Starting phenix.real_space_refine on Mon Dec 11 10:07:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/12_2023/7vz3_32219.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/12_2023/7vz3_32219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/12_2023/7vz3_32219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/12_2023/7vz3_32219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/12_2023/7vz3_32219.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vz3_32219/12_2023/7vz3_32219.pdb" } resolution = 2.46 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= 0.006 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 66 5.16 5 C 10985 2.51 5 N 2950 2.21 5 O 3414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ASP 553": "OD1" <-> "OD2" Residue "A ASP 563": "OD1" <-> "OD2" Residue "A GLU 566": "OE1" <-> "OE2" Residue "A TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 644": "NH1" <-> "NH2" Residue "A ASP 658": "OD1" <-> "OD2" Residue "A ASP 665": "OD1" <-> "OD2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "A PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 869": "OD1" <-> "OD2" Residue "A ASP 884": "OD1" <-> "OD2" Residue "A PHE 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B ASP 332": "OD1" <-> "OD2" Residue "B PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 395": "NH1" <-> "NH2" Residue "B PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 497": "OD1" <-> "OD2" Residue "B TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B ASP 553": "OD1" <-> "OD2" Residue "B TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B ARG 636": "NH1" <-> "NH2" Residue "B ARG 644": "NH1" <-> "NH2" Residue "B PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 673": "OE1" <-> "OE2" Residue "B ASP 705": "OD1" <-> "OD2" Residue "B PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 763": "OD1" <-> "OD2" Residue "B PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 799": "NH1" <-> "NH2" Residue "B ASP 801": "OD1" <-> "OD2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C GLU 423": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 446": "OE1" <-> "OE2" Residue "C TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 493": "OD1" <-> "OD2" Residue "C TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 572": "OD1" <-> "OD2" Residue "C GLU 612": "OE1" <-> "OE2" Residue "C GLU 620": "OE1" <-> "OE2" Residue "C ARG 636": "NH1" <-> "NH2" Residue "C ARG 644": "NH1" <-> "NH2" Residue "C GLU 673": "OE1" <-> "OE2" Residue "C TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 742": "OE1" <-> "OE2" Residue "C PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 799": "NH1" <-> "NH2" Residue "C TYR 819": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 851": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17415 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5798 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 720} Chain: "B" Number of atoms: 5819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 5819 Classifications: {'peptide': 754} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 723} Chain: "C" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5798 Classifications: {'peptide': 751} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 720} Time building chain proxies: 9.20, per 1000 atoms: 0.53 Number of scatterers: 17415 At special positions: 0 Unit cell: (94.569, 93.482, 192.399, 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 66 16.00 O 3414 8.00 N 2950 7.00 C 10985 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: 6.91 Conformation dependent library (CDL) restraints added in 3.4 seconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4116 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 24 sheets defined 20.1% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 155 through 182 removed outlier: 3.559A pdb=" N ALA A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 removed outlier: 4.062A pdb=" N VAL A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 301 through 316 Processing helix chain 'A' and resid 354 through 357 Processing helix chain 'A' and resid 473 through 479 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 643 through 646 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 662 through 665 Processing helix chain 'A' and resid 705 through 709 Processing helix chain 'A' and resid 741 through 746 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 823 through 827 Processing helix chain 'A' and resid 828 through 832 Processing helix chain 'A' and resid 862 through 867 Processing helix chain 'A' and resid 886 through 902 Processing helix chain 'B' and resid 153 through 183 removed outlier: 4.118A pdb=" N ASN B 159 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 195 through 200 Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 354 through 357 Processing helix chain 'B' and resid 473 through 479 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 643 through 646 Processing helix chain 'B' and resid 653 through 660 Processing helix chain 'B' and resid 662 through 665 Processing helix chain 'B' and resid 705 through 709 Processing helix chain 'B' and resid 741 through 