Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 14 20:12:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/08_2023/6k9f_9948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/08_2023/6k9f_9948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/08_2023/6k9f_9948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/08_2023/6k9f_9948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/08_2023/6k9f_9948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/08_2023/6k9f_9948.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8484 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 5244 2.51 5 N 1512 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 464": "NH1" <-> "NH2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A ARG 495": "NH1" <-> "NH2" Residue "A GLU 507": "OE1" <-> "OE2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 492": "OE1" <-> "OE2" Residue "B ARG 495": "NH1" <-> "NH2" Residue "B GLU 507": "OE1" <-> "OE2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "C ARG 495": "NH1" <-> "NH2" Residue "C GLU 507": "OE1" <-> "OE2" Residue "C ARG 519": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D GLU 492": "OE1" <-> "OE2" Residue "D ARG 495": "NH1" <-> "NH2" Residue "D GLU 507": "OE1" <-> "OE2" Residue "D ARG 519": "NH1" <-> "NH2" Residue "E ARG 464": "NH1" <-> "NH2" Residue "E GLU 487": "OE1" <-> "OE2" Residue "E GLU 492": "OE1" <-> "OE2" Residue "E ARG 495": "NH1" <-> "NH2" Residue "E GLU 507": "OE1" <-> "OE2" Residue "E ARG 519": "NH1" <-> "NH2" Residue "F ARG 464": "NH1" <-> "NH2" Residue "F GLU 487": "OE1" <-> "OE2" Residue "F GLU 492": "OE1" <-> "OE2" Residue "F ARG 495": "NH1" <-> "NH2" Residue "F GLU 507": "OE1" <-> "OE2" Residue "F ARG 519": "NH1" <-> "NH2" Residue "G ARG 464": "NH1" <-> "NH2" Residue "G GLU 487": "OE1" <-> "OE2" Residue "G GLU 492": "OE1" <-> "OE2" Residue "G ARG 495": "NH1" <-> "NH2" Residue "G GLU 507": "OE1" <-> "OE2" Residue "G ARG 519": "NH1" <-> "NH2" Residue "H ARG 464": "NH1" <-> "NH2" Residue "H GLU 487": "OE1" <-> "OE2" Residue "H GLU 492": "OE1" <-> "OE2" Residue "H ARG 495": "NH1" <-> "NH2" Residue "H GLU 507": "OE1" <-> "OE2" Residue "H ARG 519": "NH1" <-> "NH2" Residue "I PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 464": "NH1" <-> "NH2" Residue "I GLU 487": "OE1" <-> "OE2" Residue "I GLU 492": "OE1" <-> "OE2" Residue "I ARG 495": "NH1" <-> "NH2" Residue "I GLU 507": "OE1" <-> "OE2" Residue "I ARG 519": "NH1" <-> "NH2" Residue "J ARG 464": "NH1" <-> "NH2" Residue "J GLU 487": "OE1" <-> "OE2" Residue "J GLU 492": "OE1" <-> "OE2" Residue "J ARG 495": "NH1" <-> "NH2" Residue "J GLU 507": "OE1" <-> "OE2" Residue "J ARG 519": "NH1" <-> "NH2" Residue "K ARG 464": "NH1" <-> "NH2" Residue "K GLU 487": "OE1" <-> "OE2" Residue "K GLU 492": "OE1" <-> "OE2" Residue "K ARG 495": "NH1" <-> "NH2" Residue "K GLU 507": "OE1" <-> "OE2" Residue "K ARG 519": "NH1" <-> "NH2" Residue "L ARG 464": "NH1" <-> "NH2" Residue "L GLU 487": "OE1" <-> "OE2" Residue "L GLU 492": "OE1" <-> "OE2" Residue "L ARG 495": "NH1" <-> "NH2" Residue "L GLU 507": "OE1" <-> "OE2" Residue "L ARG 519": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 8484 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "D" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "E" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "F" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "H" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "I" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "J" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "K" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "L" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Time building chain proxies: 4.32, per 1000 atoms: 0.51 Number of scatterers: 8484 At special positions: 0 Unit cell: (97.9, 96.8, 103.4, 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 24 16.00 O 1704 8.00 N 1512 7.00 C 5244 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: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 95.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 451 through 457 Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'A' and resid 482 through 492 removed outlier: 4.165A pdb=" N GLU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 510 removed outlier: 3.687A pdb=" N LYS A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS A 509 " --> pdb=" O MET A 505 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 525 Processing helix chain 'A' and resid 525 through 537 removed outlier: 4.240A pdb=" N VAL A 529 " --> pdb=" O ASP A 525 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER A 530 " --> pdb=" O PRO A 526 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 537 " --> pdb=" O ARG A 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 457 through 465 Processing helix chain 'B' and resid 468 through 478 Processing helix chain 'B' and resid 482 through 492 removed outlier: 4.227A pdb=" N GLU B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.664A pdb=" N LYS