Starting phenix.real_space_refine on Sun Nov 19 18:56:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/11_2023/6lvd_0990.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/11_2023/6lvd_0990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/11_2023/6lvd_0990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/11_2023/6lvd_0990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/11_2023/6lvd_0990.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lvd_0990/11_2023/6lvd_0990.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 17444 2.51 5 N 4836 2.21 5 O 5252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 108": "NH1" <-> "NH2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "E PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 299": "NH1" <-> "NH2" Residue "E PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 120": "NH1" <-> "NH2" Residue "G PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 299": "NH1" <-> "NH2" Residue "G PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 108": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 27628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "B" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "D" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 5877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 5877 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 39, 'TRANS': 707} Chain breaks: 2 Chain: "H" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1030 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 13.89, per 1000 atoms: 0.50 Number of scatterers: 27628 At special positions: 0 Unit cell: (120.91, 155.15, 104.86, 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 96 16.00 O 5252 8.00 N 4836 7.00 C 17444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.16 Conformation dependent library (CDL) restraints added in 5.0 seconds 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6288 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 42 sheets defined 21.2% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 Creating SS restraints... Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 264 through 266 No H-bonds generated for 'chain 'A' and resid 264 through 266' Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.675A pdb=" N GLN A 326 " --> pdb=" O CYS A 323 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 327 " --> pdb=" O PRO A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 327' Processing helix chain 'A' and resid 392 through 399 removed outlier: 3.656A pdb=" N TYR A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 432 through 435 Processing helix chain 'A' and resid 458 through 462 removed outlier: 3.652A pdb=" N LEU A 461 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 462 " --> pdb=" O MET A 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 458 through 462' Processing helix chain 'A' and resid 473 through 488 removed outlier: 4.356A pdb=" N LEU A 481 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 504 through 509 removed outlier: 3.883A pdb=" N LEU A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 536 Processing helix chain 'A' and resid 593 through 597 removed outlier: 3.633A pdb=" N ALA A 597 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 4.012A pdb=" N ILE A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 691 removed outlier: 3.831A pdb=" N LYS A 691 " --> pdb=" O PRO A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 691' Processing helix chain 'A' and resid 726 through 733 removed outlier: 3.645A pdb=" N TRP A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 730 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 731 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 733 " --> pdb=" O LEU A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 754 removed outlier: 3.517A pdb=" N ILE A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 15 Processing helix chain 'B' and resid 19 through 41 Processing helix chain 'B' and resid 42 through 51 removed outlier: 4.277A pdb=" N GLU B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 71 Processing helix chain 'B' and resid 72 through 78 removed outlier: 6.264A pdb=" N THR B 75 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.770A pdb=" N ALA B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 258 Processing helix chain 'C' and resid 323 through 327 removed outlier: 3.698A pdb=" N TYR C 327 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 422 through 431 removed outlier: 3.886A pdb=" N VAL C 426 " --> pdb=" O ASN C 422 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 428 " --> pdb=" O ASN C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 488 removed outlier: 4.376A pdb=" N LEU C 481 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 504 through 509 removed outlier: 4.127A pdb=" N LEU C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 537 removed outlier: 3.773A pdb=" N ASP C 537 " --> pdb=" O ASP C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 597 Processing helix chain 'C' and resid 599 through 605 removed outlier: 3.975A pdb=" N ILE C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 732 removed outlier: 4.341A pdb=" N GLY C 731 " --> pdb=" O ILE C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 754 Processing helix chain 'D' and resid 19 through 41 Processing helix chain 'D' and resid 43 through 51 Processing helix chain 'D' and resid 60 through 71 Processing helix chain 'D' and resid 111 through 130 removed outlier: 3.508A pdb=" N ALA D 115 