746 Processing helix chain 'B' and resid 784 through 788 Processing helix chain 'B' and resid 823 through 827 Processing helix chain 'B' and resid 862 through 867 Processing helix chain 'B' and resid 886 through 902 Processing helix chain 'C' and resid 156 through 181 removed outlier: 3.701A pdb=" N ALA C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 192 Processing helix chain 'C' and resid 195 through 200 Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 277 through 280 Processing helix chain 'C' and resid 301 through 316 Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 643 through 646 Processing helix chain 'C' and resid 653 through 659 Processing helix chain 'C' and resid 662 through 665 Processing helix chain 'C' and resid 705 through 709 Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 784 through 788 removed outlier: 3.612A pdb=" N PHE C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 827 Processing helix chain 'C' and resid 828 through 832 Processing helix chain 'C' and resid 862 through 867 Processing helix chain 'C' and resid 885 through 902 removed outlier: 4.013A pdb=" N ASN C 889 " --> pdb=" O VAL C 885 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 275 removed outlier: 6.482A pdb=" N PHE A 274 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A 319 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS A 467 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE A 596 " --> pdb=" O ASP A 546 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN A 548 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.235A pdb=" N GLY A 324 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N TYR A 351 " --> pdb=" O GLY A 324 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR A 326 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR A 348 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU A 405 " --> pdb=" O ARG A 375 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N SER A 377 " --> pdb=" O LEU A 405 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N HIS A 407 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A 405 " --> pdb=" O HIS A 431 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE A 428 " --> pdb=" O HIS A 461 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE A 463 " --> pdb=" O ILE A 428 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N PHE A 430 " --> pdb=" O PHE A 463 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE A 537 " --> pdb=" O ASN A 509 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLN A 511 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE A 539 " --> pdb=" O GLN A 511 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 513 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 6.383A pdb=" N LEU A 334 " --> pdb=" O ASN A 367 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA A 364 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASN A 392 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET A 366 " --> pdb=" O ASN A 392 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS A 389 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N TYR A 418 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE A 391 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP A 415 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE A 444 " --> pdb=" O TRP A 415 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE A 417 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N GLU A 446 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 419 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLN A 441 " --> pdb=" O GLY A 499 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN A 501 " --> pdb=" O GLN A 441 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N CYS A 500 " --> pdb=" O THR A 526 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU A 528 " --> pdb=" O CYS A 500 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA A 577 " --> pdb=" O ASN A 525 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER A 527 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL A 579 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA A 529 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N SER A 581 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 531 " --> pdb=" O SER A 581 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA A 576 " --> pdb=" O THR A 601 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS A 603 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 578 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N MET A 605 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 580 " --> pdb=" O MET A 605 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TRP A 627 " --> pdb=" O SER A 600 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 602 " --> pdb=" O TRP A 627 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 480 through 482 Processing sheet with id=AA6, first strand: chain 'A' and resid 795 through 801 removed outlier: 3.507A pdb=" N TYR A 751 " --> pdb=" O VAL A 844 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR A 757 " --> pdb=" O PHE A 838 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N PHE A 838 " --> pdb=" O THR A 757 