CA or name C or name O or name \ CB )) or resid 340 through 416 or (resid 417 and (name N or name CA or name C or \ name O or name CB )) or resid 418 through 420 or (resid 421 through 423 and (na \ me N or name CA or name C or name O or name CB )) or resid 424 through 448 or (r \ esid 449 and (name N or name CA or name C or name O or name CB )) or resid 450 t \ hrough 543 or (resid 544 through 545 and (name N or name CA or name C or name O \ or name CB )) or resid 546 through 575 or (resid 576 and (name N or name CA or n \ ame C or name O or name CB )) or resid 577 through 580 or (resid 581 through 583 \ and (name N or name CA or name C or name O or name CB )) or resid 584 through 6 \ 61 or (resid 662 and (name N or name CA or name C or name O or name CB )) or res \ id 663 through 693 or (resid 694 through 695 and (name N or name CA or name C or \ name O or name CB )) or resid 696 through 703 or (resid 704 and (name N or name \ CA or name C or name O or name CB )) or resid 705 through 724 or (resid 725 and \ (name N or name CA or name C or name O or name CB )) or resid 726 through 736 o \ r (resid 737 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 38 or (resid 739 through 740 and (name N or name CA or name C or name O or name \ CB )) or resid 741 through 750 or (resid 751 and (name N or name CA or name C or \ name O or name CB )) or resid 752 through 780 or (resid 781 and (name N or name \ CA or name C or name O or name CB )) or resid 782 through 818 or (resid 819 and \ (name N or name CA or name C or name O or name CB )) or resid 820 through 841 o \ r resid 901 through 902)) selection = (chain 'C' and (resid 25 through 58 or (resid 59 and (name N or name CA or name \ C or name O or name CB )) or resid 60 or (resid 61 through 62 and (name N or nam \ e CA or name C or name O or name CB )) or resid 63 through 79 or (resid 80 and ( \ name N or name CA or name C or name O or name CB )) or resid 81 through 82 or (r \ esid 83 and (name N or name CA or name C or name O or name CB )) or resid 84 thr \ ough 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) \ or resid 103 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 224 or (resid 225 and (name \ N or name CA or name C or name O or name CB )) or resid 226 through 271 or (res \ id 272 and (name N or name CA or name C or name O or name CB )) or resid 273 thr \ ough 276 or (resid 277 and (name N or name CA or name C or name O or name CB )) \ or resid 278 through 294 or (resid 295 through 299 and (name N or name CA or nam \ e C or name O or name CB )) or resid 300 through 310 or (resid 311 and (name N o \ r name CA or name C or name O or name CB )) or resid 312 or (resid 313 and (name \ N or name CA or name C or name O or name CB )) or resid 314 through 331 or (res \ id 332 and (name N or name CA or name C or name O or name CB )) or resid 333 thr \ ough 340 or (resid 341 through 342 and (name N or name CA or name C or name O or \ name CB )) or resid 343 through 345 or (resid 346 through 347 and (name N or na \ me CA or name C or name O or name CB )) or resid 348 through 376 or (resid 377 t \ hrough 378 and (name N or name CA or name C or name O or name CB )) or resid 379 \ through 386 or (resid 387 and (name N or name CA or name C or name O or name CB \ )) or resid 388 through 393 or (resid 394 and (name N or name CA or name C or n \ ame O or name CB )) or resid 395 through 396 or (resid 397 and (name N or name C \ A or name C or name O or name CB )) or resid 398 through 706 or (resid 707 and ( \ name N or name CA or name C or name O or name CB )) or resid 708 through 810 or \ (resid 811 and (name N or name CA or name C or name O or name CB )) or resid 812 \ through 816 or (resid 817 through 819 and (name N or name CA or name C or name \ O or name CB )) or resid 820 through 841 or resid 901 through 902)) } ncs_group { reference = (chain 'B' and (resid 34 through 68 or (resid 69 and (name N or name CA or name \ C or name O or name CB )) or resid 70 through 117 or (resid 118 and (name N or n \ ame CA or name C or name O or name CB )) or resid 119 through 152 or (resid 153 \ through 154 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 5 through 212 or (resid 213 and (name N or name CA or name C or name O or name C \ B )) or resid 214 through 233 or (resid 234 through 237 and (name N or name CA o \ r name C or name O or name CB )) or resid 238 through 241 or (resid 242 and (nam \ e N or name CA or name C or name O or name CB )) or resid 243 through 