Starting phenix.real_space_refine (version: dev) on Sat Feb 18 08:41:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/02_2023/7y9u_33692_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/02_2023/7y9u_33692.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/02_2023/7y9u_33692_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/02_2023/7y9u_33692_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/02_2023/7y9u_33692_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/02_2023/7y9u_33692.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/02_2023/7y9u_33692.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/02_2023/7y9u_33692_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y9u_33692/02_2023/7y9u_33692_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.116 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 Process input model Symmetric amino acids flipped Residue "A ARG 94": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 101": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B ARG 475": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 7748 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2957 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "C" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "D" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "B" Number of atoms: 2957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2957 Classifications: {'peptide': 379} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain breaks: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'E7O': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.56, per 1000 atoms: 0.59 Number of scatterers: 7748 At special positions: 0 Unit cell: (100.1, 123.2, 96.8, 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 56 16.00 O 1342 8.00 N 1272 7.00 C 5078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.2 seconds 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 12 sheets defined 44.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.817A pdb=" N TYR A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 13 " --> pdb=" O HIS A 9 " (cutoff:3.500A) Proline residue: A 16 - end of helix removed outlier: 4.041A pdb=" N ALA A 20 " --> pdb=" O PRO A 16 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 48 removed outlier: 3.635A pdb=" N PHE A 45 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.874A pdb=" N PHE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 removed outlier: 3.542A pdb=" N ASP A 75 " --> pdb=" O PHE A 71 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A 79 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.681A pdb=" N THR A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 129 through 142 removed outlier: 3.933A pdb=" N VAL A 134 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 139 " --> pdb=" O GLN A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 164 removed outlier: 3.664A pdb=" N LEU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 458 through 473 removed outlier: 3.751A pdb=" N THR A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 483 through 492 removed outlier: 3.563A pdb=" N TRP A 488 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 491 " --> pdb=" O THR A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 511 through 528 removed outlier: 4.625A pdb=" N LEU A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 516 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 517 " --> pdb=" O GLY A 514 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 518 " --> pdb=" O LEU A 515 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET A 519 " --> pdb=" O GLY A 516 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 522 " --> pdb=" O MET A 519 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU A 524 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE A 525 " --> pdb=" O LEU A 522 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 526 " --> pdb=" O GLY A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 541 No H-bonds generated for 'chain 'A' and resid 538 through 541' Processing helix chain 'A' and resid 566 through 577 removed outlier: 3.710A pdb=" N HIS A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 574 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 590 removed outlier: 3.558A pdb=" N ALA A 588 " --> pdb=" O PRO A 584 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 590 " --> pdb=" O VAL A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 607 removed outlier: 3.529A pdb=" N ALA A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 603 " --> pdb=" O SER A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 621 removed outlier: 3.820A pdb=" N LEU A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 618 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 29 removed outlier: 3.817A pdb=" N TYR B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 13 " --> pdb=" O HIS B 9 " (cutoff:3.500A) Proline residue: B 16 - end of helix removed outlier: 4.041A pdb=" N ALA B 20 " --> pdb=" O PRO B 16 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 48 removed outlier: 3.635A pdb=" N PHE B 45 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.874A pdb=" N PHE B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 85 removed outlier: 3.542A pdb=" N ASP B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 76 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 79 " --> pdb=" O ASP B 75 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 90 No H-bonds generated for 'chain 'B' and resid 87 through 90' Processing helix chain 'B' and resid 99 through 109 removed outlier: 3.682A pdb=" N THR B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 125 Processing helix chain 'B' and resid 129 through 142 removed outlier: 3.932A pdb=" N VAL B 134 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 136 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 139 " --> pdb=" O GLN B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 164 removed outlier: 3.663A pdb=" N LEU B 159 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 458 through 473 removed outlier: 3.752A pdb=" N THR B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 466 " --> pdb=" O THR B 462 