Starting phenix.real_space_refine on Sun Mar 17 06:19:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/03_2024/6k9f_9948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/03_2024/6k9f_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_9948/03_2024/6k9f_9948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/03_2024/6k9f_9948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/03_2024/6k9f_9948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k9f_9948/03_2024/6k9f_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-dev-5265/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: 4.34, 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: 3.04 Conformation dependent library (CDL) restraints added in 1.4 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: 0.82 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: 2.20 Time building geometry restraints manager: 3.31 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: 0.050 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: 0.850 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.040 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- 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 % Allowed : 2.53 % Favored : 97.47 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 458 PHE 0.013 0.002 PHE J 518 TYR 0.015 0.002 TYR B 531 ARG 0.002 0.000 ARG F 464 *********************** 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 : 1.072 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 REVERT: A 485 GLU cc_start: 0.9625 (mt-10) cc_final: 0.9334 (mt-10) REVERT: A 498 LYS cc_start: 0.9749 (mttt) cc_final: 0.9469 (mttt) REVERT: A 503 LEU cc_start: 0.9742 (mt) cc_final: 0.9493 (mp) REVERT: B 461 LEU cc_start: 0.9684 (mt) cc_final: 0.9398 (mt) REVERT: B 462 GLN cc_start: 0.9387 (tt0) cc_final: 0.8999 (tp40) REVERT: B 464 ARG cc_start: 0.8437 (mtt-85) cc_final: 0.7981 (tpt170) REVERT: B 487 GLU cc_start: 0.9718 (mt-10) cc_final: 0.9375 (pt0) REVERT: B 496 GLN cc_start: 0.9590 (mp10) cc_final: 0.9243 (pm20) REVERT: B 503 LEU cc_start: 0.9685 (mt) cc_final: 0.9352 (mt) REVERT: C 462 GLN cc_start: 0.9502 (tt0) cc_final: 0.9144 (tp40) REVERT: C 502 LEU cc_start: 0.9815 (tp) cc_final: 0.9582 (mt) REVERT: D 461 LEU cc_start: 0.9815 (mt) cc_final: 0.9541 (mt) REVERT: D 462 GLN cc_start: 0.9465 (tt0) cc_final: 0.9063 (tp40) REVERT: D 503 LEU cc_start: 0.9803 (mt) cc_final: 0.9598 (mt) REVERT: E 461 LEU cc_start: 0.9742 (mt) cc_final: 0.9419 (mt) REVERT: E 462 GLN cc_start: 0.9608 (tt0) cc_final: 0.9233 (tp-100) REVERT: E 503 LEU cc_start: 0.9826 (mt) cc_final: 0.9567 (mt) REVERT: F 462 GLN cc_start: 0.9610 (tt0) cc_final: 0.9282 (tp40) REVERT: F 524 ARG cc_start: 0.9546 (tpm170) cc_final: 0.9343 (mmm160) REVERT: F 528 LEU cc_start: 0.9519 (tp) cc_final: 0.9277 (mp) REVERT: G 498 LYS cc_start: 0.9582 (mttt) cc_final: 0.9379 (mttm) REVERT: G 503 LEU cc_start: 0.9842 (mt) cc_final: 0.9586 (mp) REVERT: H 465 MET cc_start: 0.9234 (mtm) cc_final: 0.8904 (mtm) REVERT: H 503 LEU cc_start: 0.9874 (mt) cc_final: 0.9533 (mt) REVERT: H 506 VAL cc_start: 0.9868 (t) cc_final: 0.9587 (p) REVERT: H 528 LEU cc_start: 0.9497 (tp) cc_final: 0.9245 (mt) REVERT: I 461 LEU cc_start: 0.9680 (mt) cc_final: 0.9330 (mt) REVERT: I 462 GLN cc_start: 0.9555 (tt0) cc_final: 0.9099 (tp40) REVERT: I 496 GLN cc_start: 0.9660 (mp10) cc_final: 0.9374 (pm20) REVERT: I 503 LEU cc_start: 0.9719 (mt) cc_final: 0.9501 (mp) REVERT: I 532 LEU cc_start: 0.9772 (mt) cc_final: 0.9563 (pp) REVERT: J 461 LEU cc_start: 0.9726 (mt) cc_final: 0.9420 (mt) REVERT: J 462 GLN cc_start: 0.9375 (tt0) cc_final: 0.8923 (tp40) REVERT: J 496 GLN cc_start: 0.9620 (mp10) cc_final: 0.9253 (pm20) REVERT: J 503 LEU cc_start: 0.9697 (mt) cc_final: 0.9377 (mt) REVERT: K 461 LEU cc_start: 0.9817 (mt) cc_final: 0.9455 (mt) REVERT: K 462 GLN cc_start: 0.9534 (tt0) cc_final: 0.9216 (tp40) REVERT: K 498 LYS cc_start: 0.9678 (mttt) cc_final: 0.9434 (mttt) REVERT: K 503 LEU cc_start: 0.9552 (mt) cc_final: 0.9211 (mp) REVERT: L 462 GLN cc_start: 0.9311 (tt0) cc_final: 0.8974 (tp40) REVERT: L 464 ARG cc_start: 0.8618 (mtt-85) cc_final: 0.8020 (tpt170) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.3151 time to fit residues: 207.6565 Evaluate side-chains 285 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 285 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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: 40.0000 chunk 72 optimal weight: 30.0000 chunk 40 optimal weight: 60.0000 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 56 optimal weight: 50.0000 chunk 87 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 458 HIS ** J 