Starting phenix.real_space_refine on Fri Sep 27 05:19:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/09_2024/6zqj_11366.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/09_2024/6zqj_11366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/09_2024/6zqj_11366.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/09_2024/6zqj_11366.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/09_2024/6zqj_11366.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zqj_11366/09_2024/6zqj_11366.cif" } resolution = 4.2 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= 0.000 sd= 0.007 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 129 5.16 5 C 9501 2.51 5 N 2625 2.21 5 O 2841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15096 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "B" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "D" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "G" Number of atoms: 3835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3835 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 12, 'TRANS': 491} Chain: "H" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "I" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "F" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "C" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.65, per 1000 atoms: 0.57 Number of scatterers: 15096 At special positions: 0 Unit cell: (170.69, 179.14, 141.96, 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 129 16.00 O 2841 8.00 N 2625 7.00 C 9501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.04 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 309 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 69 " distance=2.03 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 81 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 67 " distance=2.04 Simple disulfide: pdb=" SG CYS D 3 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 121 " distance=2.03 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 116 " distance=2.04 Simple disulfide: pdb=" SG CYS D 191 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 309 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 34 " - pdb=" SG CYS E 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 81 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS G 3 " - pdb=" SG CYS G 30 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 121 " distance=2.03 Simple disulfide: pdb=" SG CYS G 74 " - pdb=" SG CYS G 105 " distance=2.03 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 116 " distance=2.04 Simple disulfide: pdb=" SG CYS G 191 " - pdb=" SG CYS G 292 " distance=2.03 Simple disulfide: pdb=" SG CYS G 309 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS H 34 " - pdb=" SG CYS H 69 " distance=2.03 Simple disulfide: pdb=" SG CYS H 45 " - pdb=" SG CYS H 81 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 67 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG B 201 " - " ASN B 70 " " NAG E 201 " - " ASN E 70 " " NAG H 201 " - " ASN H 70 " Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.9 seconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3546 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 35 sheets defined 23.4% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.716A pdb=" N ALA A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.544A pdb=" N GLY A 104 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 216 through 220 removed outlier: 3.608A pdb=" N HIS A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 220' Processing helix chain 'A' and resid 239 through 242 removed outlier: 3.971A pdb=" N ALA A 242 " --> pdb=" O ASN A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.594A pdb=" N THR A 395 " --> pdb=" O THR A 392 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 396 " --> pdb=" O GLY A 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 396' Processing helix chain 'A' and resid 406 through 425 Processing helix chain 'A' and resid 437 through 458 removed outlier: 5.782A pdb=" N SER A 452 " --> pdb=" O GLN A 448 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 479 removed outlier: 3.540A pdb=" N LEU A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 502 removed outlier: 3.697A pdb=" N PHE A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.787A pdb=" N ALA D 86 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 104 removed outlier: 3.516A pdb=" N GLY D 104 " --> pdb=" O TRP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.525A pdb=" N HIS