Starting phenix.real_space_refine on Mon Mar 11 09:21:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/03_2024/8afm_15402.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/03_2024/8afm_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_15402/03_2024/8afm_15402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/03_2024/8afm_15402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/03_2024/8afm_15402.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8afm_15402/03_2024/8afm_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.94, per 1000 atoms: 0.63 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: 2.86 Conformation dependent library (CDL) restraints added in 1.4 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: 0.95 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: 2.12 Time building geometry restraints manager: 3.13 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: 0.720 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: 0.010 Extract box with map and model: 3.560 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 24.710 Find NCS groups from input model: 0.520 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.540 ------------------------------------------------------------------------------- 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 : 0.966 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: B 375 GLU cc_start: 0.6981 (mm-30) cc_final: 0.5861 (mt-10) REVERT: B 419 ARG cc_start: 0.4921 (tpp80) cc_final: 0.4551 (tpp80) REVERT: D 820 MET cc_start: 0.5763 (mpp) cc_final: 0.5553 (mpp) REVERT: D 877 TYR cc_start: 0.5320 (m-80) cc_final: 0.4962 (m-80) REVERT: C 6 GLU cc_start: 0.6366 (tm-30) cc_final: 0.5971 (pt0) REVERT: C 798 SER cc_start: 0.8393 (t) cc_final: 0.7858 (m) REVERT: C 806 ILE cc_start: 0.7215 (tp) cc_final: 0.7013 (tp) REVERT: C 827 TRP cc_start: 0.6154 (m-90) cc_final: 0.4380 (m-90) REVERT: C 841 ILE cc_start: 0.7607 (mp) cc_final: 0.7345 (mm) REVERT: E 148 ASN cc_start: 0.8067 (m-40) cc_final: 0.7745 (t0) REVERT: F 108 GLU cc_start: 0.6685 (tp30) cc_final: 0.6201 (tp30) REVERT: F 133 ASP cc_start: 0.8257 (m-30) cc_final: 0.7702 (m-30) REVERT: F 136 LEU cc_start: 0.6453 (tp) cc_final: 0.6159 (mt) REVERT: F 139 ASN cc_start: 0.7392 (p0) cc_final: 0.7136 (p0) REVERT: G 395 MET cc_start: 0.5819 (mmm) cc_final: 0.5346 (ttt) REVERT: G 423 GLU cc_start: 0.7778 (tt0) cc_final: 0.7129 (tm-30) REVERT: G 438 ARG cc_start: 0.5662 (ptt-90) cc_final: 0.3368 (mmp-170) REVERT: J 807 MET cc_start: 0.3696 (ppp) cc_final: 0.2786 (ppp) REVERT: J 820 MET cc_start: 0.5423 (mpp) cc_final: 0.4849 (mpp) REVERT: I 807 MET cc_start: 0.6350 (ppp) cc_final: 0.5998 (ppp) REVERT: I 884 VAL cc_start: 0.7868 (t) cc_final: 0.5549 (t) REVERT: L 107 GLU cc_start: 0.7886 (tp30) cc_final: 0.7665 (mm-30) outliers start: 2 outliers final: 0 residues processed: 256 average time/residue: 0.3292 time to fit residues: 101.2008 Evaluate side-chains 191 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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: 0.9990 chunk 71 optimal weight: 8.9990 chunk 39 optimal weight: 0.0470 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN C 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5358 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7894 Z= 0.244 Angle : 0.719 9.214 10606 Z= 0.374 Chirality : 0.044 0.175 1192 Planarity : 0.005 0.048 1416 Dihedral : 5.770 24.995 1126 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.28 % 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: -2.17 (0.26), residues: 978 helix: -0.92 (0.22), residues: 520 sheet: -2.85 (0.44), residues: 112 loop : -1.48 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP J 827 HIS 0.007 0.004 HIS H 406 PHE 0.011 0.002 PHE J 840 TYR 0.020 0.002 TYR I 872 ARG 0.006 0.001 ARG A 419 *********************** 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 226 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 0.959 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: A 375 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7138 (mm-30) REVERT: A 393 ASP cc_start: 0.6345 (m-30) cc_final: 0.6121 (m-30) REVERT: D 802 ASP cc_start: 0.4416 (t0) cc_final: 0.3763 (t0) REVERT: D 812 GLN cc_start: 0.5489 (mp10) cc_final: 0.4577 (mp10) REVERT: D 839 ARG cc_start: 0.5204 (ttt-90) cc_final: 0.4996 (mtp180) REVERT: D 850 THR cc_start: 0.6385 (m) cc_final: 0.5971 (t) REVERT: D 873 ARG cc_start: 0.5987 (mpp-170) cc_final: 0.5646 (mpp-170) REVERT: D 877 TYR cc_start: 0.5924 (m-80) cc_final: 0.5381 (m-80) REVERT: C 793 LEU cc_start: 0.6410 (mm) cc_final: 0.5724 (mt) REVERT: C 798 SER cc_start: 0.8491 (t) cc_final: 0.8270 (m) REVERT: C 802 ASP cc_start: 0.6669 (t0) cc_final: 0.6192 (t0) REVERT: C 806 ILE cc_start: 0.7561 (tp) cc_final: 0.7353 (tp) REVERT: C 825 THR cc_start: 0.6329 (OUTLIER) cc_final: 0.5495 (m) REVERT: E 145 ARG cc_start: 0.6164 (mtt180) cc_final: 0.5952 (mtt180) REVERT: F 108 GLU cc_start: 0.7138 (tp30) cc_final: 0.6425 (tp30) REVERT: F 115 LEU cc_start: 0.8238 (mm) cc_final: 0.7958 (mm) REVERT: F 133 ASP cc_start: 0.7920 (m-30) cc_final: 0.7635 (m-30) REVERT: F 142 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6615 (tp30) REVERT: F 144 ASP cc_start: 0.6522 (m-30) cc_final: 0.6043 (m-30) REVERT: H 370 SER cc_start: 0.6915 (t) cc_final: 0.6632 (m) REVERT: J 807 MET cc_start: 0.3988 (ppp) cc_final: 0.3254 (ppp) REVERT: J 820 MET cc_start: 0.5619 (mpp) cc_final: 0.4863 (mpp) REVERT: J 878 TRP cc_start: 0.5225 (m100) cc_final: 0.4937 (m100) REVERT: I 807 MET cc_start: 0.6223 (ppp) cc_final: 0.5663 (ppp) REVERT: I 810 TYR cc_start: 0.6028 (m-80) cc_final: 0.5722 (m-80) REVERT: I 823 VAL cc_start: 0.7485 (p) cc_final: 0.7177 (p) REVERT: I 857 ASN cc_start: 0.7927 (t0) cc_final: 0.7642 (t0) REVERT: I 884 VAL cc_start: 0.7508 (t) cc_final: 0.5907 (t) REVERT: K 128 ARG cc_start: 0.6034 (ptt90) cc_final: 0.5747 (ptt90) REVERT: K 148 ASN cc_start: 0.7625 (t0) cc_final: 0.7364 (t0) REVERT: K 156 LYS cc_start: 0.7344 (mtmt) cc_final: 0.7129 (mtmm) REVERT: L 107 GLU cc_start: 0.8309 (tp30) cc_final: 0.7996 (mm-30) REVERT: L 115 LEU cc_start: 0.8630 (mm) cc_final: 0.8174 (mm) REVERT: L 129 ARG cc_start: 0.7565 (tmm160) cc_final: 0.7312 (ttp-110) REVERT: L 132 GLN cc_start: 0.8660 (mp-120) cc_final: 0.7734 (pp30) REVERT: L 142 GLU cc_start: 0.5924 (tm-30) cc_final: 0.5167 (tm-30) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.3068 time to fit residues: 84.2958 Evaluate side-chains 194 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** C 3 GLN C 805 ASN ** C 854 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 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7894 Z= 0.298 Angle : 0.740 7.424 10606 Z= 0.388 Chirality : 0.045 0.171 1192 Planarity : 0.005 0.056 1416 Dihedral : 5.982 29.183 1126 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.12 % Allowed : 5.85 % Favored : 94.03 % 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: -1.81 (0.27), residues: 978 helix: -0.60 (0.23), residues: 508 sheet: -3.31 (0.45), residues: 104 loop : -1.16 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 827 HIS 0.011 0.006 HIS G 406 PHE 0.009 0.002 PHE J 840 TYR 0.015 0.002 TYR D 810 ARG 0.009 0.001 ARG B 435 *********************** 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 211 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 0.944 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: A 369 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8159 (mmmt) REVERT: A 389 ARG cc_start: 0.5290 (ptp-170) cc_final: 0.4778 (ptp-170) REVERT: B 376 LYS cc_start: 0.7613 (pttm) cc_final: 0.7394 (pttt) REVERT: D 812 GLN cc_start: 0.6021 (mp10) cc_final: 0.4507 (mt0) REVERT: D 839 ARG cc_start: 0.5393 (ttt-90) cc_final: 0.4861 (mtp180) REVERT: D 850 THR cc_start: 0.6311 (m) cc_final: 0.5745 (t) REVERT: D 877 TYR cc_start: 0.6056 (m-80) cc_final: 0.5797 (m-80) REVERT: C 798 SER cc_start: 0.8567 (t) cc_final: 0.8307 (m) REVERT: C 802 ASP cc_start: 0.6880 (t0) cc_final: 0.6380 (t0) REVERT: C 825 THR cc_start: 0.7873 (m) cc_final: 0.7448 (m) REVERT: C 856 ASN cc_start: 0.7840 (t0) cc_final: 0.7516 (t0) REVERT: C 880 GLN cc_start: 0.5668 (OUTLIER) cc_final: 0.4310 (mp10) REVERT: E 152 GLN cc_start: 0.6282 (mm-40) cc_final: 0.6055 (mm-40) REVERT: F 107 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6693 (mm-30) REVERT: F 108 GLU cc_start: 0.7119 (tp30) cc_final: 0.6385 (tp30) REVERT: F 142 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7007 (tp30) REVERT: F 144 ASP cc_start: 0.6636 (m-30) cc_final: 0.6293 (m-30) REVERT: G 375 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6078 (mt-10) REVERT: I 807 MET cc_start: 0.6573 (ppp) cc_final: 0.6061 (ppp) REVERT: I 808 ARG cc_start: 0.6411 (ptt180) cc_final: 0.6022 (ptt90) REVERT: I 810 TYR cc_start: 0.6364 (m-80) cc_final: 0.6142 (m-80) REVERT: I 823 VAL cc_start: 0.7519 (p) cc_final: 0.7261 (p) REVERT: I 884 VAL cc_start: 0.7729 (t) cc_final: 0.6474 (t) REVERT: I 886 VAL cc_start: 0.7048 (p) cc_final: 0.6790 (t) REVERT: K 156 LYS cc_start: 0.7922 (mtmt) cc_final: 0.7704 (mtmm) REVERT: L 107 GLU cc_start: 0.8745 (tp30) cc_final: 0.8036 (mm-30) REVERT: L 115 LEU cc_start: 0.8721 (mm) cc_final: 0.8218 (mm) REVERT: L 131 THR cc_start: 0.8166 (p) cc_final: 0.7894 (p) REVERT: L 132 GLN cc_start: 0.8735 (mp-120) cc_final: 0.8210 (pp30) REVERT: L 142 GLU cc_start: 0.6507 (tm-30) cc_final: 0.6064 (tm-30) outliers start: 1 outliers final: 0 residues processed: 211 average time/residue: 0.3058 time to fit residues: 79.3929 Evaluate side-chains 190 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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: 0.7980 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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 374 GLN ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 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 387 GLN L 100 GLN L 130 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: 0.5454 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7894 Z= 0.189 Angle : 0.618 10.169 10606 Z= 0.321 Chirality : 0.041 0.144 1192 Planarity : 0.004 0.038 1416 Dihedral : 5.266 25.247 1126 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: -1.41 (0.27), residues: 978 helix: -0.25 (0.23), residues: 500 sheet: -2.63 (0.40), residues: 148 loop : -0.87 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 827 HIS 0.006 0.003 HIS H 406 PHE 0.004 0.001 PHE I 840 TYR 0.011 0.001 TYR I 832 ARG 0.008 0.001 ARG D 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 220 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.793 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: A 389 ARG cc_start: 0.4945 (ptp-170) cc_final: 0.4582 (ptp-170) REVERT: B 375 GLU cc_start: 0.7322 (tp30) cc_final: 0.6783 (tm-30) REVERT: B 376 LYS cc_start: 0.7382 (pttm) cc_final: 0.7095 (pttt) REVERT: D 812 GLN cc_start: 0.5347 (mp10) cc_final: 0.4460 (mt0) REVERT: D 839 ARG cc_start: 0.5372 (ttt-90) cc_final: 0.4921 (mtp180) REVERT: D 850 THR cc_start: 0.5821 (m) cc_final: 0.5293 (t) REVERT: D 873 ARG cc_start: 0.6147 (mpp-170) cc_final: 0.5880 (mpp80) REVERT: C 798 SER cc_start: 0.8377 (t) cc_final: 0.8164 (m) REVERT: C 832 TYR cc_start: 0.7293 (m-80) cc_final: 0.7057 (m-10) REVERT: C 841 ILE cc_start: 0.7411 (mm) cc_final: 0.7191 (mm) REVERT: C 856 ASN cc_start: 0.7792 (t0) cc_final: 0.7505 (t0) REVERT: E 145 ARG cc_start: 0.6981 (mtt180) cc_final: 0.6656 (mtt180) REVERT: E 152 GLN cc_start: 0.5980 (mm-40) cc_final: 0.5713 (mm-40) REVERT: E 156 LYS cc_start: 0.2884 (mptt) cc_final: 0.2455 (tttt) REVERT: F 107 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6735 (mm-30) REVERT: F 108 GLU cc_start: 0.7034 (tp30) cc_final: 0.6278 (tp30) REVERT: F 115 LEU cc_start: 0.8387 (mm) cc_final: 0.8046 (mm) REVERT: F 124 GLU cc_start: 0.8460 (pp20) cc_final: 0.8177 (pp20) REVERT: F 133 ASP cc_start: 0.7776 (m-30) cc_final: 0.7540 (m-30) REVERT: F 144 ASP cc_start: 0.6581 (m-30) cc_final: 0.6196 (m-30) REVERT: G 389 ARG cc_start: 0.6232 (ptm160) cc_final: 0.5748 (ptm-80) REVERT: J 807 MET cc_start: 0.4362 (ppp) cc_final: 0.3532 (ppp) REVERT: J 820 MET cc_start: 0.5632 (mpp) cc_final: 0.4682 (mpp) REVERT: J 869 ASN cc_start: 0.4387 (t0) cc_final: 0.3848 (t0) REVERT: J 878 TRP cc_start: 0.5367 (m100) cc_final: 0.4442 (m100) REVERT: I 807 MET cc_start: 0.6725 (ppp) cc_final: 0.6391 (ppp) REVERT: I 820 MET cc_start: 0.6425 (ptm) cc_final: 0.5641 (ppp) REVERT: I 884 VAL cc_start: 0.7712 (t) cc_final: 0.6357 (t) REVERT: I 886 VAL cc_start: 0.6860 (p) cc_final: 0.6563 (t) REVERT: K 126 ASP cc_start: 0.6980 (p0) cc_final: 0.6682 (p0) REVERT: K 156 LYS cc_start: 0.7963 (mtmt) cc_final: 0.7749 (mtmm) REVERT: L 105 GLN cc_start: 0.6745 (tm-30) cc_final: 0.6138 (tm-30) REVERT: L 107 GLU cc_start: 0.8811 (tp30) cc_final: 0.7800 (mm-30) REVERT: L 115 LEU cc_start: 0.8731 (mm) cc_final: 0.8204 (mm) REVERT: L 131 THR cc_start: 0.8446 (p) cc_final: 0.8162 (p) REVERT: L 132 GLN cc_start: 0.8717 (mp-120) cc_final: 0.8099 (pp30) REVERT: L 142 GLU cc_start: 0.6319 (tm-30) cc_final: 0.6063 (tm-30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2901 time to fit residues: 78.6178 Evaluate side-chains 199 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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: 0.7980 chunk 1 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 HIS ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN J 831 ASN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5466 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7894 Z= 0.187 Angle : 0.625 8.431 10606 Z= 0.325 Chirality : 0.041 0.151 1192 Planarity : 0.004 0.055 1416 Dihedral : 5.241 24.320 1126 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.37 % Allowed : 3.11 % Favored : 96.52 % 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 (0.28), residues: 978 helix: -0.04 (0.23), residues: 498 sheet: -2.61 (0.42), residues: 130 loop : -0.73 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 827 HIS 0.005 0.003 HIS B 406 PHE 0.004 0.001 PHE I 840 TYR 0.013 0.001 TYR D 810 ARG 0.007 0.001 ARG D 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 214 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 0.965 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: A 375 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6066 (mm-30) REVERT: A 389 ARG cc_start: 0.4889 (ptp-170) cc_final: 0.4565 (ptp-170) REVERT: B 375 GLU cc_start: 0.7227 (tp30) cc_final: 0.6875 (tm-30) REVERT: B 379 LYS cc_start: 0.6915 (mmmm) cc_final: 0.6627 (tppt) REVERT: B 387 GLN cc_start: 0.7677 (pt0) cc_final: 0.7400 (pp30) REVERT: D 812 GLN cc_start: 0.5702 (mp10) cc_final: 0.4274 (mt0) REVERT: D 839 ARG cc_start: 0.5483 (ttt-90) cc_final: 0.4962 (mtp180) REVERT: D 850 THR cc_start: 0.5840 (m) cc_final: 0.5114 (t) REVERT: C 793 LEU cc_start: 0.6519 (mm) cc_final: 0.6017 (mt) REVERT: C 825 THR cc_start: 0.7905 (m) cc_final: 0.7420 (m) REVERT: C 841 ILE cc_start: 0.7435 (mm) cc_final: 0.7184 (mm) REVERT: C 856 ASN cc_start: 0.7852 (t0) cc_final: 0.7626 (t0) REVERT: E 152 GLN cc_start: 0.5895 (mm-40) cc_final: 0.5676 (mm-40) REVERT: E 156 LYS cc_start: 0.2965 (mptt) cc_final: 0.2538 (tttt) REVERT: F 100 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7361 (mm-40) REVERT: F 107 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6589 (mm-30) REVERT: F 108 GLU cc_start: 0.7049 (tp30) cc_final: 0.6281 (tp30) REVERT: F 124 GLU cc_start: 0.8452 (pp20) cc_final: 0.8186 (pp20) REVERT: F 144 ASP cc_start: 0.6751 (m-30) cc_final: 0.6322 (m-30) REVERT: G 389 ARG cc_start: 0.6059 (ptm160) cc_final: 0.5721 (ptm-80) REVERT: G 395 MET cc_start: 0.4664 (ttt) cc_final: 0.4421 (ttt) REVERT: G 422 SER cc_start: 0.4376 (p) cc_final: 0.4080 (p) REVERT: H 372 VAL cc_start: 0.7196 (m) cc_final: 0.6995 (m) REVERT: J 807 MET cc_start: 0.4237 (ppp) cc_final: 0.3184 (ppp) REVERT: J 820 MET cc_start: 0.5489 (mpp) cc_final: 0.4828 (mpp) REVERT: J 839 ARG cc_start: 0.7284 (tpt170) cc_final: 0.7077 (tpt-90) REVERT: J 869 ASN cc_start: 0.4892 (t0) cc_final: 0.4418 (t0) REVERT: J 878 TRP cc_start: 0.5430 (m100) cc_final: 0.4498 (m100) REVERT: I 802 ASP cc_start: 0.6300 (t0) cc_final: 0.5635 (t0) REVERT: I 884 VAL cc_start: 0.7674 (t) cc_final: 0.7432 (t) REVERT: L 105 GLN cc_start: 0.6904 (tm-30) cc_final: 0.6296 (tm-30) REVERT: L 107 GLU cc_start: 