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 535 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.6052 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= 0.225 Angle : 0.825 12.506 11448 Z= 0.403 Chirality : 0.044 0.242 1296 Planarity : 0.004 0.032 1524 Dihedral : 4.318 19.419 1128 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 4.85 % Allowed : 20.89 % Favored : 74.26 % 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 (0.26), residues: 1020 helix: 0.89 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.33 (0.25), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 458 PHE 0.006 0.001 PHE I 453 TYR 0.010 0.001 TYR L 531 ARG 0.005 0.001 ARG K 495 *********************** 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 364 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 318 time to evaluate : 0.982 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: A 465 MET cc_start: 0.9346 (mtm) cc_final: 0.9030 (mtm) REVERT: A 481 LEU cc_start: 0.9057 (tp) cc_final: 0.8697 (tp) REVERT: B 461 LEU cc_start: 0.9619 (mt) cc_final: 0.9336 (mt) REVERT: B 465 MET cc_start: 0.8520 (mtm) cc_final: 0.8251 (mtm) REVERT: B 524 ARG cc_start: 0.9756 (tpm170) cc_final: 0.9498 (mmm160) REVERT: C 486 LYS cc_start: 0.9583 (ttpt) cc_final: 0.9310 (ttmt) REVERT: F 486 LYS cc_start: 0.9568 (ttpt) cc_final: 0.9180 (ttmt) REVERT: F 524 ARG cc_start: 0.9582 (tpm170) cc_final: 0.9342 (mmm160) REVERT: G 465 MET cc_start: 0.9167 (mtm) cc_final: 0.8748 (mtm) REVERT: G 486 LYS cc_start: 0.9573 (ttpt) cc_final: 0.9219 (ttmt) REVERT: G 492 GLU cc_start: 0.9671 (mm-30) cc_final: 0.9269 (mp0) REVERT: H 486 LYS cc_start: 0.9476 (ttpt) cc_final: 0.9013 (ttmt) REVERT: H 492 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9006 (mt-10) REVERT: I 465 MET cc_start: 0.8679 (mtp) cc_final: 0.8115 (mtm) REVERT: I 485 GLU cc_start: 0.9805 (mt-10) cc_final: 0.9545 (pt0) REVERT: I 487 GLU cc_start: 0.9800 (OUTLIER) cc_final: 0.9598 (pt0) REVERT: I 492 GLU cc_start: 0.9700 (mm-30) cc_final: 0.9393 (mp0) REVERT: J 465 MET cc_start: 0.9011 (mtp) cc_final: 0.8344 (mtp) REVERT: K 465 MET cc_start: 0.8742 (mtp) cc_final: 0.8357 (mtp) REVERT: L 464 ARG cc_start: 0.8809 (mtt-85) cc_final: 0.8195 (tpt170) REVERT: L 517 LEU cc_start: 0.9856 (tp) cc_final: 0.9501 (pp) outliers start: 46 outliers final: 31 residues processed: 349 average time/residue: 0.2790 time to fit residues: 121.9427 Evaluate side-chains 264 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 232 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 480 VAL Chi-restraints excluded: chain I residue 487 GLU Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 487 GLU Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 480 VAL Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 72 optimal weight: 30.0000 chunk 59 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- 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** E 458 HIS E 476 GLN F 458 HIS F 462 GLN G 476 GLN H 458 HIS H 476 GLN I 462 GLN I 476 GLN J 476 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8544 Z= 0.205 Angle : 0.847 13.789 11448 Z= 0.406 Chirality : 0.041 0.234 1296 Planarity : 0.004 0.035 1524 Dihedral : 4.441 21.896 1128 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 7.28 % Allowed : 22.05 % Favored : 70.68 % 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: 0.81 (0.25), residues: 1020 helix: 0.97 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.25 (0.27), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 458 PHE 0.007 0.001 PHE E 453 TYR 0.011 0.001 TYR J 531 ARG 0.006 0.001 ARG F 495 *********************** 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 319 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 250 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 461 LEU cc_start: 0.9741 (mt) cc_final: 0.9513 (mt) REVERT: B 486 LYS cc_start: 0.9725 (ttpt) cc_final: 0.9486 (ttmt) REVERT: C 462 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8967 (tp40) REVERT: C 486 LYS cc_start: 0.9653 (ttpt) cc_final: 0.9367 (ttmt) REVERT: D 481 LEU cc_start: 0.9165 (pp) cc_final: 0.8821 (pp) REVERT: D 485 GLU cc_start: 0.9758 (mt-10) cc_final: 0.9502 (pt0) REVERT: D 524 ARG cc_start: 0.9765 (tpm170) cc_final: 0.9354 (mmm160) REVERT: F 462 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.8977 (tp40) REVERT: F 486 LYS cc_start: 0.9666 (ttpt) cc_final: 0.9400 (tttt) REVERT: G 517 LEU cc_start: 0.9934 (tp) cc_final: 0.9677 (pp) REVERT: H 489 VAL cc_start: 0.9819 (t) cc_final: 0.9577 (p) REVERT: I 524 ARG cc_start: 0.9694 (tpm170) cc_final: 0.9422 (mmm160) REVERT: K 486 LYS cc_start: 0.9730 (ttpt) cc_final: 0.9377 (ttmt) REVERT: L 464 ARG cc_start: 0.8712 (mtt-85) cc_final: 0.8494 (mmt180) REVERT: L 524 ARG cc_start: 0.9673 (tpm170) cc_final: 0.9388 (mtp180) outliers start: 69 outliers final: 46 residues processed: 294 average time/residue: 0.2942 time to fit residues: 106.9228 Evaluate side-chains 245 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 459 ARG Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 455 LYS Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain I residue 462 GLN Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 488 LEU Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 480 VAL Chi-restraints excluded: chain J residue 487 GLU Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 58 optimal weight: 50.0000 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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** C 476 GLN ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN I 462 GLN K 458 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.8469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8544 Z= 0.191 Angle : 0.865 12.974 11448 Z= 0.415 Chirality : 0.042 0.232 1296 Planarity : 0.003 0.024 1524 Dihedral : 4.517 22.938 1128 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 6.22 % Allowed : 24.89 % Favored : 68.88 % 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: 0.60 (0.26), residues: 1020 helix: 0.83 (0.17), residues: 924 sheet: None (None), residues: 0 loop : -3.26 (0.27), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS L 458 PHE 0.007 0.001 PHE K 453 TYR 0.014 0.001 TYR H 531 ARG 0.005 0.000 ARG G 533 *********************** 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 273 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 214 time to evaluate : 1.046 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: B 481 LEU cc_start: 0.9340 (pp) cc_final: 0.9120 (tt) REVERT: B 486 LYS cc_start: 0.9751 (ttpt) cc_final: 0.9515 (ttmt) REVERT: C 462 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8880 (tp40) REVERT: D 481 LEU cc_start: 0.9244 (pp) cc_final: 0.8805 (pp) REVERT: D 492 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9145 (mt-10) REVERT: E 481 LEU cc_start: 0.9609 (pp) cc_final: 0.9315 (tt) REVERT: F 462 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.9048 (tp40) REVERT: F 486 LYS cc_start: 0.9760 (ttpt) cc_final: 0.9444 (tttt) REVERT: F 517 LEU cc_start: 0.9856 (tp) cc_final: 0.9493 (pp) REVERT: G 492 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9255 (mt-10) REVERT: G 517 LEU cc_start: 0.9929 (tp) cc_final: 0.9675 (pp) REVERT: I 492 GLU cc_start: 0.9686 (mm-30) cc_final: 0.9474 (mt-10) REVERT: K 486 LYS cc_start: 0.9742 (ttpt) cc_final: 0.9445 (ttmt) REVERT: L 486 LYS cc_start: 0.9805 (ttpt) cc_final: 0.9325 (ttmt) REVERT: L 487 GLU cc_start: 0.9904 (mm-30) cc_final: 0.9689 (pt0) outliers start: 59 outliers final: 43 residues processed: 258 average time/residue: 0.2672 time to fit residues: 87.5301 Evaluate side-chains 224 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 179 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 475 LEU Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 459 ARG Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 484 ASN Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 47 optimal weight: 50.0000 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.8883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8544 Z= 0.183 Angle : 0.870 14.165 11448 Z= 0.418 Chirality : 0.044 0.346 1296 Planarity : 0.003 0.026 1524 Dihedral : 4.465 23.008 1128 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 5.49 % Allowed : 25.63 % Favored : 68.88 % 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: 0.69 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.81 (0.27), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 458 PHE 0.008 0.001 PHE G 453 TYR 0.010 0.001 TYR H 531 ARG 0.005 0.000 ARG G 533 *********************** 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 257 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 205 time to evaluate : 1.002 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: B 481 LEU cc_start: 0.9414 (pp) cc_final: 0.9166 (tt) REVERT: B 486 LYS cc_start: 0.9806 (ttpt) cc_final: 0.9599 (ttmt) REVERT: C 462 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.8935 (tp40) REVERT: F 486 LYS cc_start: 0.9781 (ttpt) cc_final: 0.9388 (ttmt) REVERT: G 492 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9147 (mt-10) REVERT: I 492 GLU cc_start: 0.9677 (mm-30) cc_final: 0.9464 (mp0) REVERT: L 486 LYS cc_start: 0.9815 (ttpt) cc_final: 0.9537 (ttmt) outliers start: 52 outliers final: 41 residues processed: 239 average