244 or (re \ sid 245 and (name N or name CA or name C or name O or name CB )) or resid 246 th \ rough 305 or (resid 306 through 308 and (name N or name CA or name C or name O o \ r name CB )) or resid 309 or (resid 310 through 311 and (name N or name CA or na \ me C or name O or name CB )) or resid 312 through 315 or (resid 316 and (name N \ or name CA or name C or name O or name CB )) or resid 317 through 332 or (resid \ 333 through 334 and (name N or name CA or name C or name O or name CB )) or resi \ d 335 through 360 or (resid 361 and (name N or name CA or name C or name O or na \ me CB )) or resid 362 through 386 or (resid 387 and (name N or name CA or name C \ or name O or name CB )) or resid 388 through 411 or (resid 412 through 414 and \ (name N or name CA or name C or name O or name CB )) or resid 415 through 440 or \ (resid 441 and (name N or name CA or name C or name O or name CB )) or resid 44 \ 2 through 466 or (resid 467 and (name N or name CA or name C or name O or name C \ B )) or resid 468 through 472 or (resid 473 and (name N or name CA or name C or \ name O or name CB )) or resid 474 through 499 or (resid 500 and (name N or name \ CA or name C or name O or name CB )) or resid 501 through 520 or (resid 521 and \ (name N or name CA or name C or name O or name CB )) or resid 522 through 556 or \ (resid 557 and (name N or name CA or name C or name O or name CB )) or resid 55 \ 8 through 707 or (resid 708 and (name N or name CA or name C or name O or name C \ B )) or resid 709 through 785 or (resid 786 and (name N or name CA or name C or \ name O or name CB )) or resid 787 or (resid 788 and (name N or name CA or name C \ or name O or name CB )) or resid 789 through 802 or (resid 803 through 807 and \ (name N or name CA or name C or name O or name CB )) or resid 808 through 811 or \ (resid 812 and (name N or name CA or name C or name O or name CB )) or resid 81 \ 3 through 817 or (resid 818 through 819 and (name N or name CA or name C or name \ O or name CB )) or resid 820 through 828 or (resid 829 through 830 and (name N \ or name CA or name C or name O or name CB )) or resid 831 through 835 or (resid \ 836 and (name N or name CA or name C or name O or name CB )) or resid 837 throug \ h 845 or resid 901 through 902)) selection = (chain 'D' and (resid 34 through 179 or (resid 180 and (name N or name CA or nam \ e C or name O or name CB )) or resid 181 through 190 or (resid 191 and (name N o \ r name CA or name C or name O or name CB )) or resid 192 through 197 or (resid 1 \ 98 and (name N or name CA or name C or name O or name CB )) or resid 199 or (res \ id 200 through 201 and (name N or name CA or name C or name O or name CB )) or r \ esid 202 through 208 or (resid 209 through 211 and (name N or name CA or name C \ or name O or name CB )) or resid 212 through 271 or (resid 272 and (name N or na \ me CA or name C or name O or name CB )) or resid 273 through 353 or (resid 354 a \ nd (name N or name CA or name C or name O or name CB )) or resid 355 through 367 \ or (resid 368 through 370 and (name N or name CA or name C or name O or name CB \ )) or resid 371 through 412 or (resid 413 through 414 and (name N or name CA or \ name C or name O or name CB )) or resid 415 through 422 or (resid 423 and (name \ N or name CA or name C or name O or name CB )) or resid 424 through 469 or (res \ id 470 and (name N or name CA or name C or name O or name CB )) or resid 471 thr \ ough 487 or (resid 488 and (name N or name CA or name C or name O or name CB )) \ or resid 489 through 539 or (resid 540 and (name N or name CA or name C or name \ O or name CB )) or resid 541 through 574 or (resid 575 and (name N or name CA or \ name C or name O or name CB )) or resid 576 through 628 or (resid 629 and (name \ N or name CA or name C or name O or name CB )) or resid 630 through 672 or (res \ id 673 and (name N or name CA or name C or name O or name CB )) or resid 674 thr \ ough 700 or (resid 701 and (name N or name CA or name C or name O or name CB )) \ or resid 702 through 767 or (resid 768 and (name N or name CA or name C or name \ O or name CB )) or resid 769 through 792 or (resid 793 through 794 and (name N o \ r name CA or name C or name O or name CB )) or resid 795 through 845 or resid 90 \ 1 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 15.020 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 62.030 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.239 23571 Z= 0.373 Angle : 0.780 26.753 32247 