Starting phenix.real_space_refine on Fri Dec 8 08:41:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/12_2023/8afm_15402.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/12_2023/8afm_15402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/12_2023/8afm_15402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/12_2023/8afm_15402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/12_2023/8afm_15402.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/12_2023/8afm_15402.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4754 2.51 5 N 1492 2.21 5 O 1568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "B GLU 428": "OE1" <-> "OE2" Residue "D ARG 808": "NH1" <-> "NH2" Residue "D ARG 839": "NH1" <-> "NH2" Residue "D ARG 873": "NH1" <-> "NH2" Residue "C ARG 808": "NH1" <-> "NH2" Residue "C TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 839": "NH1" <-> "NH2" Residue "C ARG 873": "NH1" <-> "NH2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "G GLU 375": "OE1" <-> "OE2" Residue "G GLU 382": "OE1" <-> "OE2" Residue "G GLU 423": "OE1" <-> "OE2" Residue "H GLU 428": "OE1" <-> "OE2" Residue "J ARG 808": "NH1" <-> "NH2" Residue "J ARG 839": "NH1" <-> "NH2" Residue "J ARG 873": "NH1" <-> "NH2" Residue "I ARG 808": "NH1" <-> "NH2" Residue "I TYR 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 839": "NH1" <-> "NH2" Residue "I ARG 873": "NH1" <-> "NH2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 7842 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "B" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "G" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "H" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "I" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "K" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 518 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "L" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 455 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Time building chain proxies: 4.74, per 1000 atoms: 0.60 Number of scatterers: 7842 At special positions: 0 Unit cell: (212.544, 98.496, 86.4, 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 28 16.00 O 1568 8.00 N 1492 7.00 C 4754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 795 " - pdb=" SG CYS D 868 " distance=2.03 Simple disulfide: pdb=" SG CYS C 795 " - pdb=" SG CYS C 868 " distance=2.04 Simple disulfide: pdb=" SG CYS J 795 " - pdb=" SG CYS J 868 " distance=2.03 Simple disulfide: pdb=" SG CYS I 795 " - pdb=" SG CYS I 868 " distance=2.04 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: 3.23 Conformation dependent library (CDL) restraints added in 1.6 seconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 58.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 369 through 419 removed outlier: 3.537A pdb=" N LYS A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 378 " --> pdb=" O GLN A 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 397 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU A 407 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 434 removed outlier: 3.766A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 removed outlier: 4.228A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.846A pdb=" N LYS B 379 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN B 399 " --> pdb=" O MET B 395 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP B 400 " --> pdb=" O GLN B 396 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 429 removed outlier: 3.517A pdb=" N ALA B 408 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 418 " --> pdb=" O GLN B 414 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 434 removed outlier: 3.606A pdb=" N ALA B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 440 through 443 Processing helix chain 'D' and resid 833 through 837 removed outlier: 3.505A pdb=" N LYS D 837 " --> pdb=" O ASP D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 859 through 863 removed outlier: 4.111A pdb=" N THR D 863 " --> pdb=" O PRO D 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 863 removed outlier: 3.537A pdb=" N THR C 863 " --> pdb=" O PRO C 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 155 removed outlier: 3.911A pdb=" N GLN E 105 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU E 137 " --> pdb=" O ASP E 133 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 155 " --> pdb=" O LEU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 removed outlier: 3.631A pdb=" N SER E 159 " --> pdb=" O LEU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'F' and resid 97 through 139 removed outlier: 3.522A pdb=" N LEU F 103 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA F 106 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER F 125 " --> pdb=" O ALA F 121 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN F 139 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 154 removed outlier: 3.894A pdb=" N ILE F 143 " --> pdb=" O ASN F 139 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 144 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN F 148 " --> pdb=" O ASP F 144 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 419 removed outlier: 3.537A pdb=" N LYS G 376 " --> pdb=" O VAL G 372 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA G 377 " --> pdb=" O ALA G 373 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 378 " --> pdb=" O GLN G 374 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA G 390 " --> pdb=" O GLN G 386 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG G 391 " --> pdb=" O GLN G 387 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN G 396 " --> pdb=" O LEU G 392 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU G 407 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 408 " --> pdb=" O ARG G 404 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE G 410 " --> pdb=" O HIS G 406 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA G 411 " --> pdb=" O GLU G 407 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR G 416 " --> pdb=" O GLU G 412 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 420 through 434 removed outlier: 3.766A pdb=" N LEU G 426 " --> pdb=" O SER G 422 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU G 428 " --> pdb=" O ALA G 424 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA G 430 " --> pdb=" O LEU G 426 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU G 431 " --> pdb=" O ALA G 427 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 434 " --> pdb=" O ALA G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 443 removed outlier: 4.228A pdb=" N LEU G 441 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET G 443 " --> pdb=" O SER G 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 401 removed outlier: 3.846A pdb=" N LYS H 379 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG H 380 " --> pdb=" O LYS H 376 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA H 381 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU H 383 " --> pdb=" O LYS H 379 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG H 391 " --> pdb=" O GLN H 387 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU H 392 " --> pdb=" O LEU H 388 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN H 399 " --> pdb=" O MET H 395 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP H 400 " --> pdb=" O GLN H 396 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN H 401 " --> pdb=" O GLU H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 429 removed outlier: 3.516A pdb=" N ALA H 408 " --> pdb=" O ARG H 404 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE H 410 " --> pdb=" O HIS H 406 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 411 " --> pdb=" O GLU H 407 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR H 416 " --> pdb=" O GLU H 412 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE H 417 " --> pdb=" O LEU H 413 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU H 418 " --> pdb=" O GLN H 414 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR H 421 " --> pdb=" O ILE H 417 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 426 " --> pdb=" O SER H 422 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 429 through 434 removed outlier: 3.606A pdb=" N ALA H 434 " --> pdb=" O ALA H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 439 Processing helix chain 'H' and resid 440 through 443 Processing helix chain 'J' and resid 833 through 837 removed outlier: 3.505A pdb=" N LYS J 837 " --> pdb=" O ASP J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 859 through 863 removed outlier: 4.111A pdb=" N THR J 863 " --> pdb=" O PRO J 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 863 removed outlier: 3.536A pdb=" N THR I 863 " --> pdb=" O PRO I 860 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 155 removed outlier: 3.911A pdb=" N GLN K 105 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA K 106 " --> pdb=" O ALA K 102 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER K 112 " --> pdb=" O GLU K 108 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA K 116 " --> pdb=" O SER K 112 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU K 137 " --> pdb=" O ASP K 133 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG K 145 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU K 146 " --> pdb=" O GLU K 142 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU K 155 " --> pdb=" O LEU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 160 removed outlier: 3.631A pdb=" N SER K 159 " --> pdb=" O LEU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'L' and resid 97 through 139 removed outlier: 3.523A pdb=" N LEU L 103 " --> pdb=" O ARG L 99 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA L 106 " --> pdb=" O ALA L 102 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU L 124 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN L 139 " --> pdb=" O ALA L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 154 removed outlier: 3.893A pdb=" N ILE L 143 " --> pdb=" O ASN L 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN L 