D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 216 through 220' Processing helix chain 'D' and resid 240 through 242 No H-bonds generated for 'chain 'D' and resid 240 through 242' Processing helix chain 'D' and resid 262 through 270 Processing helix chain 'D' and resid 392 through 396 removed outlier: 3.600A pdb=" N THR D 395 " --> pdb=" O THR D 392 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS D 396 " --> pdb=" O GLY D 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 392 through 396' Processing helix chain 'D' and resid 406 through 425 Processing helix chain 'D' and resid 437 through 458 removed outlier: 5.822A pdb=" N SER D 452 " --> pdb=" O GLN D 448 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ALA D 453 " --> pdb=" O VAL D 449 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 479 removed outlier: 3.527A pdb=" N LEU D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 502 removed outlier: 3.699A pdb=" N PHE D 489 " --> pdb=" O VAL D 485 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.801A pdb=" N ALA G 86 " --> pdb=" O ASP G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 104 removed outlier: 3.505A pdb=" N GLY G 104 " --> pdb=" O TRP G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 133 No H-bonds generated for 'chain 'G' and resid 131 through 133' Processing helix chain 'G' and resid 216 through 220 removed outlier: 3.666A pdb=" N HIS G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 216 through 220' Processing helix chain 'G' and resid 240 through 242 No H-bonds generated for 'chain 'G' and resid 240 through 242' Processing helix chain 'G' and resid 262 through 270 Processing helix chain 'G' and resid 392 through 396 removed outlier: 3.598A pdb=" N THR G 395 " --> pdb=" O THR G 392 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS G 396 " --> pdb=" O GLY G 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 392 through 396' Processing helix chain 'G' and resid 406 through 425 Processing helix chain 'G' and resid 437 through 458 removed outlier: 5.801A pdb=" N SER G 452 " --> pdb=" O GLN G 448 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA G 453 " --> pdb=" O VAL G 449 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA G 456 " --> pdb=" O SER G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 464 through 479 removed outlier: 3.571A pdb=" N LEU G 468 " --> pdb=" O PHE G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 485 through 502 removed outlier: 3.690A pdb=" N PHE G 489 " --> pdb=" O VAL G 485 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 146 removed outlier: 3.565A pdb=" N ALA I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 165 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 146 removed outlier: 3.991A pdb=" N THR F 146 " --> pdb=" O VAL F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 165 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 146 removed outlier: 3.986A pdb=" N THR C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 165 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13 removed outlier: 7.189A pdb=" N ARG A 138 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR A 48 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU A 136 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13 removed outlier: 3.738A pdb=" N GLU A 277 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 25 removed outlier: 3.942A pdb=" N LYS A 291 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 55 through 64 removed outlier: 6.170A pdb=" N VAL A 56 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LYS A 128 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER A 58 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR A 126 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS A 60 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS A 124 " --> pdb=" O CYS A 60 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLU A 62 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 274 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 73 Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308 removed outlier: 6.682A pdb=" N ALA A 307 " --> pdb=" O LYS A 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.549A pdb=" N THR A 328 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 320 " --> pdb=" O THR A 328 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 315 removed outlier: 3.957A pdb=" N ARG A 358 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 347 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5 removed outlier: 