Z= 0.430 Chirality : 0.051 0.725 3924 Planarity : 0.005 0.113 4065 Dihedral : 13.287 123.434 8116 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.42 % Favored : 94.39 % Rotamer: Outliers : 0.49 % Allowed : 0.49 % Favored : 99.02 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3136 helix: 1.32 (0.15), residues: 1204 sheet: -0.16 (0.31), residues: 323 loop : -1.61 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 608 HIS 0.008 0.001 HIS C 371 PHE 0.043 0.002 PHE D 176 TYR 0.030 0.001 TYR B 646 ARG 0.005 0.000 ARG A 671 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 433 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 PHE cc_start: 0.8518 (t80) cc_final: 0.8291 (t80) REVERT: B 101 ASP cc_start: 0.7772 (m-30) cc_final: 0.6674 (t0) REVERT: B 537 MET cc_start: 0.8509 (tpt) cc_final: 0.8119 (tpt) REVERT: B 562 MET cc_start: 0.8938 (mmp) cc_final: 0.8663 (mmt) REVERT: B 702 MET cc_start: 0.8152 (ptp) cc_final: 0.7849 (ptp) REVERT: B 813 LEU cc_start: 0.8774 (mm) cc_final: 0.8086 (mm) REVERT: C 406 GLU cc_start: 0.7773 (tp30) cc_final: 0.7468 (tp30) REVERT: C 655 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9086 (tt) REVERT: C 674 ASN cc_start: 0.8522 (t0) cc_final: 0.8188 (t0) REVERT: C 724 ASN cc_start: 0.8091 (m-40) cc_final: 0.7773 (t0) REVERT: D 223 LEU cc_start: 0.8273 (mt) cc_final: 0.7935 (pp) REVERT: D 430 MET cc_start: 0.7777 (mtt) cc_final: 0.7510 (mtt) REVERT: D 742 ARG cc_start: 0.8311 (tpp80) cc_final: 0.7894 (mmm-85) REVERT: D 777 ASP cc_start: 0.7855 (t70) cc_final: 0.7642 (t70) REVERT: D 789 MET cc_start: 0.7239 (ttp) cc_final: 0.7025 (ttp) outliers start: 11 outliers final: 7 residues processed: 443 average time/residue: 0.2734 time to fit residues: 203.7322 Evaluate side-chains 330 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 322 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain C residue 654 PHE Chi-restraints excluded: chain C residue 655 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 655 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 81 optimal weight: 40.0000 chunk 160 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 246 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 183 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 145 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS D 486 HIS ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 23571 Z= 0.298 Angle : 0.649 12.335 32247 Z= 0.339 Chirality : 0.044 0.275 3924 Planarity : 0.005 0.074 4065 Dihedral : 6.973 79.151 3679 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.86 % Favored : 92.98 % Rotamer: Outliers : 2.32 % Allowed : 10.83 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.74 (0.15), residues: 3136 helix: 0.95 (0.15), residues: 1211 sheet: -0.43 (0.27), residues: 394 loop : -1.75 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 373 HIS 0.009 0.001 HIS A 404 PHE 0.030 0.002 PHE B 637 TYR 0.029 0.001 TYR B 479 ARG 0.003 0.000 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 341 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8443 (tpp) cc_final: 0.7364 (mmt) REVERT: A 642 ILE cc_start: 0.9512 (mm) cc_final: 0.9274 (mm) REVERT: B 101 ASP cc_start: 0.7838 (m-30) cc_final: 0.6527 (t0) REVERT: B 358 MET cc_start: 0.7881 (mpp) cc_final: 0.7605 (mpp) REVERT: B 654 MET cc_start: 0.8535 (tmt) cc_final: 0.8293 (tmt) REVERT: B 702 MET cc_start: 0.8261 (ptp) cc_final: 0.7937 (ptp) REVERT: C 463 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8811 (pp) REVERT: C 674 ASN cc_start: 0.8601 (t0) cc_final: 0.8152 (t0) REVERT: D 89 MET cc_start: 0.5595 (tpt) cc_final: 0.5269 (tpt) REVERT: D 430 MET cc_start: 0.7917 (mtt) cc_final: 0.7692 (mtt) REVERT: D 654 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7651 (ttm) REVERT: D 702 MET cc_start: 0.7685 (mmm) cc_final: 0.7195 (mpp) REVERT: D 742 ARG cc_start: 0.8175 (tpp80) cc_final: 0.7673 (mmm-85) outliers start: 52 outliers final: 39 residues processed: 375 average time/residue: 0.2639 time to fit residues: 168.1217 Evaluate side-chains 351 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 310 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 370 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 769 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 158 optimal weight: 7.9990 chunk 88 optimal weight: 0.0170 chunk 237 optimal weight: 0.0270 chunk 194 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 283 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 overall best weight: 1.