B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 509 " --> pdb=" O MET B 505 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 525 Processing helix chain 'B' and resid 525 through 537 removed outlier: 4.235A pdb=" N VAL B 529 " --> pdb=" O ASP B 525 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 530 " --> pdb=" O PRO B 526 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 537 " --> pdb=" O ARG B 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 457 through 465 Processing helix chain 'C' and resid 468 through 478 Processing helix chain 'C' and resid 482 through 492 removed outlier: 4.128A pdb=" N GLU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.681A pdb=" N LYS C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS C 509 " --> pdb=" O MET C 505 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 510 " --> pdb=" O VAL C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 525 Processing helix chain 'C' and resid 525 through 537 removed outlier: 4.223A pdb=" N VAL C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER C 530 " --> pdb=" O PRO C 526 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 537 " --> pdb=" O ARG C 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 457 Processing helix chain 'D' and resid 457 through 465 Processing helix chain 'D' and resid 468 through 478 Processing helix chain 'D' and resid 482 through 492 removed outlier: 4.056A pdb=" N GLU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 510 removed outlier: 3.620A pdb=" N LYS D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS D 509 " --> pdb=" O MET D 505 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 525 Processing helix chain 'D' and resid 525 through 537 removed outlier: 4.252A pdb=" N VAL D 529 " --> pdb=" O ASP D 525 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER D 530 " --> pdb=" O PRO D 526 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 537 " --> pdb=" O ARG D 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 457 Processing helix chain 'E' and resid 457 through 465 Processing helix chain 'E' and resid 468 through 478 Processing helix chain 'E' and resid 482 through 492 removed outlier: 4.168A pdb=" N GLU E 492 " --> pdb=" O LEU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 510 removed outlier: 3.691A pdb=" N LYS E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS E 509 " --> pdb=" O MET E 505 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY E 510 " --> pdb=" O VAL E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 525 Processing helix chain 'E' and resid 525 through 537 removed outlier: 4.258A pdb=" N VAL E 529 " --> pdb=" O ASP E 525 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER E 530 " --> pdb=" O PRO E 526 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 537 " --> pdb=" O ARG E 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 457 Processing helix chain 'F' and resid 457 through 465 Processing helix chain 'F' and resid 468 through 478 Processing helix chain 'F' and resid 482 through 492 removed outlier: 4.077A pdb=" N GLU F 492 " --> pdb=" O LEU F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 510 removed outlier: 3.719A pdb=" N LYS F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS F 509 " --> pdb=" O MET F 505 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY F 510 " --> pdb=" O VAL F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 525 Processing helix chain 'F' and resid 525 through 537 removed outlier: 4.148A pdb=" N VAL F 529 " --> pdb=" O ASP F 525 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER F 530 " --> pdb=" O PRO F 526 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU F 537 " --> pdb=" O ARG F 533 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 457 Processing helix chain 'G' and resid 457 through 465 Processing helix chain 'G' and resid 468 through 478 Processing helix chain 'G' and resid 482 through 492 removed outlier: 4.103A pdb=" N GLU G 492 " --> pdb=" O LEU G 488 " (cutoff:3.500A) Processing helix chain 'G' and resid 494 through 510 removed outlier: 3.752A pdb=" N LYS G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS G 509 " --> pdb=" O MET G 505 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY G 510 " --> pdb=" O VAL G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 525 Processing helix chain 'G' and resid 525 through 536 removed outlier: 4.316A pdb=" N VAL G 529 " --> pdb=" O ASP G 525 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER G 530 " --> pdb=" O PRO G 526 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 457 Processing helix chain 'H' and resid 457 through 465 Processing helix chain 'H' and resid 468 through 478 Processing helix chain 'H' and resid 482 through 492 removed outlier: 4.026A pdb=" N GLU H 492 " --> pdb=" O LEU H 488 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 510 removed outlier: 3.729A pdb=" N LYS H 508 " --> pdb=" O SER H 504 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS H 509 " --> pdb=" O MET H 505 