6.137A pdb=" N TYR B 10 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 77 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N MET B 12 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N GLY B 79 " --> pdb=" O MET B 12 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AB4, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.697A pdb=" N ASP D 10 " --> pdb=" O CYS D 30 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 32 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE D 43 " --> pdb=" O SER D 142 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N SER D 142 " --> pdb=" O PHE D 43 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU D 45 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU D 140 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N THR D 47 " --> pdb=" O ARG D 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 13 removed outlier: 3.697A pdb=" N ASP D 10 " --> pdb=" O CYS D 30 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 32 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 277 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 20 through 25 removed outlier: 3.942A pdb=" N LYS D 291 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 226 through 228 removed outlier: 7.065A pdb=" N GLY D 127 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N SER D 58 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 125 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N CYS D 60 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LYS D 123 " --> pdb=" O CYS D 60 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLU D 62 " --> pdb=" O CYS D 121 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N CYS D 121 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU D 274 " --> pdb=" O LEU D 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 90 through 98 removed outlier: 6.675A pdb=" N MET D 68 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLU E 52 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N SER D 70 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N TYR E 10 " --> pdb=" O TRP E 75 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL E 77 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N MET E 12 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY E 79 " --> pdb=" O MET E 12 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AC1, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.616A pdb=" N ALA D 307 " --> pdb=" O LYS D 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 312 through 315 removed outlier: 3.560A pdb=" N THR D 328 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 320 " --> pdb=" O THR D 328 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 312 through 315 removed outlier: 3.952A pdb=" N ARG D 358 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AC5, first strand: chain 'E' and resid 23 through 26 Processing sheet with id=AC6, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.742A pdb=" N ASP G 10 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR G 32 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N PHE G 43 " --> pdb=" O SER G 142 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER G 142 " --> pdb=" O PHE G 43 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LEU G 45 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU G 140 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR G 47 " --> pdb=" O ARG G 138 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.742A pdb=" N ASP G 10 " --> pdb=" O CYS G 30 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR G 32 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU G 277 " --> pdb=" O THR G 284 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 20 through 25 removed outlier: 3.959A pdb=" N LYS G 291 " --> pdb=" O GLU G 192 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 226 through 228 removed outlier: 5.904A pdb=" N VAL G 56 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LYS G 128 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER G 58 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR G 126 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS G 60 " --> pdb=" O LYS G 124 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS G 124 " --> pdb=" O CYS G 60 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLU G 62 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL G 122 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU G 274 " --> pdb=" O LEU G 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 