time/residue: 0.2175 time to fit residues: 68.6128 Evaluate side-chains 217 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 484 ASN Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 471 VAL Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 475 LEU Chi-restraints excluded: chain I residue 484 ASN Chi-restraints excluded: chain J residue 454 VAL Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 30.0000 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 22 optimal weight: 30.0000 chunk 92 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 40.0000 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 8.9990 chunk 89 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.9267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8544 Z= 0.191 Angle : 0.889 13.398 11448 Z= 0.436 Chirality : 0.045 0.331 1296 Planarity : 0.003 0.028 1524 Dihedral : 4.525 22.688 1128 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 5.91 % Allowed : 25.63 % Favored : 68.46 % 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: 0.39 (0.26), residues: 1020 helix: 0.62 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.97 (0.26), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 458 PHE 0.007 0.001 PHE G 453 TYR 0.008 0.001 TYR J 531 ARG 0.005 0.001 ARG A 533 *********************** 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 253 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 197 time to evaluate : 1.135 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: B 481 LEU cc_start: 0.9487 (pp) cc_final: 0.9228 (tt) REVERT: B 489 VAL cc_start: 0.9739 (t) cc_final: 0.9531 (t) REVERT: C 462 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8319 (tp40) REVERT: C 489 VAL cc_start: 0.9724 (m) cc_final: 0.9454 (p) REVERT: C 500 GLU cc_start: 0.9807 (pp20) cc_final: 0.9448 (mm-30) REVERT: G 489 VAL cc_start: 0.9803 (m) cc_final: 0.9583 (p) REVERT: G 492 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9150 (mt-10) REVERT: H 517 LEU cc_start: 0.9959 (tp) cc_final: 0.9678 (pp) REVERT: K 485 GLU cc_start: 0.9596 (mt-10) cc_final: 0.9342 (pt0) REVERT: K 488 LEU cc_start: 0.9852 (OUTLIER) cc_final: 0.9594 (pp) REVERT: L 486 LYS cc_start: 0.9837 (ttpt) cc_final: 0.9414 (ttmt) REVERT: L 487 GLU cc_start: 0.9922 (mm-30) cc_final: 0.9679 (pt0) outliers start: 56 outliers final: 46 residues processed: 237 average time/residue: 0.2523 time to fit residues: 76.8025 Evaluate side-chains 220 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 172 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 459 ARG Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 459 ARG Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 40.0000 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 92 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 56 optimal weight: 40.0000 chunk 42 optimal weight: 0.3980 chunk 36 optimal weight: 20.0000 chunk 55 optimal weight: 4.9990 overall best weight: 8.6790 ------------------------------------------------------------------------------- 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 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.9633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8544 Z= 0.197 Angle : 0.893 13.850 11448 Z= 0.438 Chirality : 0.045 0.323 1296 Planarity : 0.003 0.025 1524 Dihedral : 4.677 24.640 1128 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 24.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 5.80 % Allowed : 26.69 % Favored : 67.51 % 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: 0.29 (0.26), residues: 1020 helix: 0.56 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.02 (0.26), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 458 PHE 0.007 0.001 PHE A 453 TYR 0.007 0.001 TYR H 531 ARG 0.006 0.000 ARG C 533 *********************** 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 247 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 192 time to evaluate : 1.093 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: B 481 LEU cc_start: 0.9579 (pp) cc_final: 0.9347 (tt) REVERT: C 462 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.8903 (tp40) REVERT: C 489 VAL cc_start: 0.9695 (m) cc_final: 0.9480 (p) REVERT: E 474 ASP cc_start: 0.9591 (m-30) cc_final: 0.9365 (m-30) REVERT: G 489 VAL cc_start: 0.9827 (m) cc_final: 0.9563 (p) REVERT: G 492 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9111 (mt-10) REVERT: G 517 LEU cc_start: 0.9933 (tp) cc_final: 0.9691 (pp) REVERT: H 517 LEU cc_start: 0.9959 (tp) cc_final: 0.9678 (pp) REVERT: L 486 LYS cc_start: 0.9844 (ttpt) cc_final: 0.9595 (ttmt) outliers start: 55 outliers final: 48 residues processed: 233 average