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY H 510 " --> pdb=" O VAL H 506 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 525 Processing helix chain 'H' and resid 525 through 537 removed outlier: 4.228A pdb=" N VAL H 529 " --> pdb=" O ASP H 525 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER H 530 " --> pdb=" O PRO H 526 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 537 " --> pdb=" O ARG H 533 " (cutoff:3.500A) Processing helix chain 'I' and resid 452 through 457 Processing helix chain 'I' and resid 457 through 465 Processing helix chain 'I' and resid 468 through 478 Processing helix chain 'I' and resid 482 through 492 removed outlier: 4.179A pdb=" N GLU I 492 " --> pdb=" O LEU I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 494 through 510 removed outlier: 3.638A pdb=" N LYS I 508 " --> pdb=" O SER I 504 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS I 509 " --> pdb=" O MET I 505 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY I 510 " --> pdb=" O VAL I 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 525 Processing helix chain 'I' and resid 525 through 537 removed outlier: 4.306A pdb=" N VAL I 529 " --> pdb=" O ASP I 525 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER I 530 " --> pdb=" O PRO I 526 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU I 537 " --> pdb=" O ARG I 533 " (cutoff:3.500A) Processing helix chain 'J' and resid 452 through 457 Processing helix chain 'J' and resid 457 through 465 Processing helix chain 'J' and resid 468 through 478 Processing helix chain 'J' and resid 482 through 492 removed outlier: 4.123A pdb=" N GLU J 492 " --> pdb=" O LEU J 488 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 510 removed outlier: 3.705A pdb=" N LYS J 508 " --> pdb=" O SER J 504 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS J 509 " --> pdb=" O MET J 505 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY J 510 " --> pdb=" O VAL J 506 " (cutoff:3.500A) Processing helix chain 'J' and resid 510 through 525 Processing helix chain 'J' and resid 525 through 537 removed outlier: 4.154A pdb=" N VAL J 529 " --> pdb=" O ASP J 525 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER J 530 " --> pdb=" O PRO J 526 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU J 537 " --> pdb=" O ARG J 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 457 Processing helix chain 'K' and resid 457 through 465 Processing helix chain 'K' and resid 468 through 478 Processing helix chain 'K' and resid 482 through 492 removed outlier: 4.276A pdb=" N GLU K 492 " --> pdb=" O LEU K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 510 removed outlier: 3.700A pdb=" N LYS K 508 " --> pdb=" O SER K 504 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS K 509 " --> pdb=" O MET K 505 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY K 510 " --> pdb=" O VAL K 506 " (cutoff:3.500A) Processing helix chain 'K' and resid 510 through 525 Processing helix chain 'K' and resid 525 through 537 removed outlier: 4.156A pdb=" N VAL K 529 " --> pdb=" O ASP K 525 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER K 530 " --> pdb=" O PRO K 526 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU K 537 " --> pdb=" O ARG K 533 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 457 Processing helix chain 'L' and resid 457 through 465 Processing helix chain 'L' and resid 468 through 478 Processing helix chain 'L' and resid 482 through 492 removed outlier: 4.140A pdb=" N GLU L 492 " --> pdb=" O LEU L 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 510 removed outlier: 3.743A pdb=" N LYS L 508 " --> pdb=" O SER L 504 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS L 509 " --> pdb=" O MET L 505 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY L 510 " --> pdb=" O VAL L 506 " (cutoff:3.500A) Processing helix chain 'L' and resid 510 through 525 Processing helix chain 'L' and resid 525 through 537 removed outlier: 4.271A pdb=" N VAL L 529 " --> pdb=" O ASP L 525 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER L 530 " --> pdb=" O PRO L 526 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 537 " --> pdb=" O ARG L 533 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1731 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: 2.15 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3012 1.34 - 1.46: 628 1.46 - 1.57: 4856 1.57 - 1.69: 0 1.69 - 1.80: 48 Bond restraints: 8544 Sorted by residual: bond pdb=" C ASP J 525 " pdb=" O ASP J 525 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.75e-01 bond pdb=" C ASP K 525 " pdb=" O ASP K 525 " ideal model delta sigma weight residual 1.248 1.238 0.011 1.26e-02 6.30e+03 7.35e-01 bond pdb=" CB LYS H 508 " pdb=" CG LYS H 508 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.37e-01 bond pdb=" CB LYS G 508 " pdb=" CG LYS G 508 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.10e-01 bond pdb=" C ASP B 525 " pdb=" O ASP B 525 " ideal model delta sigma weight residual 1.248 1.239 0.010 1.26e-02 