69 through 73 Processing sheet with id=AD2, first strand: chain 'G' and resid 244 through 246 Processing sheet with id=AD3, first strand: chain 'G' and resid 307 through 308 removed outlier: 6.692A pdb=" N ALA G 307 " --> pdb=" O LYS G 341 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'G' and resid 312 through 315 removed outlier: 3.593A pdb=" N THR G 328 " --> pdb=" O SER G 320 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER G 320 " --> pdb=" O THR G 328 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 312 through 315 removed outlier: 4.044A pdb=" N ARG G 358 " --> pdb=" O ASP G 380 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 344 through 347 Processing sheet with id=AD7, first strand: chain 'H' and resid 2 through 5 removed outlier: 6.451A pdb=" N TYR H 10 " --> pdb=" O TRP H 75 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL H 77 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N MET H 12 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLY H 79 " --> pdb=" O MET H 12 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 22 through 26 629 hydrogen bonds defined for protein. 1740 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: 5.11 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4937 1.35 - 1.46: 3726 1.46 - 1.58: 6565 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 15432 Sorted by residual: bond pdb=" C1 NAG B 201 " pdb=" O5 NAG B 201 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" C1 NAG E 201 " pdb=" O5 NAG E 201 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.97e+00 bond pdb=" C1 NAG H 201 " pdb=" O5 NAG H 201 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C CYS G 74 " pdb=" N PRO G 75 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 bond pdb=" C CYS D 74 " pdb=" N PRO D 75 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 ... (remaining 15427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 20622 2.04 - 4.07: 232 4.07 - 6.11: 25 6.11 - 8.15: 1 8.15 - 10.18: 6 Bond angle restraints: 20886 Sorted by residual: angle pdb=" CA CYS A 116 " pdb=" CB CYS A 116 " pdb=" SG CYS A 116 " ideal model delta sigma weight residual 114.40 124.58 -10.18 2.30e+00 1.89e-01 1.96e+01 angle pdb=" CA CYS D 116 " pdb=" CB CYS D 116 " pdb=" SG CYS D 116 " ideal model delta sigma weight residual 114.40 124.38 -9.98 2.30e+00 1.89e-01 1.88e+01 angle pdb=" CA CYS G 116 " pdb=" CB CYS G 116 " pdb=" SG CYS G 116 " ideal model delta sigma weight residual 114.40 124.33 -9.93 2.30e+00 1.89e-01 1.87e+01 angle pdb=" CA CYS D 92 " pdb=" CB CYS D 92 " pdb=" SG CYS D 92 " ideal model delta sigma weight residual 114.40 123.88 -9.48 2.30e+00 1.89e-01 1.70e+01 angle pdb=" CA CYS A 92 " pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " ideal model delta sigma weight residual 114.40 123.72 -9.32 2.30e+00 1.89e-01 1.64e+01 ... (remaining 20881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8477 17.94 - 35.88: 552 35.88 - 53.82: 111 53.82 - 71.76: 13 71.76 - 89.70: 15 Dihedral angle restraints: 9168 sinusoidal: 3609 harmonic: 5559 Sorted by residual: dihedral pdb=" CB CYS A 74 " pdb=" SG CYS A 74 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual 93.00 178.72 -85.72 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS D 74 " pdb=" SG CYS D 74 " pdb=" SG CYS D 105 " pdb=" CB CYS D 105 " ideal model delta sinusoidal sigma weight residual 93.00 175.19 -82.19 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" CB CYS G 74 " pdb=" SG CYS G 74 " pdb=" SG CYS G 105 " pdb=" CB CYS G 105 " ideal model delta sinusoidal sigma weight residual 93.00 173.98 -80.98 1 1.00e+01 1.00e-02 8.09e+01 ... (remaining 9165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1662 0.039 - 0.077: 452 0.077 - 0.116: 163 0.116 - 0.155: 39 0.155 - 0.194: 3 Chirality restraints: 2319 Sorted by residual: chirality pdb=" CA CYS A 116 " pdb=" N CYS A 116 " pdb=" C CYS A 116 " pdb=" CB CYS A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CA CYS D 116 " pdb=" N CYS D 116 " pdb=" C CYS D 116 " pdb=" CB CYS D 116 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA CYS G 116 " pdb=" N CYS G 116 " pdb=" C CYS G 116 " pdb=" CB CYS G 116 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 2316 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 111 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C GLY D 111 " -0.033 2.00e-02 2.50e+03 pdb=" O GLY D 111 " 0.013 2.00e-02 2.50e+03 pdb=" N SER D 112 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 111 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C