0.8232 (tp30) cc_final: 0.8025 (mm-30) REVERT: L 115 LEU cc_start: 0.8639 (mm) cc_final: 0.8137 (mm) REVERT: L 132 GLN cc_start: 0.8712 (mp-120) cc_final: 0.8137 (pp30) REVERT: L 142 GLU cc_start: 0.6412 (tm-30) cc_final: 0.6205 (tm-30) outliers start: 3 outliers final: 0 residues processed: 214 average time/residue: 0.3130 time to fit residues: 81.4622 Evaluate side-chains 189 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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: 0.6980 chunk 17 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 100 GLN ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN L 100 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5478 moved from start: 0.7089 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= 0.197 Angle : 0.655 10.041 10606 Z= 0.342 Chirality : 0.042 0.141 1192 Planarity : 0.004 0.038 1416 Dihedral : 5.132 24.985 1126 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % 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: -1.35 (0.27), residues: 978 helix: -0.21 (0.23), residues: 508 sheet: -2.28 (0.39), residues: 168 loop : -0.87 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 827 HIS 0.006 0.003 HIS H 406 PHE 0.003 0.001 PHE I 840 TYR 0.014 0.001 TYR J 832 ARG 0.009 0.001 ARG D 818 *********************** 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 209 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.713 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: A 389 ARG cc_start: 0.4953 (ptp-170) cc_final: 0.4632 (ptp-170) REVERT: B 375 GLU cc_start: 0.7208 (tp30) cc_final: 0.6813 (tm-30) REVERT: B 379 LYS cc_start: 0.7003 (mmmm) cc_final: 0.6655 (tppt) REVERT: B 387 GLN cc_start: 0.7767 (pt0) cc_final: 0.7446 (pp30) REVERT: D 11 LEU cc_start: 0.6681 (mm) cc_final: 0.6477 (mm) REVERT: D 812 GLN cc_start: 0.5214 (mp10) cc_final: 0.4151 (mt0) REVERT: D 839 ARG cc_start: 0.5513 (ttt-90) cc_final: 0.4972 (mtp180) REVERT: D 850 THR cc_start: 0.5774 (m) cc_final: 0.5024 (t) REVERT: C 820 MET cc_start: 0.6596 (ppp) cc_final: 0.6389 (ppp) REVERT: C 825 THR cc_start: 0.7932 (m) cc_final: 0.7483 (m) REVERT: E 152 GLN cc_start: 0.5871 (mm-40) cc_final: 0.5624 (mm-40) REVERT: E 156 LYS cc_start: 0.2986 (mptt) cc_final: 0.2517 (tttt) REVERT: F 107 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6490 (mm-30) REVERT: F 108 GLU cc_start: 0.7072 (tp30) cc_final: 0.6466 (tp30) REVERT: F 115 LEU cc_start: 0.8568 (mm) cc_final: 0.8247 (mm) REVERT: F 133 ASP cc_start: 0.7955 (m-30) cc_final: 0.7477 (m-30) REVERT: F 144 ASP cc_start: 0.6826 (m-30) cc_final: 0.6441 (m-30) REVERT: G 389 ARG cc_start: 0.6145 (ptm160) cc_final: 0.5760 (ptm-80) REVERT: J 807 MET cc_start: 0.4608 (ppp) cc_final: 0.3602 (ppp) REVERT: J 820 MET cc_start: 0.5411 (mpp) cc_final: 0.4695 (mpp) REVERT: J 869 ASN cc_start: 0.4945 (t0) cc_final: 0.4472 (t0) REVERT: J 878 TRP cc_start: 0.5502 (m100) cc_final: 0.4681 (m100) REVERT: I 807 MET cc_start: 0.6583 (ppp) cc_final: 0.6368 (ppp) REVERT: I 817 GLN cc_start: 0.8230 (pm20) cc_final: 0.8008 (pm20) REVERT: I 823 VAL cc_start: 0.7371 (p) cc_final: 0.7150 (p) REVERT: I 857 ASN cc_start: 0.7693 (t0) cc_final: 0.7382 (t0) REVERT: I 866 TYR cc_start: 0.5348 (m-80) cc_final: 0.5138 (m-80) REVERT: I 883 GLN cc_start: 0.5387 (tt0) cc_final: 0.4992 (tt0) REVERT: I 884 VAL cc_start: 0.7710 (t) cc_final: 0.7354 (t) REVERT: L 105 GLN cc_start: 0.6733 (tm-30) cc_final: 0.6458 (tm-30) REVERT: L 119 GLU cc_start: 0.8562 (pp20) cc_final: 0.8075 (pp20) REVERT: L 132 GLN cc_start: 0.8614 (mp-120) cc_final: 0.7940 (pp30) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2861 time to fit residues: 73.5598 Evaluate side-chains 186 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 41 optimal weight: 0.0170 chunk 36 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5430 moved from start: 0.7376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7894 Z= 0.164 Angle : 0.606 9.831 10606 Z= 0.315 Chirality : 0.041 0.141 1192 Planarity : 0.004 0.031 1416 Dihedral : 4.837 23.488 1126 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % 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: -1.10 (0.28), residues: 978 helix: 0.03 (0.23), residues: 512 sheet: -1.89 (0.37), residues: 188 loop : -0.95 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 827 HIS 0.004 0.002 HIS H 406 PHE 0.004 0.001 PHE C 840 TYR 0.012 0.001 TYR D 810 ARG 0.006 0.001 ARG D 818 *********************** 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 204 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.035 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: A 389 ARG cc_start: 0.4884 (ptp-170) cc_final: 0.4538 (ptp-170) REVERT: B 375 GLU cc_start: 0.7153 (tp30) cc_final: 0.6886 (tm-30) REVERT: B 379 LYS cc_start: 0.6962 (mmmm) cc_final: 0.6599 (tppt) REVERT: B 387 GLN cc_start: 0.7803 (pt0) cc_final: 0.7497 (pp30) REVERT: D 11 LEU cc_start: 0.6387 (mm) cc_final: 0.6173 (mm) REVERT: D 812 GLN cc_start: 0.5056 (mp10) cc_final: 0.4087 (mt0) REVERT: D 839 ARG cc_start: 0.5422 (ttt-90) cc_final: 0.4901 (mtp180) REVERT: D 850 THR cc_start: 0.5773 (m) cc_final: 0.5078 (t) REVERT: C 825 THR cc_start: 0.7880 (m) cc_final: 0.7468 (m) REVERT: C 856 ASN cc_start: 0.7997 (t0) cc_final: 0.7732 (t0) REVERT: E 128 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7635 (mmm160) REVERT: F 107 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6458 (mm-30) REVERT: F 108 GLU cc_start: 0.6966 (tp30) cc_final: 0.6220 (tp30) REVERT: F 115 LEU cc_start: 0.8520 (mm) cc_final: 0.8224 (mm) REVERT: F 132 GLN cc_start: 0.7101 (pp30) cc_final: 0.6195 (pp30) REVERT: F 133 ASP cc_start: 0.7707 (m-30) cc_final: 0.7096 (m-30) REVERT: F 144 ASP cc_start: 0.6857 (m-30) cc_final: 0.6455 (m-30) REVERT: J 807 MET cc_start: 0.4410 (ppp) cc_final: 0.3453 (ppp) REVERT: J 820 MET cc_start: 0.5238 (mpp) cc_final: 0.4588 (mpp) REVERT: J 869 ASN cc_start: 0.4697 (t0) cc_final: 0.4132 (t0) REVERT: J 878 TRP cc_start: 0.5506 (m100) cc_final: 0.4700 (m100) REVERT: I 802 ASP cc_start: 0.4986 (t0) cc_final: 0.4485 (t0) REVERT: I 817 GLN cc_start: 0.7610 (pm20) cc_final: 0.7125 (pm20) REVERT: I 857 ASN cc_start: 0.7063 (t0) cc_final: 0.6852 (m-40) REVERT: I 866 TYR cc_start: 0.4996 (m-80) cc_final: 0.4692 (m-80) REVERT: I 883 GLN cc_start: 0.5172 (tt0) cc_final: 0.4884 (tt0) REVERT: I 884 VAL cc_start: 0.7655 (t) cc_final: 0.7297 (t) REVERT: K 126 ASP cc_start: 0.7463 (m-30) cc_final: 0.7247 (p0) REVERT: L 119 GLU cc_start: 0.8513 (pp20) cc_final: 0.8212 (pp20) REVERT: L 132 GLN cc_start: 0.8633 (mp-120) cc_final: 0.8135 (pp30) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2937 time to fit residues: 73.3693 Evaluate side-chains 180 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 chunk 84 optimal weight: 0.4980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5420 moved from start: 0.7640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7894 Z= 0.165 Angle : 0.620 10.020 10606 Z= 0.322 Chirality : 0.040 0.138 1192 Planarity : 0.004 0.045 1416 Dihedral : 4.693 23.414 1126 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.27), residues: 978 helix: 0.34 (0.24), residues: 502 sheet: -1.78 (0.38), residues: 176 loop : -1.07 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 827 HIS 0.004 0.002 HIS G 406 PHE 0.003 0.001 PHE I 840 TYR 0.012 0.001 TYR D 810 ARG 0.008 0.001 ARG D 818 *********************** 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 204 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.893 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: A 389 ARG cc_start: 0.4788 (ptp-170) cc_final: 0.4489 (ptp-170) REVERT: B 375 GLU cc_start: 0.7196 (tp30) cc_final: 0.6871 (tm-30) REVERT: B 379 LYS cc_start: 0.6983 (mmmm) cc_final: 0.6587 (tppt) REVERT: B 387 GLN cc_start: 0.7897 (pt0) cc_final: 0.7410 (pp30) REVERT: D 812 GLN cc_start: 0.4998 (mp10) cc_final: 0.4208 (mt0) REVERT: D 839 ARG cc_start: 0.5543 (ttt-90) cc_final: 0.4982 (mtp180) REVERT: C 793 LEU cc_start: 0.6655 (mt) cc_final: 0.6328 (mt) REVERT: C 811 ARG cc_start: 0.4787 (ttt-90) cc_final: 0.4336 (ttp-110) REVERT: C 825 THR cc_start: 0.7999 (m) cc_final: 0.7634 (p) REVERT: E 128 ARG cc_start: 