6.30e+03 5.98e-01 ... (remaining 8539 not shown) Histogram of bond angle deviations from ideal: 100.41 - 106.60: 72 106.60 - 112.79: 4602 112.79 - 118.98: 2470 118.98 - 125.18: 4280 125.18 - 131.37: 24 Bond angle restraints: 11448 Sorted by residual: angle pdb=" CA LYS K 508 " pdb=" CB LYS K 508 " pdb=" CG LYS K 508 " ideal model delta sigma weight residual 114.10 117.48 -3.38 2.00e+00 2.50e-01 2.86e+00 angle pdb=" CA LYS B 508 " pdb=" CB LYS B 508 " pdb=" CG LYS B 508 " ideal model delta sigma weight residual 114.10 117.43 -3.33 2.00e+00 2.50e-01 2.77e+00 angle pdb=" CA LYS I 508 " pdb=" CB LYS I 508 " pdb=" CG LYS I 508 " ideal model delta sigma weight residual 114.10 117.36 -3.26 2.00e+00 2.50e-01 2.65e+00 angle pdb=" CB LYS H 508 " pdb=" CG LYS H 508 " pdb=" CD LYS H 508 " ideal model delta sigma weight residual 111.30 115.03 -3.73 2.30e+00 1.89e-01 2.63e+00 angle pdb=" CA LYS J 508 " pdb=" CB LYS J 508 " pdb=" CG LYS J 508 " ideal model delta sigma weight residual 114.10 117.30 -3.20 2.00e+00 2.50e-01 2.55e+00 ... (remaining 11443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.66: 4792 11.66 - 23.32: 416 23.32 - 34.98: 107 34.98 - 46.64: 73 46.64 - 58.30: 36 Dihedral angle restraints: 5424 sinusoidal: 2352 harmonic: 3072 Sorted by residual: dihedral pdb=" CA ALA I 463 " pdb=" C ALA I 463 " pdb=" N ARG I 464 " pdb=" CA ARG I 464 " ideal model delta harmonic sigma weight residual -180.00 -163.35 -16.65 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ALA H 463 " pdb=" C ALA H 463 " pdb=" N ARG H 464 " pdb=" CA ARG H 464 " ideal model delta harmonic sigma weight residual 180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ALA L 463 " pdb=" C ALA L 463 " pdb=" N ARG L 464 " pdb=" CA ARG L 464 " ideal model delta harmonic sigma weight residual -180.00 -163.75 -16.25 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 5421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.019: 704 0.019 - 0.039: 358 0.039 - 0.058: 140 0.058 - 0.077: 69 0.077 - 0.096: 25 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA GLU K 479 " pdb=" N GLU K 479 " pdb=" C GLU K 479 " pdb=" CB GLU K 479 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.32e-01 chirality pdb=" CA PRO H 526 " pdb=" N PRO H 526 " pdb=" C PRO H 526 " pdb=" CB PRO H 526 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.16e-01 chirality pdb=" CA PRO I 526 " pdb=" N PRO I 526 " pdb=" C PRO I 526 " pdb=" CB PRO I 526 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.14e-01 ... (remaining 1293 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 527 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C TYR A 527 " 0.020 2.00e-02 2.50e+03 pdb=" O TYR A 527 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU A 528 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR J 527 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C TYR J 527 " -0.019 2.00e-02 2.50e+03 pdb=" O TYR J 527 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU J 528 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 527 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.23e+00 pdb=" C TYR H 527 " -0.019 2.00e-02 2.50e+03 pdb=" O TYR H 527 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU H 528 " 0.007 2.00e-02 2.50e+03 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 2776 2.86 - 3.37: 8644 3.37 - 3.88: 13602 3.88 - 4.39: 16015 4.39 - 4.90: 26417 Nonbonded interactions: 67454 Sorted by model distance: nonbonded pdb=" NE2 GLN H 476 " pdb=" OE1 GLU H 483 " model vdw 2.356 2.520 nonbonded pdb=" O GLU E 500 " pdb=" OG SER E 504 " model vdw 2.379 2.440 nonbonded pdb=" O GLU L 500 " pdb=" OG SER L 504 " model vdw 2.425 2.440 nonbonded pdb=" O PHE E 518 " pdb=" OG SER E 522 " model vdw 2.450 2.440 nonbonded pdb=" O GLU B 500 " pdb=" OG SER B 504 " model vdw 2.455 2.440 ... (remaining 67449 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 1.120 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 22.990 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.002 0.024 8544 Z= 0.136 Angle : 0.446 3.733 11448 Z= 0.277 Chirality : 0.030 0.096 1296 Planarity : 0.003 0.023 1524 Dihedral : 11.872 58.301 3408 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.23), residues: 1020 helix: 0.05 (0.15), residues: 900 sheet: None (None), residues: 0 loop : -3.46 (0.29), residues: 120 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.3283 time to fit residues: 216.2698 Evaluate side-chains 260 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.120 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5175 ------------------------------------------------------------------------------- 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: 6.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 60.0000 chunk 24 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 50.0000 chunk 87 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 HIS ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN I 458 HIS I 462 GLN ** L 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 535 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 8544 Z= 0.231 Angle : 0.869 12.524 11448 Z= 0.418 Chirality : 0.046 0.251 1296 Planarity : 0.004 0.026 1524 Dihedral : 4.388 20.839 1128 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 4.