GLY G 111 " -0.032 2.00e-02 2.50e+03 pdb=" O GLY G 111 " 0.012 2.00e-02 2.50e+03 pdb=" N SER G 112 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 51 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.36e+00 pdb=" C TYR H 51 " 0.032 2.00e-02 2.50e+03 pdb=" O TYR H 51 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU H 52 " -0.011 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4236 2.81 - 3.33: 13004 3.33 - 3.85: 22774 3.85 - 4.38: 24622 4.38 - 4.90: 44215 Nonbonded interactions: 108851 Sorted by model distance: nonbonded pdb=" OD1 ASP D 380 " pdb=" NH1 ARG D 403 " model vdw 2.286 3.120 nonbonded pdb=" OG SER G 348 " pdb=" NH2 ARG I 132 " model vdw 2.322 3.120 nonbonded pdb=" OD1 ASP G 380 " pdb=" NH1 ARG G 403 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASP A 380 " pdb=" NH1 ARG A 403 " model vdw 2.354 3.120 nonbonded pdb=" N ASN A 233 " pdb=" OD1 ASN A 233 " model vdw 2.370 3.120 ... (remaining 108846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 0.160 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: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.490 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15432 Z= 0.134 Angle : 0.555 10.184 20886 Z= 0.314 Chirality : 0.042 0.194 2319 Planarity : 0.003 0.032 2661 Dihedral : 12.255 89.703 5541 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.93 % Favored : 96.97 % Rotamer: Outliers : 1.55 % Allowed : 4.03 % Favored : 94.41 % 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: -2.13 (0.17), residues: 1947 helix: -0.01 (0.24), residues: 396 sheet: -0.54 (0.21), residues: 564 loop : -2.64 (0.15), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 226 HIS 0.008 0.001 HIS B 83 PHE 0.012 0.001 PHE A 445 TYR 0.009 0.001 TYR E 51 ARG 0.009 0.000 ARG G 247 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 739 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ILE cc_start: 0.8763 (pt) cc_final: 0.8560 (mt) REVERT: A 36 ASN cc_start: 0.8293 (p0) cc_final: 0.7889 (p0) REVERT: A 118 LYS cc_start: 0.8792 (tttp) cc_final: 0.8159 (ttpt) REVERT: A 140 LEU cc_start: 0.9126 (mt) cc_final: 0.8920 (mt) REVERT: A 151 MET cc_start: 0.3263 (tpt) cc_final: 0.2885 (mmp) REVERT: A 207 MET cc_start: 0.7556 (ttt) cc_final: 0.7305 (tmm) REVERT: A 294 LEU cc_start: 0.8978 (mt) cc_final: 0.8351 (mp) REVERT: A 416 MET cc_start: 0.7953 (ttt) cc_final: 0.7302 (tpt) REVERT: A 489 PHE cc_start: 0.3431 (m-10) cc_final: 0.3020 (m-10) REVERT: B 12 MET cc_start: 0.8261 (mtm) cc_final: 0.8008 (mtp) REVERT: B 26 GLU cc_start: 0.8089 (tt0) cc_final: 0.7586 (tp30) REVERT: B 63 GLU cc_start: 0.6154 (tt0) cc_final: 0.5672 (tm-30) REVERT: B 93 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.6643 (ptp90) REVERT: B 101 HIS cc_start: 0.5938 (OUTLIER) cc_final: 0.5182 (m-70) REVERT: D 118 LYS cc_start: 0.8352 (tttp) cc_final: 0.8146 (tttt) REVERT: D 253 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7241 (pttp) REVERT: D 285 ILE cc_start: 0.8154 (mp) cc_final: 0.7699 (mp) REVERT: D 302 LYS cc_start: 0.7515 (tttt) cc_final: 0.7229 (tptt) REVERT: D 383 PHE cc_start: 0.8253 (m-80) cc_final: 0.7664 (m-10) REVERT: D 403 ARG cc_start: 0.8531 (ttt180) cc_final: 0.8050 (ptm160) REVERT: D 447 HIS cc_start: 0.8068 (t-90) cc_final: 0.7504 (t-90) REVERT: D 487 MET cc_start: 0.2812 (mpp) cc_final: 0.2582 (tmm) REVERT: D 495 MET cc_start: 0.6537 (ttm) cc_final: 0.6221 (mmm) REVERT: E 44 MET cc_start: 0.6487 (tpp) cc_final: 0.5745 (tpp) REVERT: E 101 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.5527 (m-70) REVERT: G 27 HIS cc_start: 0.5741 (t-90) cc_final: 0.5282 (t-90) REVERT: G 53 MET cc_start: 0.7557 (mtm) cc_final: 0.7300 (mtm) REVERT: G 71 ASP cc_start: 0.8438 (t0) cc_final: 0.7432 (t0) REVERT: G 87 ASP cc_start: 0.6750 (t0) cc_final: 0.5697 (t0) REVERT: G 90 PHE cc_start: 0.8620 (m-80) cc_final: 0.8141 (m-80) REVERT: G 131 GLN cc_start: 0.8603 (mm110) cc_final: 0.8357 (mt0) REVERT: G 140 LEU cc_start: 0.8785 (mt) cc_final: 0.8572 (mt) REVERT: G 151 MET cc_start: 0.4884 (tpt) cc_final: 0.4056 (tpp) REVERT: G 207 MET cc_start: 0.8681 (ttt) cc_final: 0.8097 (tmm) REVERT: G 248 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7721 (pp20) REVERT: G 250 HIS cc_start: 0.6610 (t70) cc_final: 0.6223 (t-170) REVERT: G 294 LEU cc_start: 0.8230 (mt) cc_final: 0.7847 (mp) REVERT: G 302 LYS cc_start: 0.8546 (tttt) cc_final: 0.7956 (tptp) REVERT: G 313 PHE cc_start: 0.8367 (m-80) cc_final: 0.8164 (m-10) REVERT: G 341 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8347 (mtmm) REVERT: G 376 MET cc_start: 0.8754 (ttp) cc_final: 0.8180 (tmm) REVERT: G 383 PHE cc_start: 0.7201 (m-80) cc_final: 0.6898 (m-80) REVERT: G 422 MET cc_start: 0.9304 (tpp) cc_final: 0.9011 (mmm) REVERT: G 435 VAL cc_start: 0.7062 (p) cc_final: 0.6859 (p) REVERT: G 439 PHE cc_start: 0.7315 (m-80) cc_final: 0.6776 (p90) REVERT: G 440 ASN cc_start: 0.7862 (t0) cc_final: 0.7554 (t0) REVERT: H 36 ILE cc_start: 0.7679 (mt) cc_final: 0.7433 (mt) REVERT: H 51 TYR cc_start: 0.8535 (p90) cc_final: 0.8232 (p90) REVERT: H 83 HIS cc_start: 0.6778 (m170) cc_final: 0.6171 (m170) REVERT: H 101 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6209 (m-70) REVERT: I 125 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8686 (mtmt) REVERT: I 128 ASN cc_start: 0.8098 (t0) cc_final: 0.7897 (t0) outliers start: 25 outliers final: 6 residues processed: 753 average time/residue: 0.2776 time to fit residues: 296.3019 Evaluate side-chains 482 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 472 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 59 optimal weight: 0.0270 chunk 92 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 overall best weight: 2.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 236 HIS A 250 HIS A 448 GLN ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 HIS D 147 GLN D 148 HIS D 164 ASN D 400 HIS E 37 GLN E 83 HIS G 131 GLN G 254 GLN G 363 ASN G 400 HIS G 479 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 15432 Z= 0.259 Angle : 0.682 14.490 20886 Z= 0.360 Chirality : 0.047 0.263 2319 Planarity : 0.004 0.036 2661 Dihedral : 5.152 83.266 2166 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.43 % Allowed : 4.78 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.17 (0.18), residues: 1947 helix: 1.14 (0.26), residues: 399 sheet: -0.21 (0.20), residues: 609 loop : -2.08 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP I 129 HIS 0.013 0.001 HIS A 235 PHE 0.031 0.002 PHE C 157 TYR 0.024 0.002 TYR G 203 ARG 0.012 0.001 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 534 time to evaluate : 1.668 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 68 MET cc_start: 0.8692 (ttp) cc_final: 0.8423 (ttm) REVERT: A 76 THR cc_start: 0.8467 (m) cc_final: 0.8140 (m) REVERT: A 77 GLN cc_start: 0.8227 (tp40) cc_final: 0.8014 (mm110) REVERT: A 131 GLN cc_start: 0.7566 (mt0) cc_final: 0.6932 (mm-40) REVERT: A 133 GLU cc_start: 0.7667 (pm20) cc_final: 0.7397 (pm20) REVERT: A 147 GLN cc_start: 0.8482 (mt0) cc_final: 0.8226 (mt0) REVERT: A 156 THR cc_start: 0.8142 (p) cc_final: 0.7863 (t) REVERT: A 204 TYR cc_start: 0.8586 (t80) cc_final: 0.8339 (t80) REVERT: A 294 LEU cc_start: 0.8872 (mt) cc_final: 0.8503 (mp) REVERT: A 415 THR cc_start: 0.8817 (m) cc_final: 0.8588 (p) REVERT: A 416 MET cc_start: 0.7876 (ttt) cc_final: 0.7399 (tpt) REVERT: A 438 MET cc_start: 0.8902 (tpt) cc_final: 0.7113 (mpp) REVERT: B 5 LYS cc_start: 0.8967 (ptmt) cc_final: 0.8616 (pttt) REVERT: B 12 MET cc_start: 0.8153 (mtm) cc_final: 0.7897 (mtp) REVERT: B 26 GLU cc_start: 0.8083 (tt0) cc_final: 0.7697 (tp30) REVERT: B 27 THR cc_start: 0.6947 (p) cc_final: 0.6550 (p) REVERT: D 26 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8203 (mm-30) REVERT: D 108 PHE cc_start: 0.6617 (m-10) cc_final: 0.6097 (m-10) REVERT: D 297 ASP cc_start: 0.7650 (p0) cc_final: 0.7380 (p0) REVERT: D 383 PHE cc_start: 0.8605 (m-80) cc_final: 0.8256 (m-10) REVERT: D 487 MET cc_start: 0.2533 (mpp) cc_final: 0.1930 (tmm) REVERT: E 68 TRP cc_start: 0.7248 (p90) cc_final: 0.6535 (p90) REVERT: E 88 GLU cc_start: 0.7441 (mp0) cc_final: 0.7117 (mp0) REVERT: E 93 ARG cc_start: 0.7762 (mmp-170) cc_final: 0.7513 (mmp-170) REVERT: G 68 MET cc_start: 0.8479 (mtt) cc_final: 0.8207 (mtt) REVERT: G 140 LEU cc_start: 0.9189 (mt) cc_final: 0.8542 (mt) REVERT: G 151 MET cc_start: 0.5179 (tpt) cc_final: 0.4650 (tpp) REVERT: G 160 HIS cc_start: 0.7184 (m-70) cc_final: 0.6619 (m90) REVERT: G 163 GLU cc_start: 0.7578 (pm20) cc_final: 0.7352 (pm20) REVERT: G 204 TYR cc_start: 0.8621 (t80) cc_final: 0.8289 (t80) REVERT: G 250 HIS cc_start: 0.7760 (t70) cc_final: 0.7140 (t-170) REVERT: G 285 ILE cc_start: 0.8496 (mp) cc_final: 0.8180 (mt) REVERT: G 342 VAL cc_start: 0.9401 (t) cc_final: 0.9069 (p) REVERT: G 376 MET cc_start: 0.8683 (ttp) cc_final: 0.7955 (tmm) REVERT: G 383 PHE cc_start: 0.7491 (m-80) cc_final: 0.7220 (m-80) REVERT: G 439 PHE cc_start: 0.7679 (m-80) cc_final: 0.7144 (p90) REVERT: H 83 HIS cc_start: 0.5868 (m170) cc_final: 0.4643 (m170) REVERT: I 125 