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 258 Processing helix chain 'E' and resid 323 through 327 removed outlier: 3.705A pdb=" N TYR E 327 " --> pdb=" O PRO E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 399 Processing helix chain 'E' and resid 422 through 431 removed outlier: 3.920A pdb=" N VAL E 426 " --> pdb=" O ASN E 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU E 428 " --> pdb=" O ASN E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 488 removed outlier: 3.518A pdb=" N ASP E 478 " --> pdb=" O GLU E 474 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU E 481 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 504 Processing helix chain 'E' and resid 504 through 509 removed outlier: 4.127A pdb=" N LEU E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 524 through 537 removed outlier: 3.769A pdb=" N ASP E 537 " --> pdb=" O ASP E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 593 through 597 Processing helix chain 'E' and resid 599 through 605 removed outlier: 3.971A pdb=" N ILE E 603 " --> pdb=" O ALA E 599 " (cutoff:3.500A) Processing helix chain 'E' and resid 740 through 754 Processing helix chain 'F' and resid 19 through 41 Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 60 through 71 Processing helix chain 'F' and resid 111 through 130 removed outlier: 3.597A pdb=" N ALA F 115 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU F 130 " --> pdb=" O ASP F 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 258 Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'G' and resid 323 through 327 removed outlier: 3.677A pdb=" N GLN G 326 " --> pdb=" O CYS G 323 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR G 327 " --> pdb=" O PRO G 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 323 through 327' Processing helix chain 'G' and resid 392 through 399 removed outlier: 3.672A pdb=" N TYR G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 431 Processing helix chain 'G' and resid 432 through 435 Processing helix chain 'G' and resid 458 through 462 removed outlier: 3.566A pdb=" N LEU G 461 " --> pdb=" O ILE G 458 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG G 462 " --> pdb=" O MET G 459 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 458 through 462' Processing helix chain 'G' and resid 473 through 488 removed outlier: 3.676A pdb=" N ALA G 477 " --> pdb=" O TRP G 473 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU G 481 " --> pdb=" O ALA G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 504 Processing helix chain 'G' and resid 504 through 509 removed outlier: 3.881A pdb=" N LEU G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 536 Processing helix chain 'G' and resid 593 through 597 removed outlier: 3.638A pdb=" N ALA G 597 " --> pdb=" O ARG G 594 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 604 removed outlier: 3.999A pdb=" N ILE G 603 " --> pdb=" O ALA G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 688 through 691 removed outlier: 3.800A pdb=" N LYS G 691 " --> pdb=" O PRO G 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 688 through 691' Processing helix chain 'G' and resid 726 through 730 removed outlier: 3.807A pdb=" N TRP G 729 " --> pdb=" O SER G 726 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU G 730 " --> pdb=" O ILE G 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 726 through 730' Processing helix chain 'G' and resid 740 through 754 removed outlier: 3.520A pdb=" N ILE G 754 " --> pdb=" O LEU G 750 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 15 Processing helix chain 'H' and resid 19 through 41 Processing helix chain 'H' and resid 42 through 51 removed outlier: 4.284A pdb=" N GLU H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 71 Processing helix chain 'H' and resid 72 through 78 removed outlier: 6.258A pdb=" N THR H 75 " --> pdb=" O MET H 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY H 77 " --> pdb=" O PRO H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.776A pdb=" N ALA H 115 " --> pdb=" O THR H 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 10 removed outlier: 3.679A pdb=" N PHE A 346 " --> pdb=" O PHE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 15 removed outlier: 5.015A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 360 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 36 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 64 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.345A pdb=" N LYS A 54 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 360 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE A 358 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 148 removed outlier: 3.515A pdb=" N GLY A 123 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL A 239 " --> pdb=" O TRP A 101 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N TRP A 101 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA A 241 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N PHE A 99 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 145 through 148 removed outlier: 3.515A pdb=" N GLY A 123 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N SER A 122 " --> pdb=" O TRP A 116 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP A 116 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TRP A 124 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 114 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 126 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 288 