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23571 Z= 0.173 Angle : 0.580 9.733 32247 Z= 0.297 Chirality : 0.042 0.285 3924 Planarity : 0.005 0.066 4065 Dihedral : 5.992 56.127 3669 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.31 % Favored : 93.53 % Rotamer: Outliers : 2.41 % Allowed : 13.82 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.15), residues: 3136 helix: 0.99 (0.15), residues: 1198 sheet: -0.29 (0.28), residues: 393 loop : -1.72 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 768 HIS 0.012 0.001 HIS A 146 PHE 0.024 0.002 PHE B 642 TYR 0.025 0.001 TYR B 479 ARG 0.003 0.000 ARG A 704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 342 time to evaluate : 2.680 Fit side-chains revert: symmetry clash REVERT: A 642 ILE cc_start: 0.9509 (mm) cc_final: 0.8969 (mm) REVERT: B 101 ASP cc_start: 0.7789 (m-30) cc_final: 0.6500 (t0) REVERT: B 702 MET cc_start: 0.8183 (ptp) cc_final: 0.7820 (ptp) REVERT: B 829 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7361 (tmm) REVERT: C 237 MET cc_start: 0.7728 (ppp) cc_final: 0.7417 (ppp) REVERT: C 406 GLU cc_start: 0.7746 (tp30) cc_final: 0.7434 (tp30) REVERT: C 463 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8764 (pp) REVERT: C 674 ASN cc_start: 0.8613 (t0) cc_final: 0.8242 (t0) REVERT: D 89 MET cc_start: 0.5383 (tpt) cc_final: 0.5175 (tpt) REVERT: D 430 MET cc_start: 0.7897 (mtt) cc_final: 0.7691 (mtt) REVERT: D 654 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7638 (ttm) REVERT: D 702 MET cc_start: 0.7657 (mmm) cc_final: 0.7204 (mpp) REVERT: D 742 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7522 (mmm-85) outliers start: 54 outliers final: 34 residues processed: 376 average time/residue: 0.2713 time to fit residues: 173.1511 Evaluate side-chains 353 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 316 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 654 MET Chi-restraints excluded: chain D residue 769 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 282 optimal weight: 6.9990 chunk 214 optimal weight: 0.0010 chunk 148 optimal weight: 0.1980 chunk 31 optimal weight: 9.9990 chunk 136 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 286 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 271 optimal weight: 20.0000 chunk 81 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 GLN B 218 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN D 127 HIS D 711 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23571 Z= 0.145 Angle : 0.568 9.574 32247 Z= 0.286 Chirality : 0.042 0.293 3924 Planarity : 0.004 0.059 4065 Dihedral : 5.514 54.126 3669 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.09 % Favored : 93.78 % Rotamer: Outliers : 2.18 % Allowed : 15.87 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.59 (0.15), residues: 3136 helix: 1.05 (0.15), residues: 1198 sheet: -0.15 (0.28), residues: 378 loop : -1.67 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 768 HIS 0.004 0.001 HIS A 404 PHE 0.024 0.001 PHE A 554 TYR 0.029 0.001 TYR B 479 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 348 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.8452 (tpp) cc_final: 0.7371 (mmt) REVERT: A 642 ILE cc_start: 0.9438 (mm) cc_final: 0.9182 (mm) REVERT: B 101 ASP cc_start: 0.7782 (m-30) cc_final: 0.7229 (m-30) REVERT: B 410 THR cc_start: 0.9432 (t) cc_final: 0.9130 (m) REVERT: B 436 CYS cc_start: 0.5090 (OUTLIER) cc_final: 0.4857 (t) REVERT: B 537 MET cc_start: 0.8428 (tpt) cc_final: 0.8164 (tpt) REVERT: B 702 MET cc_start: 0.8092 (ptp) cc_final: 0.7773 (ptp) REVERT: C 155 MET cc_start: 0.8044 (ptm) cc_final: 0.7796 (mmp) REVERT: C 436 CYS cc_start: 0.7010 (m) cc_final: 0.6784 (m) REVERT: C 463 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8748 (pp) REVERT: C 572 VAL cc_start: 0.9313 (t) cc_final: 0.9047 (p) REVERT: C 575 VAL cc_start: 0.9536 (t) cc_final: 0.9332 (p) REVERT: C 674 ASN cc_start: 0.8584 (t0) cc_final: 0.8222 (t0) REVERT: C 762 MET cc_start: 0.8604 (ptp) cc_final: 0.8346 (ptp) REVERT: D 524 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7562 (m-30) REVERT: D 562 MET cc_start: 0.9121 (ppp) cc_final: 0.8901 (ppp) REVERT: D 600 PHE cc_start: 0.8026 (t80) cc_final: 0.7806 (t80) REVERT: D 702 MET cc_start: 0.7677 (mmm) cc_final: 0.7310 (mpp) REVERT: D 711 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: D 742 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7600 (mmm-85) outliers start: 49 outliers final: 33 residues processed: 380 average time/residue: 0.2722 time to fit residues: 176.8830 Evaluate side-chains 362 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 325 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 711 GLN Chi-restraints excluded: chain D residue 769 ASP Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 252 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 209 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 154 optimal weight: 0.9980 chunk 272 optimal weight: 0.7980 chunk 76 optimal weight: 20.