LYS cc_start: 0.9199 (mtpt) cc_final: 0.8803 (mtmt) outliers start: 7 outliers final: 3 residues processed: 534 average time/residue: 0.2521 time to fit residues: 198.2705 Evaluate side-chains 435 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 432 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 142 optimal weight: 0.2980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 103 ASN A 236 HIS A 250 HIS ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 HIS D 289 HIS D 448 GLN E 43 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 250 HIS ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 15432 Z= 0.214 Angle : 0.640 16.048 20886 Z= 0.336 Chirality : 0.046 0.286 2319 Planarity : 0.004 0.041 2661 Dihedral : 5.103 83.890 2166 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.31 % Allowed : 4.16 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 1947 helix: 1.28 (0.26), residues: 414 sheet: 0.02 (0.21), residues: 624 loop : -1.99 (0.18), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 68 HIS 0.008 0.001 HIS A 27 PHE 0.020 0.002 PHE A 445 TYR 0.019 0.001 TYR C 122 ARG 0.004 0.001 ARG I 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 518 time to evaluate : 1.673 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 36 ASN cc_start: 0.7994 (p0) cc_final: 0.7762 (p0) REVERT: A 53 MET cc_start: 0.7261 (ptp) cc_final: 0.7041 (ptm) REVERT: A 77 GLN cc_start: 0.8239 (tp40) cc_final: 0.7998 (mm110) REVERT: A 82 LEU cc_start: 0.9160 (tp) cc_final: 0.8747 (tp) REVERT: A 204 TYR cc_start: 0.8274 (t80) cc_final: 0.8071 (t80) REVERT: A 207 MET cc_start: 0.8281 (ttt) cc_final: 0.8006 (tmm) REVERT: A 415 THR cc_start: 0.8803 (m) cc_final: 0.8535 (p) REVERT: A 416 MET cc_start: 0.7666 (ttt) cc_final: 0.7204 (tpt) REVERT: A 438 MET cc_start: 0.8896 (tpt) cc_final: 0.7076 (mpp) REVERT: A 489 PHE cc_start: 0.3079 (m-10) cc_final: 0.2846 (m-10) REVERT: B 5 LYS cc_start: 0.8924 (ptmt) cc_final: 0.8604 (pttt) REVERT: B 26 GLU cc_start: 0.8187 (tt0) cc_final: 0.7834 (tp30) REVERT: B 27 THR cc_start: 0.7095 (p) cc_final: 0.6815 (p) REVERT: B 77 VAL cc_start: 0.8594 (p) cc_final: 0.8373 (p) REVERT: B 86 THR cc_start: 0.6900 (p) cc_final: 0.6694 (p) REVERT: D 26 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8142 (mm-30) REVERT: D 45 LEU cc_start: 0.9029 (tt) cc_final: 0.8368 (pp) REVERT: D 82 LEU cc_start: 0.8219 (tp) cc_final: 0.8014 (tt) REVERT: D 245 GLU cc_start: 0.8445 (tt0) cc_final: 0.8147 (tt0) REVERT: D 297 ASP cc_start: 0.7565 (p0) cc_final: 0.7175 (p0) REVERT: D 372 ASN cc_start: 0.8670 (p0) cc_final: 0.8430 (p0) REVERT: D 383 PHE cc_start: 0.8469 (m-80) cc_final: 0.8157 (m-10) REVERT: D 389 ILE cc_start: 0.9270 (mp) cc_final: 0.8961 (tp) REVERT: D 461 MET cc_start: 0.6520 (mpp) cc_final: 0.5327 (mpp) REVERT: D 476 MET cc_start: 0.7770 (tmm) cc_final: 0.7421 (tmm) REVERT: D 487 MET cc_start: 0.2446 (mpp) cc_final: 0.1889 (tmm) REVERT: G 68 MET cc_start: 0.8555 (mtt) cc_final: 0.8227 (mtp) REVERT: G 151 MET cc_start: 0.4806 (tpt) cc_final: 0.4264 (tpp) REVERT: G 160 HIS cc_start: 0.7415 (m-70) cc_final: 0.7077 (m-70) REVERT: G 204 TYR cc_start: 0.8496 (t80) cc_final: 0.8197 (t80) REVERT: G 207 MET cc_start: 0.8843 (tmm) cc_final: 0.7665 (tmm) REVERT: G 306 TYR cc_start: 0.7338 (m-10) cc_final: 0.7062 (m-10) REVERT: G 439 PHE cc_start: 0.7759 (m-80) cc_final: 0.7244 (p90) REVERT: G 461 MET cc_start: 0.5758 (mpp) cc_final: 0.4454 (mmp) REVERT: G 487 MET cc_start: 0.5514 (mtm) cc_final: 0.3689 (tmm) REVERT: H 66 ASP cc_start: 0.7812 (m-30) cc_final: 0.7524 (m-30) REVERT: H 88 GLU cc_start: 0.8858 (tp30) cc_final: 0.8655 (tp30) REVERT: I 125 LYS cc_start: 0.9238 (mtpt) cc_final: 0.8793 (mtmt) REVERT: I 127 GLU cc_start: 0.9023 (tp30) cc_final: 0.8781 (tp30) REVERT: C 161 LEU cc_start: 0.8614 (tp) cc_final: 0.8400 (tp) outliers start: 5 outliers final: 2 residues processed: 518 average time/residue: 0.2457 time to fit residues: 188.6872 Evaluate side-chains 432 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 430 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 19 optimal weight: 0.0870 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 chunk 188 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 168 optimal weight: 0.0980 chunk 50 optimal weight: 9.9990 overall best weight: 2.