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU A 839 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN A 672 " --> pdb=" O LEU A 839 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 841 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AA8, first strand: chain 'A' and resid 727 through 732 removed outlier: 3.943A pdb=" N LEU A 727 " --> pdb=" O PHE A 813 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 858 through 859 removed outlier: 6.887A pdb=" N SER B 667 " --> pdb=" O TYR B 845 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR B 845 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LEU B 669 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 843 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 671 " --> pdb=" O ILE B 841 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE B 838 " --> pdb=" O THR B 757 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR B 757 " --> pdb=" O PHE B 838 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 751 " --> pdb=" O VAL B 844 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 220 through 225 removed outlier: 5.615A pdb=" N SER B 225 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY B 239 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 263 " --> pdb=" O GLY B 260 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 275 removed outlier: 6.547A pdb=" N PHE B 274 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 405 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS B 407 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ARG B 434 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 408 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLN B 436 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL B 410 " --> pdb=" O GLN B 436 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA B 435 " --> pdb=" O ASN B 468 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS B 467 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 9.746A pdb=" N ASP B 543 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N LYS B 595 " --> pdb=" O ASP B 543 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLU B 545 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N LYS B 597 " --> pdb=" O GLU B 545 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE B 547 " --> pdb=" O LYS B 597 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.069A pdb=" N THR B 348 " --> pdb=" O SER B 378 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 405 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER B 377 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS B 407 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 405 " --> pdb=" O HIS B 431 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 428 " --> pdb=" O HIS B 461 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE B 463 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE B 430 " --> pdb=" O PHE B 463 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 460 " --> pdb=" O GLN B 511 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B 513 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE B 462 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N PHE B 537 " --> pdb=" O ASN B 509 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLN B 511 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE B 539 " --> pdb=" O GLN B 511 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 513 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 334 through 336 removed outlier: 6.342A pdb=" N LEU B 334 " --> pdb=" O ASN B 367 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA B 364 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASN B 392 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N MET B 366 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N PHE B 417 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASN B 392 " --> pdb=" O PHE B 417 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL B 419 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY B 442 " --> pdb=" O TRP B 415 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLN B 441 " --> pdb=" O GLY B 499 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLN B 501 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N CYS B 500 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N LEU B 528 " --> pdb=" O CYS B 500 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA B 577 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR B 601 " --> pdb=" O ALA B 576 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 480 through 482 Processing sheet with id=AB6, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 727 through 732 removed outlier: 3.922A pdb=" N LEU B 727 " --> pdb=" O PHE B 813 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 858 through 859 removed outlier: 6.421A pdb=" N ILE C 841 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN C 672 " --> pdb=" O LEU C 839 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU C 839 " --> pdb=" O ASN C 672 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE C 838 " --> pdb=" O THR C 757 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR C 757 " --> pdb=" O PHE C 838 