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 650 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23571 Z= 0.275 Angle : 0.611 9.508 32247 Z= 0.317 Chirality : 0.043 0.275 3924 Planarity : 0.005 0.061 4065 Dihedral : 5.741 57.638 3666 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.68 % Favored : 92.22 % Rotamer: Outliers : 3.43 % Allowed : 16.94 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.73 (0.15), residues: 3136 helix: 0.98 (0.15), residues: 1194 sheet: -0.32 (0.27), residues: 397 loop : -1.77 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 494 HIS 0.009 0.001 HIS A 404 PHE 0.026 0.002 PHE A 321 TYR 0.027 0.001 TYR B 479 ARG 0.004 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 327 time to evaluate : 2.657 Fit side-chains revert: symmetry clash REVERT: A 642 ILE cc_start: 0.9512 (mm) cc_final: 0.9253 (mm) REVERT: B 101 ASP cc_start: 0.7600 (m-30) cc_final: 0.7149 (m-30) REVERT: B 386 MET cc_start: 0.8791 (mmm) cc_final: 0.8390 (mmm) REVERT: B 702 MET cc_start: 0.8217 (ptp) cc_final: 0.7942 (ptp) REVERT: B 829 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7316 (tmm) REVERT: C 155 MET cc_start: 0.8133 (ptm) cc_final: 0.7829 (mmp) REVERT: C 436 CYS cc_start: 0.6739 (m) cc_final: 0.6534 (m) REVERT: C 572 VAL cc_start: 0.9354 (t) cc_final: 0.9081 (p) REVERT: C 575 VAL cc_start: 0.9556 (t) cc_final: 0.9307 (p) REVERT: C 674 ASN cc_start: 0.8614 (t0) cc_final: 0.8151 (t0) REVERT: C 762 MET cc_start: 0.8579 (ptp) cc_final: 0.8282 (ptp) REVERT: D 600 PHE cc_start: 0.8109 (t80) cc_final: 0.7885 (t80) REVERT: D 702 MET cc_start: 0.7731 (mmm) cc_final: 0.7354 (mpp) REVERT: D 742 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7538 (mmm-85) outliers start: 77 outliers final: 59 residues processed: 380 average time/residue: 0.2636 time to fit residues: 170.1745 Evaluate side-chains 378 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 318 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 635 VAL Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 645 SER Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 772 TRP Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 687 SER Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 461 CYS Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 769 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 102 optimal weight: 40.0000 chunk 273 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 140 optimal weight: 0.0060 chunk 25 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 23571 Z= 0.154 Angle : 0.580 9.146 32247 Z= 0.291 Chirality : 0.041 0.285 3924 Planarity : 0.004 0.061 4065 Dihedral : 5.271 54.684 3666 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.31 % Favored : 93.56 % Rotamer: Outliers : 2.67 % Allowed : 18.32 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.62 (0.15), residues: 3136 helix: 1.09 (0.15), residues: 1198 sheet: -0.18 (0.28), residues: 383 loop : -1.75 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 768 HIS 0.004 0.000 HIS A 404 PHE 0.020 0.001 PHE B 642 TYR 0.030 0.001 TYR B 479 ARG 0.001 0.000 ARG B 742 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 346 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 641 MET cc_start: 0.8796 (tmm) cc_final: 0.8587 (tmm) REVERT: A 642 ILE cc_start: 0.9488 (mm) cc_final: 0.9015 (mm) REVERT: A 711 TYR cc_start: 0.8044 (m-10) cc_final: 0.7793 (m-80) REVERT: B 101 ASP cc_start: 0.7597 (m-30) cc_final: 0.7114 (m-30) REVERT: B 702 MET cc_start: 0.8118 (ptp) cc_final: 0.7828 (ptp) REVERT: B 829 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7334 (tmm) REVERT: C 155 MET cc_start: 0.8131 (ptm) cc_final: 0.7829 (mmp) REVERT: C 237 MET cc_start: 0.7259 (ppp) cc_final: 0.5356 (ttm) REVERT: C 436 CYS cc_start: 0.6945 (m) cc_final: 0.6726 (m) REVERT: C 572 VAL cc_start: 0.9313 (t) cc_final: 0.9055 (p) REVERT: C 575 VAL cc_start: 0.9517 (t) cc_final: 0.9301 (p) REVERT: C 674 ASN cc_start: 0.8614 (t0) cc_final: 0.8236 (t0) REVERT: C 762 MET cc_start: 0.8616 (ptp) cc_final: 0.7885 (ptm) REVERT: D 542 ASN cc_start: 0.5268 (OUTLIER) cc_final: 0.4835 (m-40) REVERT: D 562 MET cc_start: 0.9078 (ppp) cc_final: 0.8850 (ppp) REVERT: D 742 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7591 (mmm-85) outliers start: 60 outliers final: 46 residues processed: 381 average time/residue: 0.2650 time to fit residues: 171.1584 Evaluate side-chains 376 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 328 time to evaluate : 2.