0.7835 (mtt180) cc_final: 0.7619 (mmm160) REVERT: F 107 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6402 (mm-30) REVERT: F 108 GLU cc_start: 0.6944 (tp30) cc_final: 0.6149 (tp30) REVERT: F 115 LEU cc_start: 0.8663 (mm) cc_final: 0.8269 (mm) REVERT: F 132 GLN cc_start: 0.7394 (pp30) cc_final: 0.6911 (pp30) REVERT: F 133 ASP cc_start: 0.7402 (m-30) cc_final: 0.7084 (m-30) REVERT: F 144 ASP cc_start: 0.7112 (m-30) cc_final: 0.6775 (m-30) REVERT: J 807 MET cc_start: 0.4561 (ppp) cc_final: 0.3674 (ppp) REVERT: J 820 MET cc_start: 0.5311 (mpp) cc_final: 0.4520 (mpp) REVERT: J 869 ASN cc_start: 0.4793 (t0) cc_final: 0.4214 (t0) REVERT: J 878 TRP cc_start: 0.5539 (m100) cc_final: 0.4707 (m100) REVERT: I 802 ASP cc_start: 0.4721 (t0) cc_final: 0.4135 (t0) REVERT: I 817 GLN cc_start: 0.8050 (pm20) cc_final: 0.7573 (pm20) REVERT: I 866 TYR cc_start: 0.5031 (m-80) cc_final: 0.4804 (m-80) REVERT: I 883 GLN cc_start: 0.5064 (tt0) cc_final: 0.4819 (tt0) REVERT: I 884 VAL cc_start: 0.7617 (t) cc_final: 0.7237 (t) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2919 time to fit residues: 73.0185 Evaluate side-chains 186 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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: 0.9990 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 0.0030 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 89 optimal weight: 0.1980 chunk 54 optimal weight: 0.4980 overall best weight: 0.3990 ------------------------------------------------------------------------------- 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** E 139 ASN F 105 GLN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5407 moved from start: 0.7828 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= 0.175 Angle : 0.640 9.583 10606 Z= 0.335 Chirality : 0.041 0.157 1192 Planarity : 0.004 0.056 1416 Dihedral : 4.636 23.767 1126 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -0.92 (0.28), residues: 978 helix: 0.19 (0.24), residues: 510 sheet: -1.71 (0.38), residues: 176 loop : -1.02 (0.38), residues: 292 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 C 840 TYR 0.013 0.001 TYR D 810 ARG 0.010 0.001 ARG D 818 *********************** 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 203 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.846 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: A 389 ARG cc_start: 0.4589 (ptp-170) cc_final: 0.4321 (ptp-170) REVERT: B 375 GLU cc_start: 0.7127 (tp30) cc_final: 0.6846 (tm-30) REVERT: B 379 LYS cc_start: 0.6941 (mmmm) cc_final: 0.6605 (tppt) REVERT: B 387 GLN cc_start: 0.7909 (pt0) cc_final: 0.7417 (pp30) REVERT: D 812 GLN cc_start: 0.4683 (mp10) cc_final: 0.4289 (mt0) REVERT: D 839 ARG cc_start: 0.5580 (ttt-90) cc_final: 0.5035 (mtp180) REVERT: C 825 THR cc_start: 0.8201 (m) cc_final: 0.7819 (p) REVERT: E 128 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7621 (mmm160) REVERT: F 107 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6279 (mm-30) REVERT: F 108 GLU cc_start: 0.6769 (tp30) cc_final: 0.6037 (tp30) REVERT: F 115 LEU cc_start: 0.8642 (mm) cc_final: 0.8300 (mm) REVERT: F 132 GLN cc_start: 0.7249 (pp30) cc_final: 0.6647 (pp30) REVERT: F 144 ASP cc_start: 0.7120 (m-30) cc_final: 0.6757 (m-30) REVERT: J 807 MET cc_start: 0.4538 (ppp) cc_final: 0.3753 (ppp) REVERT: J 869 ASN cc_start: 0.4777 (t0) cc_final: 0.4043 (t0) REVERT: J 878 TRP cc_start: 0.5574 (m100) cc_final: 0.4723 (m100) REVERT: I 802 ASP cc_start: 0.4260 (t0) cc_final: 0.3839 (t0) REVERT: I 817 GLN cc_start: 0.7645 (pm20) cc_final: 0.7165 (pm20) REVERT: I 884 VAL cc_start: 0.7598 (t) cc_final: 0.7283 (t) REVERT: K 100 GLN cc_start: 0.7937 (mp10) cc_final: 0.7375 (mp10) REVERT: K 128 ARG cc_start: 0.7576 (ptp90) cc_final: 0.7363 (ptt90) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.3000 time to fit residues: 74.2928 Evaluate side-chains 180 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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: 0.0070 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 74 optimal weight: 0.0030 