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 479 No H-bonds generated for 'chain 'B' and resid 477 through 479' Processing helix chain 'B' and resid 483 through 492 removed outlier: 3.563A pdb=" N TRP B 488 " --> pdb=" O PHE B 484 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 507 Processing helix chain 'B' and resid 511 through 528 removed outlier: 4.624A pdb=" N LEU B 515 " --> pdb=" O ASP B 512 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY B 516 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET B 517 " --> pdb=" O GLY B 514 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B 518 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 519 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 522 " --> pdb=" O MET B 519 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 524 " --> pdb=" O SER B 521 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE B 525 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 526 " --> pdb=" O GLY B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 541 No H-bonds generated for 'chain 'B' and resid 538 through 541' Processing helix chain 'B' and resid 566 through 577 removed outlier: 3.710A pdb=" N HIS B 570 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 574 " --> pdb=" O HIS B 570 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 590 removed outlier: 3.558A pdb=" N ALA B 588 " --> pdb=" O PRO B 584 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 590 " --> pdb=" O VAL B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 607 removed outlier: 3.529A pdb=" N ALA B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 603 " --> pdb=" O SER B 599 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 621 removed outlier: 3.820A pdb=" N LEU B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.962A pdb=" N SER A 174 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 7 through 11 removed outlier: 3.630A pdb=" N GLN C 7 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 29 " --> pdb=" O GLN C 7 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 14 through 16 removed outlier: 3.612A pdb=" N THR C 116 " --> pdb=" O GLY C 14 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.916A pdb=" N LEU C 22 " --> pdb=" O MET C 87 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.594A pdb=" N VAL C 97 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR C 99 " --> pdb=" O TYR C 41 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C 41 " --> pdb=" O TYR C 99 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TRP C 40 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 53 " --> pdb=" O TRP C 40 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG C 42 " --> pdb=" O TRP C 51 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TRP C 51 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 101 through 103 Processing sheet with id= G, first strand: chain 'D' and resid 7 through 11 removed outlier: 3.630A pdb=" N GLN D 7 " --> pdb=" O SER D 29 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER D 29 " --> pdb=" O GLN D 7 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 14 through 16 removed outlier: 3.613A pdb=" N THR D 116 " --> pdb=" O GLY D 14 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.915A pdb=" N LEU D 22 " --> pdb=" O MET D 87 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 97 through 100 removed outlier: 3.594A pdb=" N VAL D 97 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR D 99 " --> pdb=" O TYR D 41 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 41 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TRP D 40 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 53 " --> pdb=" O TRP D 40 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG D 42 " --> pdb=" O TRP D 51 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TRP D 51 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 101 through 103 Processing sheet with id= L, first strand: chain 'B' and resid 174 through 177 removed outlier: 3.961A pdb=" N SER B 174 " --> pdb=" O LEU B 202 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 585 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: 2.11 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1184 1.28 - 1.41: 2092 1.41 - 1.54: 4528 1.54 - 1.67: 32 1.67 - 1.80: 100 Bond restraints: 7936 Sorted by residual: bond pdb=" CA ASN A 112 " pdb=" C ASN A 112 " ideal model delta sigma weight residual 1.525 1.374 0.151 1.29e-02 6.01e+03 1.38e+02 bond pdb=" CA ASN B 112 " pdb=" C ASN B 112 " ideal model delta sigma weight residual 1.525 1.374 0.151 1.29e-02 6.01e+03 1.37e+02 bond pdb=" C08 E7O B 701 " pdb=" C09 E7O B 701 " ideal model delta sigma weight residual 1.396 1.541 -0.145 2.00e-02 2.50e+03 5.22e+01 bond pdb=" C08 E7O A 701 " pdb=" C09 E7O A 701 " ideal model delta sigma weight residual 1.396 1.540 -0.144 2.00e-02 2.50e+03 5.19e+01 bond pdb=" C04 E7O B 701 " pdb=" C10 E7O B 701 " ideal model delta sigma weight residual 1.414 1.272 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 7931 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.81: 198 105.81 - 112.88: 4102 112.88 - 119.95: 2998 119.95 - 127.02: 3386 127.02 - 134.09: 106 Bond angle restraints: 10790 Sorted by residual: angle pdb=" C09 E7O B 701 " pdb=" C10 E7O B 701 " pdb=" N11 E7O B 701 " ideal model delta sigma weight residual 81.04 118.31 -37.27 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C04 E7O B 701 " pdb=" C10 E7O B 701 " pdb=" N11 E7O B 701 " ideal model delta sigma weight residual 155.44 118.19 37.25 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C09 E7O A 701 " pdb=" C10 E7O A 701 " pdb=" N11 E7O A 701 " ideal model delta sigma weight residual 81.04 118.28 -37.24 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C04 E7O A 701 " pdb=" C10 E7O A 701 " pdb=" N11 E7O A 701 " ideal model delta sigma weight residual 155.44 118.21 37.23 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C ASN B 112 " pdb=" CA ASN B 112 " pdb=" CB ASN B 112 " ideal model delta sigma weight residual 111.31 100.98 10.33 1.68e+00 3.54e-01 3.78e+01 ... (remaining 10785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 4410 15.31 - 30.61: 192 30.61 - 45.92: 46 45.92 - 61.23: 6 61.23 - 76.54: 2 