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 780 HIS Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 542 ASN Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 292 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 221 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 169 optimal weight: 0.9980 chunk 302 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 chunk 139 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23571 Z= 0.157 Angle : 0.571 10.307 32247 Z= 0.288 Chirality : 0.042 0.368 3924 Planarity : 0.004 0.082 4065 Dihedral : 5.093 56.664 3665 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.57 % Favored : 93.30 % Rotamer: Outliers : 2.59 % Allowed : 19.30 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.60 (0.15), residues: 3136 helix: 1.09 (0.15), residues: 1209 sheet: -0.15 (0.28), residues: 383 loop : -1.75 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 768 HIS 0.004 0.001 HIS A 404 PHE 0.025 0.001 PHE B 637 TYR 0.028 0.001 TYR B 479 ARG 0.001 0.000 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 343 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 642 ILE cc_start: 0.9489 (mm) cc_final: 0.8996 (mm) REVERT: B 101 ASP cc_start: 0.7542 (m-30) cc_final: 0.7061 (m-30) REVERT: B 141 SER cc_start: 0.8046 (m) cc_final: 0.7831 (p) REVERT: B 562 MET cc_start: 0.8988 (mmp) cc_final: 0.8675 (mmt) REVERT: B 702 MET cc_start: 0.8123 (ptp) cc_final: 0.7865 (ptp) REVERT: B 829 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7318 (tmm) REVERT: C 130 ASP cc_start: 0.7303 (t0) cc_final: 0.6524 (p0) REVERT: C 155 MET cc_start: 0.8165 (ptm) cc_final: 0.7842 (mmp) REVERT: C 237 MET cc_start: 0.7288 (ppp) cc_final: 0.5363 (ttm) REVERT: C 240 MET cc_start: 0.7300 (mmm) cc_final: 0.6977 (mmm) REVERT: C 436 CYS cc_start: 0.6938 (m) cc_final: 0.6722 (m) REVERT: C 463 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8755 (pp) REVERT: C 572 VAL cc_start: 0.9332 (t) cc_final: 0.9068 (p) REVERT: C 575 VAL cc_start: 0.9526 (t) cc_final: 0.9315 (p) REVERT: C 674 ASN cc_start: 0.8622 (t0) cc_final: 0.8275 (t0) REVERT: C 762 MET cc_start: 0.8598 (ptp) cc_final: 0.7863 (ptm) REVERT: D 542 ASN cc_start: 0.5200 (OUTLIER) cc_final: 0.4755 (m-40) REVERT: D 559 TRP cc_start: 0.8056 (m100) cc_final: 0.7678 (m-10) REVERT: D 562 MET cc_start: 0.9061 (ppp) cc_final: 0.8812 (ppp) REVERT: D 742 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7601 (mmm-85) outliers start: 58 outliers final: 43 residues processed: 380 average time/residue: 0.2706 time to fit residues: 174.5888 Evaluate side-chains 377 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 331 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 737 GLU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 814 ASP Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 143 PHE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 542 ASN Chi-restraints excluded: chain D residue 563 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 187 optimal weight: 0.4980 chunk 120 optimal weight: 0.0970 chunk 180 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 192 optimal weight: 0.0980 chunk 206 optimal weight: 0.0050 chunk 149 optimal weight: 7.9990 chunk 28 optimal weight: 0.2980 chunk 237 optimal weight: 0.0170 overall best weight: 0.1030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23571 Z= 0.148 Angle : 0.586 11.623 32247 Z= 0.291 Chirality : 0.042 0.317 3924 Planarity : 0.004 0.059 4065 Dihedral : 4.732 54.512 3665 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.90 % Favored : 93.97 % Rotamer: Outliers : 2.18 % Allowed : 20.33 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.57 (0.15), residues: 3136 helix: 1.05 (0.15), residues: 1214 sheet: -0.07 (0.28), residues: 384 loop : -1.71 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 635 HIS 0.002 0.000 HIS C 67 PHE 0.022 0.001 PHE B 637 TYR 0.029 0.001 TYR B 479 ARG 0.002 0.000 ARG A 763 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 