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL A 289 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE A 244 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N HIS A 271 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ASP A 273 " --> pdb=" O ASP A 240 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ASP A 240 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 330 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.528A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 658 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE A 611 " --> pdb=" O TYR A 656 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR A 656 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N PHE A 613 " --> pdb=" O GLY A 654 " (cutoff:3.500A) removed outlier: 13.620A pdb=" N GLY A 654 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.528A pdb=" N ILE A 387 " --> pdb=" O ASP A 493 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA A 495 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N VAL A 389 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 388 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 514 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 719 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 710 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 618 " --> pdb=" O VAL A 678 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA9, first strand: chain 'A' and resid 451 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.579A pdb=" N PHE C 346 " --> pdb=" O PHE C 23 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.990A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LYS C 54 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 14 through 15 removed outlier: 4.990A pdb=" N PHE C 358 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 64 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.989A pdb=" N SER C 122 " --> pdb=" O TRP C 116 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TRP C 116 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N TRP C 124 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N SER C 114 " --> pdb=" O TRP C 124 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 126 " --> pdb=" O ILE C 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 197 through 202 removed outlier: 4.759A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ASP C 240 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ASP C 273 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS C 271 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE C 244 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL C 289 " --> pdb=" O ASP C 273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 197 through 202 removed outlier: 4.759A pdb=" N PHE C 99 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA C 241 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.290A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 12.441A pdb=" N PHE C 611 " --> pdb=" O ARG C 660 " (cutoff:3.500A) removed outlier: 12.381A pdb=" N ARG C 660 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 11.796A pdb=" N PHE C 613 " --> pdb=" O LEU C 658 " (cutoff:3.500A) removed outlier: 12.400A pdb=" N LEU C 658 " --> pdb=" O PHE C 613 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N HIS C 615 " --> pdb=" O TYR C 656 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR C 656 " --> pdb=" O HIS C 615 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.290A pdb=" N LEU C 388 " --> pdb=" O LEU C 515 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL C 514 " --> pdb=" O MET C 542 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE C 710 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR C 618 " --> pdb=" O VAL C 678 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE C 611 " --> pdb=" O THR C 685 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AC2, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 522 through 523 Processing sheet with id=AC4, first strand: chain 'E' and resid 9 through 10 removed outlier: 3.581A pdb=" N PHE E 346 " --> pdb=" O PHE E 23 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.993A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU E 38 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS E 54 " --> pdb=" O ILE E 42 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 14 through 15 removed outlier: 4.993A pdb=" N PHE E 358 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY E 64 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 144 through 148 removed outlier: 6.985A pdb=" N SER E 122 " --> pdb=" O TRP E 116 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP E 116 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TRP E 124 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER E 114 " --> pdb=" O TRP E 124 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU E 126 " --> pdb=" O ILE E 112 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 197 through 202 removed outlier: 4.765A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N ASP E 240 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ASP E 273 " --> pdb=" O ASP E 240 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N HIS E 271 " --> pdb=" O PRO E 242 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 244 " --> pdb=" O LEU E 269 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL E 289 " --> pdb=" O ASP E 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 197 through 202 removed outlier: 4.765A pdb=" N PHE E 99 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ALA