time/residue: 0.2557 time to fit residues: 77.2512 Evaluate side-chains 221 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 172 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 459 ARG Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 468 LEU Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 485 GLU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 471 VAL Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 480 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 459 ARG Chi-restraints excluded: chain L residue 471 VAL Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 40.0000 chunk 58 optimal weight: 50.0000 chunk 63 optimal weight: 50.0000 chunk 45 optimal weight: 8.9990 chunk 8 optimal weight: 50.0000 chunk 72 optimal weight: 0.0980 chunk 84 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 overall best weight: 7.0190 ------------------------------------------------------------------------------- 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 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** ** K 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.9910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8544 Z= 0.207 Angle : 0.966 15.967 11448 Z= 0.469 Chirality : 0.050 0.420 1296 Planarity : 0.003 0.024 1524 Dihedral : 4.704 23.908 1128 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 5.17 % Allowed : 28.90 % Favored : 65.93 % 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: 0.24 (0.26), residues: 1020 helix: 0.54 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -3.10 (0.29), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 458 PHE 0.008 0.001 PHE D 453 TYR 0.006 0.001 TYR J 531 ARG 0.005 0.000 ARG C 533 *********************** 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 236 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 1.044 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: C 462 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8478 (tp40) REVERT: C 500 GLU cc_start: 0.9816 (pp20) cc_final: 0.9603 (mm-30) REVERT: G 489 VAL cc_start: 0.9834 (m) cc_final: 0.9562 (p) REVERT: G 517 LEU cc_start: 0.9929 (tp) cc_final: 0.9684 (pp) REVERT: H 517 LEU cc_start: 0.9960 (tp) cc_final: 0.9663 (pp) outliers start: 49 outliers final: 43 residues processed: 223 average time/residue: 0.2411 time to fit residues: 69.3462 Evaluate side-chains 213 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 169 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 484 ASN Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 459 ARG Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 480 VAL Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 471 VAL Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 480 VAL Chi-restraints excluded: chain H residue 484 ASN Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 459 ARG Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 56 optimal weight: 50.0000 chunk 91 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 499 ASN ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 1.0223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8544 Z= 0.209 Angle : 0.993 14.137 11448 Z= 0.486 Chirality : 0.050 0.425 1296 Planarity : 0.003 0.018 1524 Dihedral : 4.808 26.051 1128 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 4.96 % Allowed : 29.85 % Favored : 65.19 % 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: 0.12 (0.26), residues: 1020 helix: 0.43 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -2.79 (0.37), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 458 PHE 0.008 0.001 PHE B 453 TYR 0.006 0.001 TYR J 531 ARG 0.005 0.000 ARG C 533 *********************** 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 240 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 193 time to evaluate : 1.100 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: A 500 GLU cc_start: 0.9815 (pp20) cc_final: 0.9590 (mp0) REVERT: B 517 LEU cc_start: 0.9854 (tp) cc_final: 0.9635 (pp) REVERT: C 462 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.9018 (tp-100) REVERT: C 489 VAL cc_start: 0.9695 (m) cc_final: 0.9477 (p) REVERT: G 500 GLU cc_start: 0.9738 (pp20) cc_final: 0.9535 (mm-30) REVERT: G 517 LEU cc_start: 0.9931 (tp) cc_final: 0.9682 (pp) outliers start: 47 outliers final: 42 residues processed: 232 average time/residue: 0.2705 time to fit residues: 80.2165 Evaluate side-chains 209 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 166 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 459 ARG Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain C residue 462 GLN Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 459 