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR C 751 " --> pdb=" O VAL C 844 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 220 through 225 removed outlier: 5.473A pdb=" N SER C 225 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLY C 239 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 273 through 275 removed outlier: 6.576A pdb=" N PHE C 274 " --> pdb=" O ASN C 320 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N CYS C 467 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N ASP C 543 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N LYS C 595 " --> pdb=" O ASP C 543 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU C 545 " --> pdb=" O LYS C 595 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LYS C 597 " --> pdb=" O GLU C 545 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 547 " --> pdb=" O LYS C 597 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 324 through 328 removed outlier: 5.031A pdb=" N THR C 348 " --> pdb=" O SER C 378 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU C 405 " --> pdb=" O ARG C 375 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N SER C 377 " --> pdb=" O LEU C 405 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS C 407 " --> pdb=" O SER C 377 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU C 405 " --> pdb=" O HIS C 431 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 428 " --> pdb=" O HIS C 461 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE C 463 " --> pdb=" O ILE C 428 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 430 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 460 " --> pdb=" O GLN C 511 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE C 513 " --> pdb=" O VAL C 460 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 462 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER C 536 " --> pdb=" O SER C 508 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 334 through 336 removed outlier: 6.402A pdb=" N LEU C 334 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ILE C 391 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN C 367 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE C 393 " --> pdb=" O ASN C 367 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS C 389 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR C 418 " --> pdb=" O LYS C 389 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE C 391 " --> pdb=" O TYR C 418 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TRP C 415 " --> pdb=" O GLY C 442 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N PHE C 444 " --> pdb=" O TRP C 415 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE C 417 " --> pdb=" O PHE C 444 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU C 446 " --> pdb=" O PHE C 417 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL C 419 " --> pdb=" O GLU C 446 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N GLN C 441 " --> pdb=" O GLY C 499 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLN C 501 " --> pdb=" O GLN C 441 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS C 500 " --> pdb=" O LEU C 528 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR C 530 " --> pdb=" O CYS C 500 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA C 502 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR C 532 " --> pdb=" O ALA C 502 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE C 504 " --> pdb=" O THR C 532 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N ALA C 577 " --> pdb=" O ASN C 525 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER C 527 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N VAL C 579 " --> pdb=" O SER C 527 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA C 529 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER C 581 " --> pdb=" O ALA C 529 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE C 531 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA C 576 " --> pdb=" O THR C 601 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS C 603 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 578 " --> pdb=" O LYS C 603 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N MET C 605 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 580 " --> pdb=" O MET C 605 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N TRP C 627 " --> pdb=" O SER C 600 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE C 602 " --> pdb=" O TRP C 627 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 480 through 482 Processing sheet with id=AC5, first strand: chain 'C' and resid 711 through 712 Processing sheet with id=AC6, first strand: chain 'C' and resid 727 through 732 removed outlier: 3.974A pdb=" N LEU C 727 " --> pdb=" O PHE C 813 " (cutoff:3.500A) 526 hydrogen bonds defined for protein. 1425 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: 7.72 Time building geometry restraints manager: 7.