148 " --> pdb=" O ASP L 144 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER L 153 " --> pdb=" O ALA L 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 4.036A pdb=" N CYS D 795 " --> pdb=" O VAL D 851 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL D 851 " --> pdb=" O CYS D 795 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 841 " --> pdb=" O GLN D 854 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 818 through 824 removed outlier: 3.561A pdb=" N GLY D 819 " --> pdb=" O ARG D 811 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP D 809 " --> pdb=" O VAL D 821 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL D 823 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET D 807 " --> pdb=" O VAL D 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 869 through 872 removed outlier: 3.693A pdb=" N ALA D 870 " --> pdb=" O TYR D 877 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 790 through 795 removed outlier: 3.516A pdb=" N CYS C 795 " --> pdb=" O VAL C 851 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN C 831 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 823 " --> pdb=" O ASN C 831 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 821 " --> pdb=" O TRP C 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 870 " --> pdb=" O TYR C 877 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN C 831 " --> pdb=" O VAL C 823 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 823 " --> pdb=" O ASN C 831 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL C 821 " --> pdb=" O TRP C 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 5 through 7 removed outlier: 4.036A pdb=" N CYS J 795 " --> pdb=" O VAL J 851 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL J 851 " --> pdb=" O CYS J 795 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE J 841 " --> pdb=" O GLN J 854 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 818 through 824 removed outlier: 3.562A pdb=" N GLY J 819 " --> pdb=" O ARG J 811 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP J 809 " --> pdb=" O VAL J 821 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL J 823 " --> pdb=" O MET J 807 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET J 807 " --> pdb=" O VAL J 823 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 869 through 872 removed outlier: 3.694A pdb=" N ALA J 870 " --> pdb=" O TYR J 877 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 790 through 795 removed outlier: 3.515A pdb=" N CYS I 795 " --> pdb=" O VAL I 851 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN I 831 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL I 823 " --> pdb=" O ASN I 831 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 821 " --> pdb=" O TRP I 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA I 870 " --> pdb=" O TYR I 877 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 830 through 832 removed outlier: 3.633A pdb=" N ASN I 831 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL I 823 " --> pdb=" O ASN I 831 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 821 " --> pdb=" O TRP I 809 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1236 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: 2.27 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2844 1.34 - 1.46: 1129 1.46 - 1.58: 3873 1.58 - 1.70: 0 1.70 - 1.81: 48 Bond restraints: 7894 Sorted by residual: bond pdb=" N LEU E 115 " pdb=" CA LEU E 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.78e+00 bond pdb=" N LEU K 115 " pdb=" CA LEU K 115 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.74e+00 bond pdb=" N ARG K 114 " pdb=" CA ARG K 114 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.71e+00 bond pdb=" N ARG E 114 " pdb=" CA ARG E 114 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.46e+00 bond pdb=" N ALA K 113 " pdb=" CA ALA K 113 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.69e+00 ... (remaining 7889 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.51: 73 106.51 - 113.39: 4341 113.39 - 120.27: 3026 120.27 - 127.15: 3132 127.15 - 134.03: 34 Bond angle restraints: 10606 Sorted by residual: angle pdb=" N GLY I 803 " pdb=" CA GLY I 803 " pdb=" C GLY I 803 " ideal model delta sigma weight residual 113.18 106.21 6.97 2.37e+00 1.78e-01 8.65e+00 angle pdb=" N GLY C 803 " pdb=" CA GLY C 803 " pdb=" C GLY C 803 " ideal model delta sigma weight residual 113.18 106.25 6.93 2.37e+00 1.78e-01 8.55e+00 angle pdb=" N ALA C 864 " pdb=" CA ALA C 864 " pdb=" C ALA C 864 " ideal model delta sigma weight residual 107.88 111.58 -3.70 1.41e+00 5.03e-01 6.88e+00 angle pdb=" CA ARG K 99 " pdb=" CB ARG K 99 " pdb=" CG ARG K 99 " ideal model delta sigma weight residual 114.10 119.33 -5.23 2.00e+00 2.50e-01 6.85e+00 angle pdb=" N ALA I 864 " pdb=" CA ALA I 864 " pdb=" C ALA I 864 " ideal model delta sigma weight residual 107.88 111.56 -3.68 1.41e+00 5.03e-01 6.82e+00 ... (remaining 10601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4412 17.76 - 35.52: 412 35.52 - 53.27: 88 53.27 - 71.03: 12 71.03 - 88.79: 18 Dihedral angle restraints: 4942 sinusoidal: 2012 harmonic: 2930 Sorted by residual: dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.66 45.34 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 47.67 45.33 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA ILE D 804 " pdb=" C ILE D 804 " pdb=" N ASN D 805 " pdb=" CA ASN D 805 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 683 0.028 - 0.057: 311 0.057 - 0.085: 126 0.085 - 0.114: 46 0.114 - 0.142: 26 Chirality restraints: 1192 Sorted by residual: chirality pdb=" CA LEU E 115 " pdb=" N LEU E 115 " pdb=" C LEU E 115 " pdb=" CB LEU E 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASN J 857 " pdb=" N ASN J 857 " pdb=" C ASN J 857 " pdb=" CB ASN J 857 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA LEU K 115 " pdb=" N LEU K 115 " pdb=" C LEU K 115 " pdb=" CB LEU K 115 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 1189 not shown) Planarity restraints: 1416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 827 " -0.015 2.00e-02 2.50e+03 9.58e-03 2.29e+00 pdb=" CG TRP D 827 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP D 827 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 827 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 827 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 827 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 827 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 827 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 827 " 0.015 2.00e-02 2.50e+03 9.38e-03 2.20e+00 pdb=" CG TRP J 827 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP J 827 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP J 827 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 827 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP J 827 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 827 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 827 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 827 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 809 " -0.013 2.00e-02 2.50e+03 9.04e-03 2.04e+00 pdb=" CG TRP I 809 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 809 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP I 809 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP I 809 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 809 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 809 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 809 " 0.001 2.00e-02 2.50e+03 ... (remaining 1413 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 309 2.70 - 3.25: 8455 3.25 - 3.80: 11709 3.80 - 4.35: 15177 4.35 - 4.90: 23284 Nonbonded interactions: 58934 Sorted by model distance: nonbonded pdb=" OE1 GLN J 883 " pdb=" OG1 THR J 885 " model vdw 2.153 2.440 nonbonded pdb=" OE1 GLN D 883 " pdb=" OG1 THR D 885 " model vdw 2.153 2.440 nonbonded pdb=" O LEU C 791 " pdb=" NE2 GLN C 854 " model vdw 2.157 2.520 nonbonded pdb=" O LEU I 791 " pdb=" NE2 GLN I 854 " model vdw 2.157 2.520 nonbonded pdb=" O LEU K 160 " pdb=" OG SER K 163 " model vdw 2.157 2.440 ... (remaining 58929 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 'G' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'E' and resid 96 through 154) selection = chain 'F' selection = (chain 'K' and resid 96 through 154) 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.590 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 25.730 Find NCS groups from input model: 0.550 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5120 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 : 0.004 0.033 7894 Z= 0.263 Angle : 0.743 8.610 10606 Z= 0.446 Chirality : 0.042 0.142 1192 Planarity : 0.003 0.029 1416 Dihedral : 15.273 88.790 3022 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 0.25 % Allowed : 0.25 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.24), residues: 978 helix: -2.28 (0.20), residues: 504 sheet: -2.15 (0.40), residues: 166 loop : -1.97 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP D 827 HIS 0.002 0.001 HIS H 406 PHE 0.010 0.003 PHE D 840 TYR 0.019 0.002 TYR C 872 ARG 0.020 0.001 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 256 time to evaluate : 0.914 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 outliers start: 2 outliers final: 0 residues processed: 256 average time/residue: 0.3337 time to fit residues: 102.5081 Evaluate side-chains 189 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 805 ASN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7894 Z= 0.273 Angle : 0.744 9.286 10606 Z= 0.389 Chirality : 0.045 0.169 1192 Planarity : 0.006 0.053 1416 Dihedral : 5.860 25.534 1126 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.12 % Allowed : 6.72 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.26), residues: 978 helix: -1.01 (0.22), residues: 514 sheet: -2.86 (0.45), residues: 108 loop : -1.56 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP J 827 HIS 0.010 0.005 HIS H 406 PHE 0.011 0.002 PHE J 840 TYR 0.018 0.002 TYR I 872 ARG 0.008 0.001 ARG K 128 