E 241 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N TRP E 101 " --> pdb=" O VAL E 239 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL E 239 " --> pdb=" O TRP E 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.262A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL E 514 " --> pdb=" O MET E 542 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 12.471A pdb=" N PHE E 611 " --> pdb=" O ARG E 660 " (cutoff:3.500A) removed outlier: 12.439A pdb=" N ARG E 660 " --> pdb=" O PHE E 611 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N PHE E 613 " --> pdb=" O LEU E 658 " (cutoff:3.500A) removed outlier: 12.494A pdb=" N LEU E 658 " --> pdb=" O PHE E 613 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N HIS E 615 " --> pdb=" O TYR E 656 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR E 656 " --> pdb=" O HIS E 615 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 492 through 496 removed outlier: 6.262A pdb=" N LEU E 388 " --> pdb=" O LEU E 515 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL E 514 " --> pdb=" O MET E 542 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE E 710 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR E 618 " --> pdb=" O VAL E 678 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE E 611 " --> pdb=" O THR E 685 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 420 through 421 Processing sheet with id=AD4, first strand: chain 'E' and resid 451 through 453 Processing sheet with id=AD5, first strand: chain 'E' and resid 522 through 523 Processing sheet with id=AD6, first strand: chain 'G' and resid 9 through 10 removed outlier: 3.676A pdb=" N PHE G 346 " --> pdb=" O PHE G 23 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 14 through 15 removed outlier: 5.067A pdb=" N PHE G 358 " --> pdb=" O LEU G 41 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA G 360 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 33 through 36 removed outlier: 3.568A pdb=" N GLY G 64 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 145 through 148 removed outlier: 3.509A pdb=" N GLY G 123 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL G 239 " --> pdb=" O TRP G 101 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N TRP G 101 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ALA G 241 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N PHE G 99 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 145 through 148 removed outlier: 3.509A pdb=" N GLY G 123 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N SER G 122 " --> pdb=" O TRP G 116 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TRP G 116 " --> pdb=" O SER G 122 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N TRP G 124 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER G 114 " --> pdb=" O TRP G 124 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU G 126 " --> pdb=" O ILE G 112 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL G 288 " --> pdb=" O GLY G 298 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 289 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE G 244 " --> pdb=" O LEU G 269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS G 271 " --> pdb=" O PRO G 242 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ASP G 273 " --> pdb=" O ASP G 240 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N ASP G 240 " --> pdb=" O ASP G 273 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 330 " --> pdb=" O VAL G 239 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 492 through 496 removed outlier: 6.543A pdb=" N ILE G 387 " --> pdb=" O ASP G 493 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA G 495 " --> pdb=" O ILE G 387 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL G 389 " --> pdb=" O ALA G 495 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 388 " --> pdb=" O LEU G 515 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL G 514 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE G 710 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR G 618 " --> pdb=" O VAL G 678 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 420 through 421 removed outlier: 3.515A pdb=" N TYR H 80 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 451 through 453 Processing sheet with id=AE5, first strand: chain 'G' and resid 522 through 523 Processing sheet with id=AE6, first strand: chain 'G' and resid 657 through 660 removed outlier: 6.697A pdb=" N LEU G 658 " --> pdb=" O SER G 609 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2697 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: 12.00 Time building geometry restraints manager: 11.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 8905 1.33 - 1.45: 5400 1.45 - 1.57: 13951 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 28412 Sorted by residual: bond pdb=" CG1 ILE G 161 " pdb=" CD1 ILE G 161 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.60e+00 bond pdb=" CG1 ILE A 161 " pdb=" CD1 ILE A 161 " ideal model delta sigma weight residual 1.513 1.413 0.100 3.90e-02 6.57e+02 6.57e+00 bond pdb=" C LEU C 461 " pdb=" N ARG C 462 " ideal model delta sigma weight residual 1.329 1.295 0.034 1.60e-02 3.91e+03 4.40e+00 bond pdb=" CG LEU C 330 " pdb=" CD1 LEU C 330 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.90e+00 bond pdb=" CG1 ILE G 244 " pdb=" CD1 ILE G 244 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.76e+00 ... (remaining 28407 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.80: 566 104.80 - 112.13: 12977 