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5547 1.34 - 1.47: 4710 1.47 - 1.59: 7464 1.59 - 1.72: 3 1.72 - 1.85: 105 Bond restraints: 17829 Sorted by residual: bond pdb=" CB GLN C 177 " pdb=" CG GLN C 177 " ideal model delta sigma weight residual 1.520 1.612 -0.092 3.00e-02 1.11e+03 9.42e+00 bond pdb=" CB ILE C 466 " pdb=" CG2 ILE C 466 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.28e+00 bond pdb=" CG LEU A 311 " pdb=" CD1 LEU A 311 " ideal model delta sigma weight residual 1.521 1.428 0.093 3.30e-02 9.18e+02 8.03e+00 bond pdb=" CB ARG A 267 " pdb=" CG ARG A 267 " ideal model delta sigma weight residual 1.520 1.436 0.084 3.00e-02 1.11e+03 7.81e+00 bond pdb=" CB THR A 325 " pdb=" CG2 THR A 325 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.35e+00 ... (remaining 17824 not shown) Histogram of bond angle deviations from ideal: 95.54 - 103.25: 153 103.25 - 110.97: 6380 110.97 - 118.69: 7375 118.69 - 126.41: 10094 126.41 - 134.13: 204 Bond angle restraints: 24206 Sorted by residual: angle pdb=" N ASN B 607 " pdb=" CA ASN B 607 " pdb=" C ASN B 607 " ideal model delta sigma weight residual 112.24 118.64 -6.40 1.28e+00 6.10e-01 2.50e+01 angle pdb=" N ASN B 468 " pdb=" CA ASN B 468 " pdb=" C ASN B 468 " ideal model delta sigma weight residual 109.06 116.74 -7.68 1.70e+00 3.46e-01 2.04e+01 angle pdb=" N ASN B 606 " pdb=" CA ASN B 606 " pdb=" C ASN B 606 " ideal model delta sigma weight residual 111.39 117.57 -6.18 1.38e+00 5.25e-01 2.00e+01 angle pdb=" C PHE B 904 " pdb=" N MET B 905 " pdb=" CA MET B 905 " ideal model delta sigma weight residual 121.70 129.22 -7.52 1.80e+00 3.09e-01 1.74e+01 angle pdb=" N ALA A 745 " pdb=" CA ALA A 745 " pdb=" C ALA A 745 " ideal model delta sigma weight residual 111.28 115.77 -4.49 1.09e+00 8.42e-01 1.70e+01 ... (remaining 24201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 9668 17.77 - 35.54: 637 35.54 - 53.30: 87 53.30 - 71.07: 26 71.07 - 88.84: 17 Dihedral angle restraints: 10435 sinusoidal: 3961 harmonic: 6474 Sorted by residual: dihedral pdb=" C VAL B 885 " pdb=" N VAL B 885 " pdb=" CA VAL B 885 " pdb=" CB VAL B 885 " ideal model delta harmonic sigma weight residual -122.00 -134.95 12.95 0 2.50e+00 1.60e-01 2.68e+01 dihedral pdb=" N VAL B 885 " pdb=" C VAL B 885 " pdb=" CA VAL B 885 " pdb=" CB VAL B 885 " ideal model delta harmonic sigma weight residual 123.40 136.08 -12.68 0 2.50e+00 1.60e-01 2.57e+01 dihedral pdb=" CA ASP C 847 " pdb=" C ASP C 847 " pdb=" N LEU C 848 " pdb=" CA LEU C 848 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 10432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2135 0.081 - 0.162: 440 0.162 - 0.243: 47 0.243 - 0.324: 5 0.324 - 0.405: 4 Chirality restraints: 2631 Sorted by residual: chirality pdb=" CA VAL B 885 " pdb=" N VAL B 885 " pdb=" C VAL B 885 " pdb=" CB VAL B 885 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA ASN B 607 " pdb=" N ASN B 607 " pdb=" C ASN B 607 " pdb=" CB ASN B 607 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA LEU C 746 " pdb=" N LEU C 746 " pdb=" C LEU C 746 " pdb=" CB LEU C 746 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 ... (remaining 2628 not shown) Planarity restraints: 3191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 782 " -0.064 2.00e-02 2.50e+03 4.06e-02 4.13e+01 pdb=" CG TRP C 782 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP C 782 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP C 782 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP C 782 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 782 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 782 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 782 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 782 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 782 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 782 " 0.062 2.00e-02 2.50e+03 4.02e-02 4.04e+01 pdb=" CG TRP A 782 " -0.104 2.00e-02 2.50e+03 pdb=" CD1 TRP A 782 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 782 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP A 782 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 782 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 782 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 782 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 782 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 782 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 782 " 0.058 2.00e-02 2.50e+03 3.90e-02 3.81e+01 pdb=" CG TRP B 782 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 TRP B 782 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP B 782 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP B 782 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 782 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 782 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 782 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 782 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 782 " 0.007 2.00e-02 2.50e+03 ... (remaining 3188 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1736 2.74 - 3.28: 16575 3.28 - 3.82: 28578 3.82 - 4.36: 38042 4.36 - 4.90: 64039 Nonbonded interactions: 148970 Sorted by model distance: nonbonded pdb=" O SER B 648 " pdb=" OH TYR B 751 " model vdw 2.203 2.440 nonbonded pdb=" NH1 ARG A 395 " pdb=" O GLU A 423 " model vdw 2.222 2.520 nonbonded pdb=" O ALA A 161 " pdb=" OG SER A 164 " model vdw 2.236 2.440 nonbonded pdb=" NH1 ARG B 395 " pdb=" O GLU B 423 " model vdw 2.239 2.520 nonbonded