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.25), residues: 1020 helix: 0.79 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.31 (0.26), residues: 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 309 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 30 residues processed: 340 average time/residue: 0.2683 time to fit residues: 115.4808 Evaluate side-chains 249 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 219 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.0973 time to fit residues: 6.3642 ------------------------------------------------------------------------------- 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: 20.0000 chunk 72 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 87 optimal weight: 40.0000 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 70 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 476 GLN E 458 HIS E 476 GLN F 458 HIS ** G 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 476 GLN H 458 HIS H 476 GLN I 476 GLN K 458 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.8106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 8544 Z= 0.205 Angle : 0.854 12.689 11448 Z= 0.421 Chirality : 0.040 0.188 1296 Planarity : 0.003 0.029 1524 Dihedral : 4.571 24.162 1128 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.26), residues: 1020 helix: 0.76 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.08 (0.28), residues: 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 256 average time/residue: 0.2543 time to fit residues: 83.4740 Evaluate side-chains 214 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 198 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1380 time to fit residues: 4.6650 ------------------------------------------------------------------------------- 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: 6.9990 chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 58 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN A 536 ASN ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 458 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.8755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 8544 Z= 0.192 Angle : 0.880 14.679 11448 Z= 0.419 Chirality : 0.041 0.250 1296 Planarity : 0.003 0.030 1524 Dihedral : 4.437 23.388 1128 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1020 helix: 0.72 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.04 (0.29), residues: 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 233 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 250 average time/residue: 0.2343 time to fit residues: 76.3128 Evaluate side-chains 205 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1865 time to fit residues: 5.8677 ------------------------------------------------------------------------------- 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: 0.4980 chunk 1 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 47 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 30.0000 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 HIS ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 GLN ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.9189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8544 Z= 0.187 Angle : 0.887 12.892 11448 Z= 0.423 Chirality : 0.043 0.279 1296 Planarity : 0.003 0.020 1524 Dihedral : 4.477 21.964 1128 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1020 helix: 0.52 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.74 (0.29), residues: 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 224 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 239 average time/residue: 0.2369 time to fit residues: 74.1867 Evaluate side-chains 190 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1278 time to fit residues: 3.5951 ------------------------------------------------------------------------------- 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: 8.9990 chunk 18 optimal weight: 40.0000 chunk 54 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 92 optimal weight: 50.0000 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.9682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8544 Z= 0.203 Angle : 0.917 13.247 11448 Z= 0.454 Chirality : 0.044 0.303 1296 Planarity : 0.003 0.032 1524 Dihedral : 4.603 21.823 1128 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 25.