112.13 - 119.46: 10114 119.46 - 126.79: 14351 126.79 - 134.11: 588 Bond angle restraints: 38596 Sorted by residual: angle pdb=" N GLY C 548 " pdb=" CA GLY C 548 " pdb=" C GLY C 548 " ideal model delta sigma weight residual 112.77 119.46 -6.69 1.28e+00 6.10e-01 2.73e+01 angle pdb=" C GLY A 655 " pdb=" N TYR A 656 " pdb=" CA TYR A 656 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.00e+01 angle pdb=" C GLY E 655 " pdb=" N TYR E 656 " pdb=" CA TYR E 656 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C GLY C 655 " pdb=" N TYR C 656 " pdb=" CA TYR C 656 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" CA TYR C 522 " pdb=" CB TYR C 522 " pdb=" CG TYR C 522 " ideal model delta sigma weight residual 113.90 121.43 -7.53 1.80e+00 3.09e-01 1.75e+01 ... (remaining 38591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 15676 15.40 - 30.81: 735 30.81 - 46.21: 110 46.21 - 61.62: 9 61.62 - 77.02: 6 Dihedral angle restraints: 16536 sinusoidal: 6628 harmonic: 9908 Sorted by residual: dihedral pdb=" CA ASN G 547 " pdb=" C ASN G 547 " pdb=" N GLY G 548 " pdb=" CA GLY G 548 " ideal model delta harmonic sigma weight residual -180.00 -152.86 -27.14 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA ASN E 547 " pdb=" C ASN E 547 " pdb=" N GLY E 548 " pdb=" CA GLY E 548 " ideal model delta harmonic sigma weight residual -180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLY A 579 " pdb=" C GLY A 579 " pdb=" N GLU A 580 " pdb=" CA GLU A 580 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 16533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3441 0.092 - 0.184: 446 0.184 - 0.276: 21 0.276 - 0.368: 4 0.368 - 0.460: 4 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CB ILE G 283 " pdb=" CA ILE G 283 " pdb=" CG1 ILE G 283 " pdb=" CG2 ILE G 283 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CB ILE A 283 " pdb=" CA ILE A 283 " pdb=" CG1 ILE A 283 " pdb=" CG2 ILE A 283 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.22e+00 chirality pdb=" CB ILE C 283 " pdb=" CA ILE C 283 " pdb=" CG1 ILE C 283 " pdb=" CG2 ILE C 283 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.70e+00 ... (remaining 3913 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 331 " -0.021 2.00e-02 2.50e+03 1.99e-02 9.85e+00 pdb=" CG TRP A 331 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 331 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 331 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 331 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 331 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 331 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 331 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 331 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 331 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 331 " -0.019 2.00e-02 2.50e+03 1.87e-02 8.75e+00 pdb=" CG TRP G 331 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP G 331 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP G 331 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 331 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP G 331 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP G 331 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 331 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 331 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 331 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 656 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.32e+00 pdb=" C TYR C 656 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR C 656 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU C 657 " -0.016 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4726 2.76 - 3.29: 23782 3.29 - 3.83: 46353 3.83 - 4.36: 57039 4.36 - 4.90: 99884 Nonbonded interactions: 231784 Sorted by model distance: nonbonded pdb=" O ILE E 552 " pdb=" OH TYR E 583 " model vdw 2.223 2.440 nonbonded pdb=" O ILE C 552 " pdb=" OH TYR C 583 " model vdw 2.227 2.440 nonbonded pdb=" O HIS G 615 " pdb=" OH TYR G 684 " model vdw 2.246 2.440 nonbonded pdb=" O HIS C 615 " pdb=" OH TYR C 684 " model vdw 2.246 2.440 nonbonded pdb=" O HIS A 615 " pdb=" OH TYR A 684 " model vdw 2.248 2.440 ... (remaining 231779 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' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.590 Check model and map are aligned: 0.380 Set scattering table: 0.240 Process input model: 73.050 Find NCS groups from input model: 1.630 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 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 : 0.009 0.100 28412 Z= 0.621 Angle : 0.925 8.837 38596 Z= 0.519 Chirality : 0.061 0.460 3916 Planarity : 0.008 0.061 5116 Dihedral : 9.355 77.019 10248 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.31 % Allowed : 1.29 % Favored : 98.40 % 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: -3.48 (0.11), residues: 3424 helix: -2.37 (0.15), residues: 592 sheet: -1.93 (0.19), residues: 652 loop : -2.52 (0.10), residues: 2180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 476 time to evaluate : 3.071 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 485 average time/residue: 0.4500 time to fit residues: 328.9376 Evaluate side-chains 272 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 270 time to evaluate : 3.213 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2378 time to fit residues: 5.1899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 266 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 198 optimal weight: 0.0770 chunk 308 optimal weight: 0.