Dihedral angle restraints: 4656 sinusoidal: 1794 harmonic: 2862 Sorted by residual: dihedral pdb=" C ASN B 112 " pdb=" N ASN B 112 " pdb=" CA ASN B 112 " pdb=" CB ASN B 112 " ideal model delta harmonic sigma weight residual -122.60 -107.69 -14.91 0 2.50e+00 1.60e-01 3.56e+01 dihedral pdb=" C ASN A 112 " pdb=" N ASN A 112 " pdb=" CA ASN A 112 " pdb=" CB ASN A 112 " ideal model delta harmonic sigma weight residual -122.60 -107.70 -14.90 0 2.50e+00 1.60e-01 3.55e+01 dihedral pdb=" CA GLN C 56 " pdb=" C GLN C 56 " pdb=" N SER C 57 " pdb=" CA SER C 57 " ideal model delta harmonic sigma weight residual 180.00 -151.54 -28.46 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 4653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 984 0.069 - 0.137: 239 0.137 - 0.206: 17 0.206 - 0.275: 4 0.275 - 0.343: 2 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CB ILE C 55 " pdb=" CA ILE C 55 " pdb=" CG1 ILE C 55 " pdb=" CG2 ILE C 55 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB ILE D 55 " pdb=" CA ILE D 55 " pdb=" CG1 ILE D 55 " pdb=" CG2 ILE D 55 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB VAL B 554 " pdb=" CA VAL B 554 " pdb=" CG1 VAL B 554 " pdb=" CG2 VAL B 554 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1243 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 551 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO A 552 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 552 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 552 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 551 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO B 552 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 552 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 552 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 15 " -0.041 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO B 16 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 16 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 16 " -0.034 5.00e-02 4.00e+02 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2396 2.83 - 3.35: 6415 3.35 - 3.86: 11798 3.86 - 4.38: 13765 4.38 - 4.90: 23897 Nonbonded interactions: 58271 Sorted by model distance: nonbonded pdb=" OE2 GLU A 193 " pdb=" NE ARG C 109 " model vdw 2.311 2.520 nonbonded pdb=" OE2 GLU A 191 " pdb=" NH2 ARG C 101 " model vdw 2.340 2.520 nonbonded pdb=" NH2 ARG C 71 " pdb=" O SER C 89 " model vdw 2.352 2.520 nonbonded pdb=" NH2 ARG D 71 " pdb=" O SER D 89 " model vdw 2.352 2.520 nonbonded pdb=" O TRP A 89 " pdb=" OG SER A 93 " model vdw 2.369 2.440 ... (remaining 58266 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' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5078 2.51 5 N 1272 2.21 5 O 1342 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.200 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: 0.000 Extract box with map and model: 4.090 Check model and map are aligned: 0.120 Process input model: 22.360 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 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 : 0.011 0.151 7936 Z= 0.672 Angle : 1.270 37.273 10790 Z= 0.608 Chirality : 0.060 0.343 1246 Planarity : 0.009 0.068 1326 Dihedral : 9.983 76.536 2810 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.22 % 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: -6.23 (0.17), residues: 976 helix: -4.89 (0.07), residues: 524 sheet: -2.72 (0.40), residues: 106 loop : -2.86 (0.27), residues: 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.819 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2559 time to fit residues: 57.0883 Evaluate side-chains 118 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.843 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 30.0000 chunk 38 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.0870 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 112 ASN B 43 ASN B 112 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7936 Z= 0.209 Angle : 0.652 16.194 10790 Z= 0.328 Chirality : 0.043 0.152 1246 Planarity : 0.006 0.054 1326 Dihedral : 5.478 31.091 1072 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 2.53 % 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: -4.68 (0.21), residues: 976 helix: -3.70 (0.15), residues: 508 sheet: -2.17 (0.44), residues: 92 loop : -2.12 (0.28), residues: 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.888 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 143 average time/residue: 0.1740 time to fit residues: 34.7539 Evaluate side-chains 121 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 111 time to evaluate : 0.668 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0671 time to fit residues: 2.3238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 24 optimal weight: 0.0370 chunk 87 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 29 optimal weight: 0.0030 chunk 70 optimal weight: 0.8980 overall best weight: 0.5068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7936 Z= 0.153 Angle : 0.564 10.535 10790 Z= 0.285 Chirality : 0.042 0.143 1246 Planarity : 0.005 0.049 1326 Dihedral : 4.838 24.041 1072 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.93 % 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: -3.98 (0.22), residues: 976 helix: -3.03 (0.17), residues: 516 sheet: -1.40 (0.45), residues: 104 loop : -2.06 (0.30), residues: 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 0.816 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 137 average time/residue: 0.1841 time to fit residues: 35.0384 Evaluate side-chains 121 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 0.882 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0717 time to fit residues: 1.9514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 0.0980 chunk 41 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.0570 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 7936 Z= 0.114 Angle : 0.516 8.744 10790 Z= 0.263 Chirality : 0.041 0.156 1246 Planarity : 0.004 0.048 1326 Dihedral : 4.405 22.670 1072 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 1.08 % 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: -3.18 (0.24), residues: 976 helix: -2.39 (0.20), residues: 506 sheet: -0.81 (0.49), residues: 102 loop : -1.78 (0.31), residues: 368 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 0.901 Fit side-chains outliers start: 9 outliers final: 2 residues processed: 134 average time/residue: 0.1878 time to fit residues: 35.0463 Evaluate side-chains 119 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0679 time to fit residues: 1.5044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 31 optimal weight: 0.0030 overall best weight: 0.6770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7936 Z= 0.175 Angle : 0.532 7.419 10790 Z= 0.270 Chirality : 0.043 0.255 1246 Planarity : 0.005 0.048 1326 Dihedral : 4.388 22.306 1072 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 1.08 % 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: -2.94 (0.24), residues: 976 helix: -2.18 (0.20), residues: 512 sheet: -0.57 (0.51), residues: 102 loop : -1.72 (0.31), residues: 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 117 time to evaluate : 0.909 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 122 average time/residue: 0.1758 time to fit residues: 30.6110 Evaluate side-chains 116 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 113 time to evaluate : 0.886 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0709 time to fit residues: 1.6176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 54 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 43 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 7936 Z= 0.151 Angle : 0.505 6.501 10790 Z= 0.256 Chirality : 0.042 0.145 1246 Planarity : 0.005 0.048 1326 Dihedral : 4.279 20.966 1072 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 2.17 % 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: -2.47 (0.25), residues: 976 helix: -1.74 (0.20), residues: 512 sheet: -0.28 (0.53), residues: 102 loop : -1.62 (0.31), residues: 362 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.910 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 123 average time/residue: 0.1714 time to fit residues: 30.4164 Evaluate side-chains 118 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0849 time to fit residues: 2.7388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 42 optimal weight: 9.9990 chunk 36 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 7936 Z= 0.240 Angle : 0.556 6.643 10790 Z= 0.279 Chirality : 0.044 0.160 1246 Planarity : 0.005 0.048 1326 Dihedral : 4.427 19.788 1072 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.45 % 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: -2.52 (0.25), residues: 976 helix: -1.72 (0.20), residues: 528 sheet: -0.22 (0.53), residues: 102 loop : -1.76 (0.31), residues: 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.751 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 133 average time/residue: 0.1757 time to fit residues: 32.9900 Evaluate side-chains 117 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.913 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1142 time to fit residues: 2.6406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7936 Z= 0.242 Angle : 0.546 6.216 10790 Z= 0.274 Chirality : 0.043 0.135 1246 Planarity : 0.005 0.048 1326 Dihedral : 4.453 19.569 1072 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 0.96 % 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: -2.37 (0.25), residues: 976 helix: -1.56 (0.21), residues: 528 sheet: -0.15 (0.53), residues: 102 loop : -1.75 (0.31), residues: 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.769 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 115 average time/residue: 0.1872 time to fit residues: 29.8313 Evaluate side-chains 114 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0755 time to fit residues: 2.1223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 7936 Z= 0.189 Angle : 0.538 12.016 10790 Z= 0.265 Chirality : 0.042 0.143 1246 Planarity : 0.005 0.048 1326 Dihedral : 4.357 18.595 1072 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.72 % 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: -2.33 (0.25), residues: 976 helix: -1.36 (0.21), residues: 528 sheet: -1.02 (0.48), residues: 126 loop : -1.76 (0.32), residues: 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 0.874 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 113 average time/residue: 0.1783 time to fit residues: 28.2077 Evaluate side-chains 110 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 107 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0677 time to fit residues: 1.5123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 7936 Z= 0.221 Angle : 0.545 10.338 10790 Z= 0.271 Chirality : 0.043 0.130 1246 Planarity : 0.005 0.048 1326 Dihedral : 4.393 18.341 1072 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.12 % 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: -2.29 (0.25), residues: 976 helix: -1.32 (0.21), residues: 528 sheet: -1.00 (0.48), residues: 126 loop : -1.75 (0.32), residues: 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1952 Ramachandran restraints generated. 976 Oldfield, 0 Emsley, 976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 0.934 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 115 average time/residue: 0.2097 time to fit residues: 33.2243 Evaluate side-chains 108 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 0.867 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0678 time to fit residues: 1.3439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.169584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.113187 restraints weight = 9061.250| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.17 r_work: 0.2823 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7936 Z= 0.172 Angle : 0.518 9.366 10790 Z= 0.258 Chirality : 0.042 0.134 1246 Planarity : 0.005 0.048 1326 Dihedral : 4.292 18.628 1072 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.24 % 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: -1.82 (0.26), residues: 976 helix: -1.02 (0.22), residues: 522 sheet: -0.06 (0.55), residues: 102 loop : -1.63 (0.31), residues: 352 =============================================================================== Job complete usr+sys time: 1817.95 seconds wall clock time: 33 minutes 49.67 seconds (2029.67 seconds total)