pdb=" OG SER B 383 " pdb=" OG SER B 385 " model vdw 2.250 2.440 ... (remaining 148965 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 'B' and resid 155 through 905) selection = chain 'C' } 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: 3.990 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: 1.280 Extract box with map and model: 3.570 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 50.200 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.080 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0205 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 0.098 17829 Z= 0.617 Angle : 1.083 10.842 24206 Z= 0.627 Chirality : 0.066 0.405 2631 Planarity : 0.007 0.048 3191 Dihedral : 12.804 88.841 6319 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.49 % Rotamer: Outliers : 0.26 % Allowed : 2.31 % Favored : 97.42 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 10.00 % 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: -1.44 (0.17), residues: 2250 helix: -0.07 (0.27), residues: 374 sheet: -0.52 (0.20), residues: 699 loop : -1.51 (0.16), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.008 TRP C 782 HIS 0.013 0.003 HIS A 671 PHE 0.042 0.005 PHE A 657 TYR 0.037 0.005 TYR C 842 ARG 0.018 0.002 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 120 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 124 average time/residue: 0.9840 time to fit residues: 142.7165 Evaluate side-chains 96 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.7221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 58 optimal weight: 0.0050 chunk 115 optimal weight: 0.0670 chunk 91 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 GLN A 292 ASN A 400 ASN A 427 GLN A 461 HIS A 533 GLN A 826 HIS ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 GLN B 292 ASN B 341 HIS B 380 ASN B 496 ASN B 755 GLN C 211 ASN C 219 GLN C 292 ASN C 400 ASN C 496 ASN C 568 ASN C 672 ASN ** C 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 726 HIS C 755 GLN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0389 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.095 17829 Z= 0.148 Angle : 0.536 10.414 24206 Z= 0.291 Chirality : 0.045 0.173 2631 Planarity : 0.004 0.049 3191 Dihedral : 5.166 24.946 2436 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.96 % Favored : 95.96 % Rotamer: Outliers : 1.00 % Allowed : 5.31 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.91 (0.17), residues: 2250 helix: 0.80 (0.28), residues: 361 sheet: -0.24 (0.20), residues: 676 loop : -1.25 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 782 HIS 0.004 0.001 HIS C 341 PHE 0.014 0.001 PHE C 382 TYR 0.017 0.001 TYR B 256 ARG 0.003 0.000 ARG B 864 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 108 average time/residue: 0.9391 time to fit residues: 120.2784 Evaluate side-chains 99 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 1.728 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.9604 time to fit residues: 6.1146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 204 optimal weight: 6.9990 chunk 221 optimal weight: 0.8980 chunk 182 optimal weight: 5.9990 chunk 202 optimal weight: 0.0070 chunk 69 optimal weight: 5.9990 chunk 164 optimal weight: 0.0970 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 535 ASN ** A 889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 ASN B 193 GLN B 292 ASN B 902 ASN C 219 GLN C 436 GLN C 468 ASN C 687 ASN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0529 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17829 Z= 0.140 Angle : 0.494 8.927 24206 Z= 0.266 Chirality : 0.043 0.163 2631 Planarity : 0.004 0.045 3191 Dihedral : 4.658 25.434 2436 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.82 % Favored : 96.09 % Rotamer: Outliers : 1.21 % Allowed : 6.37 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.74 (0.17), residues: 2250 helix: 0.91 (0.28), residues: 379 sheet: -0.11 (0.20), residues: 694 loop : -1.19 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 695 HIS 0.004 0.001 HIS A 671 PHE 0.024 0.001 PHE C 291 TYR 0.013 0.001 TYR A 439 ARG 0.004 0.000 ARG B 850 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 110 average time/residue: 0.8847 time to fit residues: 116.8156 Evaluate side-chains 111 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 1.738 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 8 residues processed: 8 average time/residue: 0.7442 time to fit residues: 9.6495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 341 HIS ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 431 HIS B 525 ASN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 GLN C 219 GLN C 270 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 697 ASN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1335 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 17829 Z= 0.354 Angle : 0.832 13.621 24206 Z= 0.453 Chirality : 0.054 0.260 2631 Planarity : 0.007 0.088 3191 Dihedral : 6.436 26.478 2436 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.78 % Favored : 94.09 % Rotamer: Outliers : 2.21 % Allowed : 7.68 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.49 (0.17), residues: 2250 helix: 