361 time to evaluate : 2.795 Fit side-chains revert: symmetry clash REVERT: A 209 MET cc_start: 0.8348 (tpp) cc_final: 0.7314 (mmt) REVERT: A 506 LEU cc_start: 0.8669 (mt) cc_final: 0.8402 (tt) REVERT: A 642 ILE cc_start: 0.9419 (mm) cc_final: 0.9149 (mm) REVERT: B 101 ASP cc_start: 0.7479 (m-30) cc_final: 0.6992 (m-30) REVERT: B 562 MET cc_start: 0.8936 (mmp) cc_final: 0.8714 (mmt) REVERT: B 702 MET cc_start: 0.8086 (ptp) cc_final: 0.7794 (ptp) REVERT: B 829 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7367 (tmm) REVERT: C 130 ASP cc_start: 0.7280 (t0) cc_final: 0.6503 (p0) REVERT: C 155 MET cc_start: 0.8198 (ptm) cc_final: 0.7833 (mmp) REVERT: C 237 MET cc_start: 0.7422 (ppp) cc_final: 0.5483 (ttm) REVERT: C 240 MET cc_start: 0.7352 (mmm) cc_final: 0.6986 (mmm) REVERT: C 436 CYS cc_start: 0.7091 (m) cc_final: 0.6846 (m) REVERT: C 463 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8725 (pp) REVERT: C 674 ASN cc_start: 0.8538 (t0) cc_final: 0.8208 (t0) REVERT: C 762 MET cc_start: 0.8607 (ptp) cc_final: 0.8295 (ptp) REVERT: D 162 GLU cc_start: 0.8733 (tp30) cc_final: 0.8416 (tm-30) REVERT: D 559 TRP cc_start: 0.8061 (m100) cc_final: 0.7646 (m-10) REVERT: D 562 MET cc_start: 0.9110 (ppp) cc_final: 0.8865 (ppp) REVERT: D 742 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7481 (mmm-85) REVERT: D 793 GLU cc_start: 0.8630 (pp20) cc_final: 0.8409 (pp20) outliers start: 49 outliers final: 37 residues processed: 386 average time/residue: 0.2647 time to fit residues: 173.4302 Evaluate side-chains 370 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 331 time to evaluate : 2.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 275 optimal weight: 0.0570 chunk 289 optimal weight: 8.9990 chunk 264 optimal weight: 0.6980 chunk 282 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 254 optimal weight: 5.9990 chunk 266 optimal weight: 20.0000 chunk 281 optimal weight: 3.9990 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23571 Z= 0.178 Angle : 0.591 10.123 32247 Z= 0.297 Chirality : 0.042 0.281 3924 Planarity : 0.004 0.060 4065 Dihedral : 4.797 53.994 3665 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.60 % Favored : 93.27 % Rotamer: Outliers : 2.27 % Allowed : 21.00 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.51 (0.15), residues: 3136 helix: 1.11 (0.15), residues: 1213 sheet: -0.12 (0.27), residues: 398 loop : -1.65 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 635 HIS 0.003 0.001 HIS A 404 PHE 0.021 0.001 PHE B 637 TYR 0.030 0.001 TYR B 479 ARG 0.002 0.000 ARG A 663 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 338 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8369 (tpp) cc_final: 0.7254 (tpp) REVERT: A 506 LEU cc_start: 0.8759 (mt) cc_final: 0.8494 (tt) REVERT: A 642 ILE cc_start: 0.9475 (mm) cc_final: 0.9217 (mm) REVERT: B 101 ASP cc_start: 0.7407 (m-30) cc_final: 0.6908 (m-30) REVERT: B 702 MET cc_start: 0.8140 (ptp) cc_final: 0.7883 (ptp) REVERT: B 829 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7318 (tmm) REVERT: C 130 ASP cc_start: 0.7313 (t0) cc_final: 0.6472 (p0) REVERT: C 155 MET cc_start: 0.8207 (ptm) cc_final: 0.7841 (mmp) REVERT: C 237 MET cc_start: 0.7477 (ppp) cc_final: 0.5514 (ttm) REVERT: C 240 MET cc_start: 0.7393 (mmm) cc_final: 0.7016 (mmm) REVERT: C 436 CYS cc_start: 0.6997 (m) cc_final: 0.6780 (m) REVERT: C 674 ASN cc_start: 0.8561 (t0) cc_final: 0.8226 (t0) REVERT: C 762 MET cc_start: 0.8619 (ptp) cc_final: 0.8301 (ptp) REVERT: D 162 GLU cc_start: 0.8738 (tp30) cc_final: 0.8459 (tm-30) REVERT: D 542 ASN cc_start: 0.5177 (OUTLIER) cc_final: 0.4729 (m-40) REVERT: D 559 TRP cc_start: 0.8108 (m100) cc_final: 0.7768 (m-10) REVERT: D 702 MET cc_start: 0.7506 (mmm) cc_final: 0.7186 (mpp) REVERT: D 742 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7653 (mmm-85) outliers start: 51 outliers final: 41 residues processed: 368 average time/residue: 0.2719 time to fit residues: 169.5096 Evaluate side-chains 379 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 336 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 436 CYS Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 542 ASN Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 185 optimal weight: 30.0000 chunk 298 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 312 optimal weight: 5.9990 chunk 287 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23571 Z= 0.170 Angle : 0.605 14.369 32247 Z= 0.299 Chirality : 0.042 0.380 3924 Planarity : 0.004 0.060 