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5431 moved from start: 0.8007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7894 Z= 0.187 Angle : 0.661 10.610 10606 Z= 0.343 Chirality : 0.042 0.153 1192 Planarity : 0.005 0.063 1416 Dihedral : 4.761 24.463 1126 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % 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: -0.94 (0.27), residues: 978 helix: 0.15 (0.23), residues: 512 sheet: -1.69 (0.38), residues: 174 loop : -1.03 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 809 HIS 0.004 0.002 HIS G 406 PHE 0.008 0.002 PHE C 840 TYR 0.014 0.001 TYR D 810 ARG 0.012 0.001 ARG D 818 ********************** 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 206 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.951 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: A 369 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7853 (mmtm) REVERT: A 389 ARG cc_start: 0.4770 (ptp-170) cc_final: 0.4528 (ptp-170) REVERT: B 375 GLU cc_start: 0.7202 (tp30) cc_final: 0.6887 (tm-30) REVERT: B 379 LYS cc_start: 0.6996 (mmmm) cc_final: 0.6603 (tppt) REVERT: B 387 GLN cc_start: 0.7925 (pt0) cc_final: 0.7366 (pp30) REVERT: D 11 LEU cc_start: 0.6480 (mm) cc_final: 0.6267 (mm) REVERT: D 812 GLN cc_start: 0.5089 (mp10) cc_final: 0.4148 (mt0) REVERT: D 837 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8325 (mmmm) REVERT: D 839 ARG cc_start: 0.5744 (ttt-90) cc_final: 0.5194 (mtp180) REVERT: C 825 THR cc_start: 0.8204 (m) cc_final: 0.7867 (p) REVERT: F 107 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6303 (mm-30) REVERT: F 108 GLU cc_start: 0.6888 (tp30) cc_final: 0.6098 (tp30) REVERT: F 115 LEU cc_start: 0.8624 (mm) cc_final: 0.8271 (mm) REVERT: F 132 GLN cc_start: 0.6814 (pp30) cc_final: 0.6143 (pp30) REVERT: F 133 ASP cc_start: 0.7509 (m-30) cc_final: 0.7271 (m-30) REVERT: F 144 ASP cc_start: 0.7134 (m-30) cc_final: 0.6904 (m-30) REVERT: G 395 MET cc_start: 0.3797 (ttt) cc_final: 0.3271 (tpp) REVERT: J 807 MET cc_start: 0.4819 (ppp) cc_final: 0.4010 (ppp) REVERT: J 869 ASN cc_start: 0.4893 (t0) cc_final: 0.4123 (t0) REVERT: J 878 TRP cc_start: 0.5551 (m100) cc_final: 0.4807 (m100) REVERT: I 817 GLN cc_start: 0.7650 (pm20) cc_final: 0.7153 (pm20) REVERT: K 152 GLN cc_start: 0.7726 (tm-30) cc_final: 0.7190 (tp40) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2957 time to fit residues: 74.7913 Evaluate side-chains 182 residues out of total 804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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: 0.0670 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 76 optimal weight: 0.0870 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN E 139 ASN ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 387 GLN ** H 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 805 ASN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.209253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 170)---------------| | r_work = 0.4520 r_free = 0.4520 target = 0.184738 restraints weight = 12991.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.184909 restraints weight = 11622.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.184981 restraints weight = 10554.971| |-----------------------------------------------------------------------------| r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 moved from start: 0.8178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7894 Z= 0.162 Angle : 0.649 10.111 10606 Z= 0.337 Chirality : 0.041 0.167 1192 Planarity : 0.004 0.057 1416 Dihedral : 4.516 23.521 1126 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % 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: -0.87 (0.27), residues: 978 helix: 0.21 (0.24), residues: 512 sheet: -1.63 (0.37), residues: 186 loop : -0.96 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 827 HIS 0.002 0.001 HIS H 406 PHE 0.006 0.001 PHE C 840 TYR 0.013 0.001 TYR D 810 ARG 0.013 0.001 ARG D 818 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2226.62 seconds wall clock time: 40 minutes 41.19 seconds (2441.19 seconds total)