0.56 (0.28), residues: 368 sheet: -0.65 (0.22), residues: 588 loop : -1.66 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 782 HIS 0.015 0.003 HIS B 642 PHE 0.044 0.004 PHE B 430 TYR 0.042 0.003 TYR B 512 ARG 0.011 0.001 ARG A 644 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 99 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 21 residues processed: 127 average time/residue: 1.0293 time to fit residues: 154.0553 Evaluate side-chains 111 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 10 average time/residue: 0.8833 time to fit residues: 13.0697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 111 optimal weight: 4.9990 chunk 195 optimal weight: 2.9990 chunk 54 optimal weight: 0.0270 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN B 441 GLN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1222 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17829 Z= 0.168 Angle : 0.549 8.487 24206 Z= 0.299 Chirality : 0.045 0.180 2631 Planarity : 0.004 0.057 3191 Dihedral : 5.351 22.086 2436 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.07 % Favored : 94.84 % Rotamer: Outliers : 1.95 % Allowed : 8.84 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.37 (0.17), residues: 2250 helix: 0.71 (0.28), residues: 377 sheet: -0.73 (0.21), residues: 617 loop : -1.53 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 782 HIS 0.005 0.001 HIS C 407 PHE 0.020 0.002 PHE B 430 TYR 0.024 0.002 TYR A 540 ARG 0.003 0.001 ARG C 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 99 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 123 average time/residue: 0.8743 time to fit residues: 128.9457 Evaluate side-chains 120 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 17 residues processed: 10 average time/residue: 0.8252 time to fit residues: 12.5023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 53 optimal weight: 0.5980 chunk 217 optimal weight: 0.0470 chunk 180 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 114 optimal weight: 2.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN A 320 ASN ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1125 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17829 Z= 0.126 Angle : 0.480 7.725 24206 Z= 0.261 Chirality : 0.043 0.154 2631 Planarity : 0.004 0.055 3191 Dihedral : 4.754 20.575 2436 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.31 % Favored : 95.60 % Rotamer: Outliers : 1.79 % Allowed : 9.26 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.95 (0.17), residues: 2250 helix: 1.09 (0.28), residues: 371 sheet: -0.52 (0.21), residues: 623 loop : -1.23 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 782 HIS 0.007 0.001 HIS B 341 PHE 0.017 0.001 PHE A 382 TYR 0.019 0.001 TYR A 439 ARG 0.007 0.000 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 92 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 29 residues processed: 113 average time/residue: 0.8941 time to fit residues: 122.4442 Evaluate side-chains 118 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 89 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 18 residues processed: 11 average time/residue: 0.7398 time to fit residues: 12.7081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 209 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 183 optimal weight: 30.0000 chunk 121 optimal weight: 0.0870 chunk 216 optimal weight: 20.0000 chunk 135 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN A 431 HIS ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1336 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17829 Z= 0.176 Angle : 0.546 8.363 24206 Z= 0.296 Chirality : 0.045 0.160 2631 Planarity : 0.005 0.062 3191 Dihedral : 4.987 23.321 2436 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 1.79 % Allowed : 9.78 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.12 (0.17), residues: 2250 helix: 1.03 (0.28), residues: 366 sheet: -0.68 (0.21), residues: 627 loop : -1.31 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 782 HIS 0.007 0.001 HIS C 461 PHE 0.030 0.002 PHE B 430 TYR 0.023 0.002 TYR A 439 ARG 0.008 0.001 ARG B 850 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 31 residues processed: 110 average time/residue: 0.9137 time to fit residues: 120.3270 Evaluate side-chains 117 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 86 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 19 residues processed: 12 average time/residue: 0.7989 time to fit residues: 14.0577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 134 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 137 optimal weight: 0.0030 chunk 147 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 170 optimal weight: 0.0040 chunk 197 optimal weight: 0.0970 overall best weight: 1.0202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 671 HIS B 392 ASN ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1349 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17829 Z= 0.165 Angle : 0.516 8.265 24206 Z= 0.281 Chirality : 0.044 0.158 2631 Planarity : 0.004 0.062 3191 Dihedral : 4.901 20.487 2436 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 2.21 % Allowed : 10.21 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.17), residues: 