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 121 GLN B 68 ASN C 121 GLN C 171 GLN C 316 HIS C 403 GLN C 424 ASN C 699 ASN E 171 GLN E 316 HIS E 403 GLN E 424 ASN E 519 HIS E 699 ASN G 89 GLN G 121 GLN G 480 HIS G 486 ASN ** G 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 68 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28412 Z= 0.171 Angle : 0.551 6.431 38596 Z= 0.300 Chirality : 0.044 0.194 3916 Planarity : 0.005 0.044 5116 Dihedral : 5.312 23.349 3856 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.19 % Allowed : 4.67 % Favored : 94.14 % 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: -2.38 (0.12), residues: 3424 helix: -0.47 (0.19), residues: 604 sheet: -1.28 (0.21), residues: 568 loop : -2.09 (0.11), residues: 2252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 319 time to evaluate : 3.290 Fit side-chains outliers start: 34 outliers final: 20 residues processed: 340 average time/residue: 0.4296 time to fit residues: 228.0847 Evaluate side-chains 267 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 247 time to evaluate : 3.079 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2819 time to fit residues: 14.3091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 309 optimal weight: 2.9990 chunk 334 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 chunk 306 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 403 GLN H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 28412 Z= 0.371 Angle : 0.595 6.398 38596 Z= 0.320 Chirality : 0.047 0.203 3916 Planarity : 0.005 0.047 5116 Dihedral : 5.259 21.591 3856 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.12 % Allowed : 6.83 % Favored : 92.05 % 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: -1.89 (0.13), residues: 3424 helix: 0.51 (0.20), residues: 604 sheet: -1.28 (0.20), residues: 608 loop : -1.85 (0.12), residues: 2212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 258 time to evaluate : 2.878 Fit side-chains outliers start: 32 outliers final: 22 residues processed: 274 average time/residue: 0.4289 time to fit residues: 182.5145 Evaluate side-chains 263 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 3.262 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2659 time to fit residues: 15.0869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 28412 Z= 0.234 Angle : 0.524 5.976 38596 Z= 0.282 Chirality : 0.044 0.181 3916 Planarity : 0.004 0.048 5116 Dihedral : 4.929 22.546 3856 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.49 % Allowed : 8.30 % Favored : 91.21 % 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: -1.47 (0.13), residues: 3424 helix: 1.15 (0.21), residues: 604 sheet: -0.88 (0.21), residues: 568 loop : -1.70 (0.12), residues: 2252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 248 time to evaluate : 3.438 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 258 average time/residue: 0.4486 time to fit residues: 180.3612 Evaluate side-chains 244 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 236 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3573 time to fit residues: 9.0386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 4.9990 chunk 186 optimal weight: 0.0050 chunk 4 optimal weight: 10.0000 chunk 244 optimal weight: 0.2980 chunk 135 optimal weight: 1.9990 chunk 280 optimal weight: 0.9980 chunk 227 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 294 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 486 ASN ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28412 Z= 0.222 Angle : 0.509 5.899 38596 Z= 0.272 Chirality : 0.044 0.180 3916 Planarity : 0.004 0.048 5116 Dihedral : 4.753 21.953 3856 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.87 % Allowed : 8.61 % Favored : 90.52 % 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: -1.18 (0.14), residues: 3424 helix: 1.51 (0.21), residues: 608 sheet: -0.66 (0.22), residues: 568 loop : -1.56 (0.12), residues: 2248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 3.092 Fit side-chains outliers start: 25 outliers final: 22 residues processed: 255 average time/residue: 0.4364 time to fit residues: 175.0461 Evaluate side-chains 253 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 231 time to evaluate : 3.365 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2513 time to fit residues: 14.8262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 4.9990 chunk 295 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 192 optimal weight: 0.1980 chunk 81 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 273 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 172 optimal weight: 0.7980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN B 73 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28412 Z= 0.287 Angle : 0.535 5.816 38596 Z= 0.286 Chirality : 0.045 0.183 3916 Planarity : 0.004 0.051 5116 Dihedral : 4.814 21.901 3856 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.63 % Allowed : 9.07 % Favored : 90.31 % 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: -1.10 (0.14), residues: 3424 helix: 1.60 (0.21), residues: 608 sheet: -0.62 (0.22), residues: 568 loop : -1.51 (0.12), residues: 2248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 3.745 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 245 average time/residue: 0.4542 time to fit residues: 175.0284 Evaluate side-chains 243 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 232 time to evaluate : 3.344 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3401 