ARG Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 453 PHE Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 459 ARG Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 459 ARG Chi-restraints excluded: chain G residue 475 LEU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 455 LYS Chi-restraints excluded: chain H residue 484 ASN Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain J residue 459 ARG Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain J residue 484 ASN Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 471 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 471 VAL Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 8.9990 chunk 43 optimal weight: 0.5980 chunk 63 optimal weight: 50.0000 chunk 95 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 0.0050 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 overall best weight: 3.5200 ------------------------------------------------------------------------------- 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** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 476 GLN ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 1.0403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8544 Z= 0.219 Angle : 1.090 17.385 11448 Z= 0.529 Chirality : 0.051 0.440 1296 Planarity : 0.003 0.019 1524 Dihedral : 4.920 25.988 1128 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.69 % Allowed : 32.17 % Favored : 64.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.27), residues: 1020 helix: 0.37 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.51 (0.45), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 458 PHE 0.008 0.001 PHE A 453 TYR 0.006 0.000 TYR J 531 ARG 0.005 0.000 ARG C 533 ********************** 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 225 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 190 time to evaluate : 1.064 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: A 500 GLU cc_start: 0.9804 (pp20) cc_final: 0.9572 (mp0) REVERT: B 498 LYS cc_start: 0.9715 (mttt) cc_final: 0.9501 (mttt) REVERT: B 517 LEU cc_start: 0.9853 (tp) cc_final: 0.9623 (pp) REVERT: C 489 VAL cc_start: 0.9687 (m) cc_final: 0.9448 (p) REVERT: G 517 LEU cc_start: 0.9929 (tp) cc_final: 0.9679 (pp) REVERT: J 489 VAL cc_start: 0.9691 (t) cc_final: 0.9479 (p) outliers start: 35 outliers final: 31 residues processed: 217 average time/residue: 0.2194 time to fit residues: 63.1997 Evaluate side-chains 196 residues out of total 948 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 484 ASN Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 529 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain E residue 455 LYS Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 529 VAL Chi-restraints excluded: chain F residue 453 PHE Chi-restraints excluded: chain F residue 459 ARG Chi-restraints excluded: chain F residue 502 LEU Chi-restraints excluded: chain G residue 529 VAL Chi-restraints excluded: chain H residue 453 PHE Chi-restraints excluded: chain H residue 484 ASN Chi-restraints excluded: chain I residue 453 PHE Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain J residue 471 VAL Chi-restraints excluded: chain K residue 488 LEU Chi-restraints excluded: chain L residue 455 LYS Chi-restraints excluded: chain L residue 471 VAL Chi-restraints excluded: chain L residue 529 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN ** F 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 478 ASN ** J 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.053745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.048260 restraints weight = 90642.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.049155 restraints weight = 44697.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.049683 restraints weight = 26592.785| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 1.0759 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= 0.241 Angle : 1.068 15.387 11448 Z= 0.529 Chirality : 0.051 0.432 1296 Planarity : 0.004 0.021 1524 Dihedral : 5.037 32.722 1128 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 28.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.11 % Allowed : 33.23 % Favored : 62.66 % 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: -0.16 (0.27), residues: 1020 helix: 0.23 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -2.66 (0.44), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 458 PHE 0.009 0.001 PHE B 453 TYR 0.006 0.001 TYR J 531 ARG 0.005 0.001 ARG C 533 =============================================================================== Job complete usr+sys time: 1973.81 seconds wall clock time: 36 minutes 31.73 seconds (2191.73 seconds total)