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.26), residues: 1020 helix: 0.45 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.84 (0.29), residues: 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 223 average time/residue: 0.2327 time to fit residues: 68.2775 Evaluate side-chains 193 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0760 time to fit residues: 4.0126 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 40.0000 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 1.0006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 8544 Z= 0.200 Angle : 0.961 15.731 11448 Z= 0.466 Chirality : 0.046 0.318 1296 Planarity : 0.003 0.023 1524 Dihedral : 4.633 23.762 1128 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1020 helix: 0.38 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.83 (0.28), residues: 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 212 average time/residue: 0.2516 time to fit residues: 69.2102 Evaluate side-chains 183 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0799 time to fit residues: 3.0714 ------------------------------------------------------------------------------- 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: 7.9990 chunk 18 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 58 optimal weight: 40.0000 chunk 63 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 8 optimal weight: 50.0000 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 1.0369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 8544 Z= 0.200 Angle : 0.969 14.290 11448 Z= 0.474 Chirality : 0.047 0.341 1296 Planarity : 0.003 0.034 1524 Dihedral : 4.815 21.927 1128 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 25.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.26), residues: 1020 helix: 0.23 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.94 (0.33), residues: 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 198 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 207 average time/residue: 0.2467 time to fit residues: 66.8288 Evaluate side-chains 177 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 171 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0901 time to fit residues: 2.3597 ------------------------------------------------------------------------------- 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: 7.9990 chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 30.0000 chunk 67 optimal weight: 40.0000 chunk 26 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 1.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8544 Z= 0.208 Angle : 1.045 15.316 11448 Z= 0.495 Chirality : 0.051 0.413 1296 Planarity : 0.003 0.026 1524 Dihedral : 4.901 31.459 1128 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.39 (0.26), residues: 1020 helix: 0.10 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.95 (0.35), residues: 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 195 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 198 average time/residue: 0.2392 time to fit residues: 62.4475 Evaluate side-chains 181 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0847 time to fit residues: 2.6690 ------------------------------------------------------------------------------- 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: 7.9990 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 0.0050 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 overall best weight: 5.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 478 ASN ** J 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 1.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 8544 Z= 0.226 Angle : 1.123 15.554 11448 Z= 0.534 Chirality : 0.053 0.447 1296 Planarity : 0.004 0.069 1524 Dihedral : 5.076 39.210 1128 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1020 helix: -0.04 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.02 (0.32), residues: 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 195 average time/residue: 0.2285 time to fit residues: 59.4665 Evaluate side-chains 169 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3778 ------------------------------------------------------------------------------- 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: 10.0000 chunk 70 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN F 478 ASN ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 476 GLN ** K 499 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 = 0.3371 r_free = 0.3371 target = 0.055323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.049806 restraints weight = 88742.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.050740 restraints weight = 42974.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.051284 restraints weight = 25499.582| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 1.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 8544 Z= 0.246 Angle : 1.154 16.619 11448 Z= 0.553 Chirality : 0.051 0.413 1296 Planarity : 0.003 0.026 1524 Dihedral : 5.251 41.518 1128 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 28.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.68 (0.26), residues: 1020 helix: -0.07 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.21 (0.30), residues: 84 =============================================================================== Job complete usr+sys time: 1876.32 seconds wall clock time: 35 minutes 1.71 seconds (2101.71 seconds total)