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.023 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 outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.3071 time to fit residues: 82.9430 Evaluate side-chains 190 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 GLN H 387 GLN L 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7894 Z= 0.276 Angle : 0.739 7.523 10606 Z= 0.387 Chirality : 0.044 0.173 1192 Planarity : 0.005 0.053 1416 Dihedral : 5.923 26.052 1126 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.25 % Allowed : 6.22 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.27), residues: 978 helix: -0.68 (0.23), residues: 504 sheet: -3.33 (0.43), residues: 110 loop : -1.08 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 827 HIS 0.010 0.005 HIS G 406 PHE 0.007 0.002 PHE J 840 TYR 0.021 0.002 TYR C 866 ARG 0.011 0.001 ARG C 811 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 219 time to evaluate : 0.897 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 outliers start: 2 outliers final: 1 residues processed: 221 average time/residue: 0.3086 time to fit residues: 82.8960 Evaluate side-chains 187 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 0.903 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0972 time to fit residues: 1.4371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 ASN C 805 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7894 Z= 0.206 Angle : 0.654 7.741 10606 Z= 0.341 Chirality : 0.042 0.176 1192 Planarity : 0.004 0.043 1416 Dihedral : 5.471 25.200 1126 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.27), residues: 978 helix: -0.33 (0.23), residues: 494 sheet: -3.13 (0.43), residues: 110 loop : -0.92 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 827 HIS 0.006 0.003 HIS H 406 PHE 0.004 0.001 PHE I 840 TYR 0.015 0.002 TYR C 866 ARG 0.010 0.001 ARG J 818 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.916 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 outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2982 time to fit residues: 79.5051 Evaluate side-chains 197 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.3980 chunk 1 optimal weight: 0.0030 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.0270 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 overall best weight: 0.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 moved from start: 0.6822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7894 Z= 0.167 Angle : 0.627 7.517 10606 Z= 0.329 Chirality : 0.041 0.179 1192 Planarity : 0.004 0.048 1416 Dihedral : 5.120 23.394 1126 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.12 % Allowed : 2.61 % Favored : 97.26 % 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: -1.26 (0.27), residues: 978 helix: -0.03 (0.23), residues: 500 sheet: -2.69 (0.37), residues: 160 loop : -0.81 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 878 HIS 0.003 0.002 HIS B 406 PHE 0.002 0.001 PHE I 840 TYR 0.021 0.001 TYR C 866 ARG 0.007 0.001 ARG J 818 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 0.921 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 outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.3199 time to fit residues: 84.1659 Evaluate side-chains 186 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 GLN ** J 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5474 moved from start: 0.7169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7894 Z= 0.214 Angle : 0.658 8.517 10606 Z= 0.348 Chirality : 0.042 0.176 1192 Planarity : 0.004 0.044 1416 Dihedral : 5.235 25.376 1126 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.27), residues: 978 helix: -0.13 (0.23), residues: 510 sheet: -2.14 (0.42), residues: 134 loop : -1.13 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 809 HIS 0.007 0.003 HIS G 406 PHE 0.003 0.001 PHE I 840 TYR 0.022 0.002 TYR C 866 ARG 0.009 0.001 ARG C 811 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.917 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 outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2991 time to fit residues: 74.3891 Evaluate side-chains 178 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.839 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 0.1980 chunk 90 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 831 ASN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5449 moved from start: 0.7458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7894 Z= 0.190 Angle : 0.657 8.762 10606 Z= 0.344 Chirality : 0.042 0.168 1192 Planarity : 0.004 0.035 1416 Dihedral : 5.145 25.115 1126 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.12 % Allowed : 1.12 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.27), residues: 978 helix: 0.08 (0.23), residues: 500 sheet: -1.91 (0.43), residues: 122 loop : -1.22 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 809 HIS 0.005 0.002 HIS H 406 PHE 0.002 0.001 PHE I 840 TYR 0.011 0.001 TYR C 866 ARG 0.008 0.001 ARG B 380 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 0.973 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 