2250 helix: 1.01 (0.28), residues: 373 sheet: -0.80 (0.21), residues: 636 loop : -1.33 (0.17), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 782 HIS 0.011 0.001 HIS A 671 PHE 0.025 0.002 PHE B 430 TYR 0.022 0.001 TYR A 439 ARG 0.006 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 95 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 32 residues processed: 121 average time/residue: 0.9814 time to fit residues: 141.2375 Evaluate side-chains 122 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 90 time to evaluate : 2.398 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 19 residues processed: 13 average time/residue: 0.7292 time to fit residues: 14.1412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 207 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 202 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 158 optimal weight: 0.0570 chunk 62 optimal weight: 6.9990 chunk 182 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1403 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17829 Z= 0.168 Angle : 0.528 7.832 24206 Z= 0.287 Chirality : 0.044 0.159 2631 Planarity : 0.004 0.065 3191 Dihedral : 4.884 19.378 2436 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 1.68 % Allowed : 10.84 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.19 (0.17), residues: 2250 helix: 1.03 (0.28), residues: 372 sheet: -0.84 (0.21), residues: 636 loop : -1.32 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 782 HIS 0.006 0.001 HIS A 642 PHE 0.025 0.002 PHE B 430 TYR 0.022 0.002 TYR C 540 ARG 0.005 0.000 ARG B 850 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 97 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 26 residues processed: 121 average time/residue: 0.9671 time to fit residues: 138.1823 Evaluate side-chains 122 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 1.779 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 20 residues processed: 6 average time/residue: 1.0335 time to fit residues: 9.8282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 213 optimal weight: 3.9990 chunk 130 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN A 561 ASN A 606 ASN A 676 GLN ** A 708 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 893 ASN B 234 ASN ** B 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 HIS B 464 ASN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 HIS ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1813 moved from start: 0.6991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 17829 Z= 0.373 Angle : 0.839 11.329 24206 Z= 0.462 Chirality : 0.054 0.272 2631 Planarity : 0.007 0.104 3191 Dihedral : 6.692 30.337 2436 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.02 % Favored : 90.89 % Rotamer: Outliers : 1.84 % Allowed : 11.15 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.11 (0.17), residues: 2250 helix: 0.15 (0.28), residues: 369 sheet: -1.33 (0.21), residues: 594 loop : -1.96 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP A 695 HIS 0.014 0.002 HIS A 520 PHE 0.068 0.004 PHE B 430 TYR 0.040 0.003 TYR C 540 ARG 0.010 0.001 ARG A 644 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 104 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 27 residues processed: 130 average time/residue: 0.9756 time to fit residues: 149.9953 Evaluate side-chains 120 residues out of total 1901 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 7 average time/residue: 1.3017 time to fit residues: 12.9462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 190 optimal weight: 0.0010 chunk 54 optimal weight: 0.4980 chunk 164 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 178 optimal weight: 0.0770 chunk 74 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 509 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 676 GLN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 GLN ** C 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5479 r_free = 0.5479 target = 0.363419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.5422 r_free = 0.5422 target = 0.354826 restraints weight = 26278.081| |-----------------------------------------------------------------------------| r_work (start): 0.5429 rms_B_bonded: 1.51 r_work: 0.5387 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.5305 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.5305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1601 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17829 Z= 0.158 Angle : 0.564 11.861 24206 Z= 0.304 Chirality : 0.045 0.186 2631 Planarity : 0.004 0.067 3191 Dihedral : 5.245 26.283 2436 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.58 % Favored : 95.33 % Rotamer: Outliers : 1.42 % Allowed : 12.15 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.68 (0.17), residues: 2250 helix: 0.71 (0.27), residues: 377 sheet: -1.19 (0.21), residues: 610 loop : -1.67 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 695 HIS 0.004 0.001 HIS C 671 PHE 0.016 0.002 PHE C 279 TYR 0.037 0.002 TYR C 512 ARG 0.009 0.001 ARG C 711 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4626.65 seconds wall clock time: 85 minutes 10.56 seconds (5110.56 seconds total)