4065 Dihedral : 4.778 54.096 3665 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.22 % Favored : 93.65 % Rotamer: Outliers : 1.92 % Allowed : 21.49 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.50 (0.15), residues: 3136 helix: 1.13 (0.15), residues: 1211 sheet: -0.10 (0.27), residues: 397 loop : -1.65 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 635 HIS 0.004 0.001 HIS A 404 PHE 0.020 0.001 PHE B 637 TYR 0.030 0.001 TYR B 479 ARG 0.001 0.000 ARG A 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 342 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 MET cc_start: 0.8372 (tpp) cc_final: 0.7296 (mmt) REVERT: A 506 LEU cc_start: 0.8735 (mt) cc_final: 0.8466 (tt) REVERT: A 642 ILE cc_start: 0.9479 (mm) cc_final: 0.9226 (mm) REVERT: B 101 ASP cc_start: 0.7385 (m-30) cc_final: 0.6906 (m-30) REVERT: B 386 MET cc_start: 0.8719 (mmm) cc_final: 0.8416 (mmm) REVERT: B 702 MET cc_start: 0.8153 (ptp) cc_final: 0.7861 (ptp) REVERT: B 829 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7334 (tmm) REVERT: C 130 ASP cc_start: 0.7234 (t0) cc_final: 0.6373 (p0) REVERT: C 155 MET cc_start: 0.8209 (ptm) cc_final: 0.7827 (mmp) REVERT: C 237 MET cc_start: 0.7491 (ppp) cc_final: 0.5584 (ttm) REVERT: C 240 MET cc_start: 0.7322 (mmm) cc_final: 0.6943 (mmm) REVERT: C 350 GLN cc_start: 0.6612 (mm110) cc_final: 0.6358 (mm110) REVERT: C 436 CYS cc_start: 0.6927 (m) cc_final: 0.6694 (m) REVERT: C 674 ASN cc_start: 0.8585 (t0) cc_final: 0.8239 (t0) REVERT: C 762 MET cc_start: 0.8620 (ptp) cc_final: 0.8294 (ptp) REVERT: D 162 GLU cc_start: 0.8684 (tp30) cc_final: 0.8423 (tm-30) REVERT: D 542 ASN cc_start: 0.5208 (OUTLIER) cc_final: 0.4767 (m-40) REVERT: D 559 TRP cc_start: 0.8074 (m100) cc_final: 0.7698 (m-10) REVERT: D 562 MET cc_start: 0.9019 (ppp) cc_final: 0.8812 (ppp) REVERT: D 702 MET cc_start: 0.7471 (mmm) cc_final: 0.7154 (mpp) REVERT: D 742 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7680 (mmm-85) REVERT: D 793 GLU cc_start: 0.8637 (pp20) cc_final: 0.8393 (pp20) outliers start: 43 outliers final: 40 residues processed: 368 average time/residue: 0.2699 time to fit residues: 168.4257 Evaluate side-chains 380 residues out of total 2746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 338 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 261 TYR Chi-restraints excluded: chain A residue 264 ASP Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 461 CYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 751 ILE Chi-restraints excluded: chain B residue 829 MET Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 232 CYS Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 356 TYR Chi-restraints excluded: chain D residue 405 HIS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 542 ASN Chi-restraints excluded: chain D residue 550 PHE Chi-restraints excluded: chain D residue 575 PHE Chi-restraints excluded: chain D residue 608 LEU Chi-restraints excluded: chain D residue 622 ASN Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 735 VAL Chi-restraints excluded: chain D residue 825 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 8.9990 chunk 265 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 249 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 256 optimal weight: 5.9990 chunk 31 optimal weight: 0.2980 chunk 45 optimal weight: 8.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.124106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.098038 restraints weight = 68494.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101214 restraints weight = 43241.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102100 restraints weight = 28853.222| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23571 Z= 0.231 Angle : 0.626 14.274 32247 Z= 0.316 Chirality : 0.044 0.407 3924 Planarity : 0.004 0.061 4065 Dihedral : 5.088 56.225 3665 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.46 % Favored : 92.41 % Rotamer: Outliers : 2.36 % Allowed : 21.44 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.82 % 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: -0.58 (0.15), residues: 3136 helix: 1.06 (0.15), residues: 1193 sheet: -0.21 (0.27), residues: 395 loop : -1.64 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 635 HIS 0.006 0.001 HIS A 404 PHE 0.021 0.002 PHE D 143 TYR 0.031 0.001 TYR B 479 ARG 0.003 0.000 ARG A 663 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4690.78 seconds wall clock time: 85 minutes 31.35 seconds (5131.35 seconds total)