time to fit residues: 10.8517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 276 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 327 optimal weight: 6.9990 chunk 205 optimal weight: 0.6980 chunk 199 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 699 ASN H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28412 Z= 0.288 Angle : 0.534 5.718 38596 Z= 0.285 Chirality : 0.045 0.184 3916 Planarity : 0.004 0.050 5116 Dihedral : 4.797 22.086 3856 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.42 % Allowed : 9.62 % Favored : 89.96 % 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: -1.01 (0.14), residues: 3424 helix: 1.67 (0.21), residues: 608 sheet: -0.54 (0.22), residues: 576 loop : -1.46 (0.12), residues: 2240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 249 time to evaluate : 3.104 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 252 average time/residue: 0.4686 time to fit residues: 183.5752 Evaluate side-chains 243 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 235 time to evaluate : 3.310 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2610 time to fit residues: 8.1888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 223 optimal weight: 0.5980 chunk 162 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN C 486 ASN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28412 Z= 0.203 Angle : 0.504 5.924 38596 Z= 0.269 Chirality : 0.044 0.179 3916 Planarity : 0.004 0.051 5116 Dihedral : 4.638 22.483 3856 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.38 % Allowed : 9.80 % Favored : 89.82 % 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: -0.89 (0.14), residues: 3424 helix: 1.80 (0.21), residues: 608 sheet: -0.46 (0.22), residues: 576 loop : -1.39 (0.12), residues: 2240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 3.495 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 252 average time/residue: 0.4499 time to fit residues: 178.4065 Evaluate side-chains 242 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 3.240 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3815 time to fit residues: 6.1645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 chunk 305 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 5.9990 chunk 93 optimal weight: 0.1980 chunk 275 optimal weight: 10.0000 chunk 288 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 748 ASN B 73 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28412 Z= 0.222 Angle : 0.506 5.860 38596 Z= 0.270 Chirality : 0.044 0.179 3916 Planarity : 0.004 0.047 5116 Dihedral : 4.595 22.005 3856 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.52 % Allowed : 9.76 % Favored : 89.71 % 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: -0.80 (0.14), residues: 3424 helix: 1.81 (0.21), residues: 612 sheet: -0.42 (0.22), residues: 560 loop : -1.31 (0.12), residues: 2252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 243 time to evaluate : 3.303 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 248 average time/residue: 0.4516 time to fit residues: 175.8582 Evaluate side-chains 251 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 239 time to evaluate : 3.428 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2619 time to fit residues: 10.4948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 4.9990 chunk 322 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 224 optimal weight: 0.2980 chunk 338 optimal weight: 10.0000 chunk 311 optimal weight: 4.9990 chunk 269 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 208 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28412 Z= 0.268 Angle : 0.526 6.007 38596 Z= 0.280 Chirality : 0.045 0.180 3916 Planarity : 0.004 0.047 5116 Dihedral : 4.660 21.863 3856 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.21 % Allowed : 10.22 % Favored : 89.57 % 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: -0.84 (0.14), residues: 3424 helix: 1.77 (0.21), residues: 612 sheet: -0.40 (0.22), residues: 528 loop : -1.33 (0.12), residues: 2284 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6848 Ramachandran restraints generated. 3424 Oldfield, 0 Emsley, 3424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 240 time to evaluate : 3.012 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 243 average time/residue: 0.4488 time to fit residues: 170.9245 Evaluate side-chains 241 residues out of total 2872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 235 time to evaluate : 3.159 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2639 time to fit residues: 7.3864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 0.0060 chunk 287 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 270 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 GLN ** D 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.083176 restraints weight = 42061.798| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.84 r_work: 0.2803 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28412 Z= 0.254 Angle : 0.521 6.556 38596 Z= 0.277 Chirality : 0.045 0.181 3916 Planarity : 0.004 0.048 5116 Dihedral : 4.640 22.075 3856 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.14 % Allowed : 10.56 % Favored : 89.30 % 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: -0.80 (0.14), residues: 3424 helix: 1.79 (0.21), residues: 612 sheet: -0.38 (0.23), residues: 528 loop : -1.30 (0.12), residues: 2284 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5379.71 seconds wall clock time: 99 minutes 3.65 seconds (5943.65 seconds total)