outliers start: 1 outliers final: 0 residues processed: 200 average time/residue: 0.3109 time to fit residues: 75.7898 Evaluate side-chains 175 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 0.0670 chunk 17 optimal weight: 0.5980 chunk 57 optimal weight: 0.4980 chunk 61 optimal weight: 0.0470 chunk 44 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 805 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 805 ASN I 857 ASN L 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5399 moved from start: 0.7776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7894 Z= 0.177 Angle : 0.668 8.812 10606 Z= 0.348 Chirality : 0.041 0.186 1192 Planarity : 0.003 0.034 1416 Dihedral : 4.862 23.788 1126 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -0.96 (0.27), residues: 978 helix: 0.13 (0.24), residues: 502 sheet: -1.76 (0.44), residues: 122 loop : -1.15 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 809 HIS 0.003 0.002 HIS H 406 PHE 0.003 0.001 PHE J 840 TYR 0.015 0.001 TYR C 13 ARG 0.006 0.001 ARG K 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.952 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 outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3117 time to fit residues: 73.3144 Evaluate side-chains 174 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 0.892 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 0.0670 chunk 54 optimal weight: 0.6980 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 831 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5433 moved from start: 0.8047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7894 Z= 0.195 Angle : 0.693 8.685 10606 Z= 0.365 Chirality : 0.042 0.227 1192 Planarity : 0.005 0.081 1416 Dihedral : 4.977 24.961 1126 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.12 % Allowed : 1.12 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.27), residues: 978 helix: 0.02 (0.23), residues: 512 sheet: -1.75 (0.43), residues: 126 loop : -1.25 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP J 809 HIS 0.005 0.002 HIS H 406 PHE 0.003 0.001 PHE D 840 TYR 0.018 0.001 TYR C 810 ARG 0.012 0.001 ARG C 811 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 0.829 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 outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.3092 time to fit residues: 74.6949 Evaluate side-chains 173 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0787 time to fit residues: 1.4442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 74 optimal weight: 0.0000 chunk 7 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 0.0050 chunk 59 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 831 ASN I 805 ASN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5411 moved from start: 0.8265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7894 Z= 0.194 Angle : 0.714 8.993 10606 Z= 0.374 Chirality : 0.043 0.202 1192 Planarity : 0.004 0.060 1416 Dihedral : 4.972 25.490 1126 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.12 % Allowed : 0.12 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.27), residues: 978 helix: -0.07 (0.23), residues: 512 sheet: -1.41 (0.42), residues: 146 loop : -1.25 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 827 HIS 0.004 0.002 HIS H 406 PHE 0.003 0.001 PHE J 840 TYR 0.010 0.001 TYR C 13 ARG 0.011 0.001 ARG E 128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.014 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 outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.3047 time to fit residues: 72.6311 Evaluate side-chains 179 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.947 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 74 optimal weight: 0.0050 chunk 31 optimal weight: 0.0030 chunk 76 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 overall best weight: 0.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 805 ASN ** L 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.207197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.189529 restraints weight = 13116.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.188732 restraints weight = 14247.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.186978 restraints weight = 13420.368| |-----------------------------------------------------------------------------| r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5518 moved from start: 0.8482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7894 Z= 0.177 Angle : 0.681 8.975 10606 Z= 0.356 Chirality : 0.042 0.194 1192 Planarity : 0.005 0.052 1416 Dihedral : 4.719 24.466 1126 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.27), residues: 978 helix: -0.01 (0.23), residues: 512 sheet: -1.27 (0.42), residues: 146 loop : -1.27 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 809 HIS 0.003 0.001 HIS H 406 PHE 0.002 0.001 PHE I 840 TYR 0.012 0.001 TYR D 13 ARG 0.012 0.001 ARG D 873 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2192.60 seconds wall clock time: 40 minutes 21.28 seconds (2421.28 seconds total)