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 164 ASN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 HIS ** D 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 GLN ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15432 Z= 0.309 Angle : 0.706 18.336 20886 Z= 0.372 Chirality : 0.047 0.273 2319 Planarity : 0.004 0.063 2661 Dihedral : 5.585 86.246 2166 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.37 % Allowed : 4.03 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.82 (0.19), residues: 1947 helix: 1.49 (0.27), residues: 414 sheet: -0.03 (0.20), residues: 624 loop : -1.96 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 129 HIS 0.013 0.002 HIS A 27 PHE 0.021 0.002 PHE C 157 TYR 0.019 0.002 TYR A 61 ARG 0.007 0.001 ARG A 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 505 time to evaluate : 1.694 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 36 ASN cc_start: 0.8179 (p0) cc_final: 0.7748 (p0) REVERT: A 37 ASN cc_start: 0.8589 (m-40) cc_final: 0.8172 (m-40) REVERT: A 65 ILE cc_start: 0.9241 (pt) cc_final: 0.9023 (pt) REVERT: A 82 LEU cc_start: 0.9013 (tp) cc_final: 0.8667 (tp) REVERT: A 85 MET cc_start: 0.7702 (mtp) cc_final: 0.7318 (mtp) REVERT: A 89 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7832 (mm110) REVERT: A 131 GLN cc_start: 0.7856 (mt0) cc_final: 0.6887 (mm-40) REVERT: A 133 GLU cc_start: 0.7579 (pm20) cc_final: 0.6959 (tm-30) REVERT: A 282 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8242 (pttm) REVERT: A 304 MET cc_start: 0.8167 (ppp) cc_final: 0.7763 (ppp) REVERT: A 349 ASP cc_start: 0.7362 (t0) cc_final: 0.7072 (t0) REVERT: A 416 MET cc_start: 0.7614 (ttt) cc_final: 0.7288 (mmm) REVERT: A 438 MET cc_start: 0.8513 (tpt) cc_final: 0.7014 (mpp) REVERT: A 489 PHE cc_start: 0.3018 (m-10) cc_final: 0.2769 (m-10) REVERT: B 5 LYS cc_start: 0.9023 (ptmt) cc_final: 0.8620 (pttt) REVERT: B 26 GLU cc_start: 0.8108 (tt0) cc_final: 0.7697 (tp30) REVERT: B 27 THR cc_start: 0.7116 (p) cc_final: 0.6835 (p) REVERT: D 20 TRP cc_start: 0.8679 (m100) cc_final: 0.8367 (m100) REVERT: D 26 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8186 (mm-30) REVERT: D 57 ARG cc_start: 0.8424 (ttm170) cc_final: 0.7994 (mmm-85) REVERT: D 108 PHE cc_start: 0.6411 (m-10) cc_final: 0.5946 (m-10) REVERT: D 245 GLU cc_start: 0.8409 (tt0) cc_final: 0.8204 (tt0) REVERT: D 297 ASP cc_start: 0.7749 (p0) cc_final: 0.7404 (p0) REVERT: D 349 ASP cc_start: 0.7463 (t0) cc_final: 0.7087 (t0) REVERT: D 389 ILE cc_start: 0.9315 (mp) cc_final: 0.8871 (tp) REVERT: D 487 MET cc_start: 0.2838 (mpp) cc_final: 0.2053 (tmm) REVERT: E 39 MET cc_start: 0.5602 (mmm) cc_final: 0.5215 (mmm) REVERT: E 51 TYR cc_start: 0.8044 (p90) cc_final: 0.7547 (p90) REVERT: E 93 ARG cc_start: 0.8521 (ptp-110) cc_final: 0.8250 (ptp-170) REVERT: G 42 ASP cc_start: 0.8647 (m-30) cc_final: 0.8278 (m-30) REVERT: G 44 GLU cc_start: 0.8301 (tt0) cc_final: 0.7522 (tt0) REVERT: G 151 MET cc_start: 0.5306 (tpt) cc_final: 0.4538 (tpp) REVERT: G 160 HIS cc_start: 0.7600 (m-70) cc_final: 0.7335 (m-70) REVERT: G 204 TYR cc_start: 0.8721 (t80) cc_final: 0.8453 (t80) REVERT: G 207 MET cc_start: 0.9215 (tmm) cc_final: 0.8209 (tmm) REVERT: G 476 MET cc_start: 0.5808 (ppp) cc_final: 0.5606 (ppp) REVERT: H 83 HIS cc_start: 0.7577 (m170) cc_final: 0.7146 (m-70) REVERT: I 125 LYS cc_start: 0.9389 (mtpt) cc_final: 0.8920 (mtmt) REVERT: I 127 GLU cc_start: 0.8986 (tp30) cc_final: 0.8742 (tp30) REVERT: I 131 LEU cc_start: 0.9067 (mm) cc_final: 0.8769 (mm) REVERT: C 134 PRO cc_start: 0.7412 (Cg_endo) cc_final: 0.7176 (Cg_exo) REVERT: C 161 LEU cc_start: 0.8619 (tp) cc_final: 0.8414 (tp) outliers start: 6 outliers final: 2 residues processed: 506 average time/residue: 0.2467 time to fit residues: 183.8141 Evaluate side-chains 415 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 413 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 254 GLN D 400 HIS D 448 GLN E 43 HIS E 83 HIS G 250 HIS ** G 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 15432 Z= 0.534 Angle : 0.889 21.586 20886 Z= 0.470 Chirality : 0.053 0.365 2319 Planarity : 0.005 0.050 2661 Dihedral : 6.580 84.272 2166 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.19 % Allowed : 5.65 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.38 (0.19), residues: 1947 helix: 0.89 (0.26), residues: 414 sheet: -0.49 (0.20), residues: 660 loop : -2.19 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 475 HIS 0.012 0.002 HIS G 27 PHE 0.033 0.003 PHE A 219 TYR 0.033 0.003 TYR A 61 ARG 0.006 0.001 ARG G 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 469 time to evaluate : 1.758 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: A 1 ILE cc_start: 0.8772 (mp) cc_final: 0.8282 (mt) REVERT: A 82 LEU cc_start: 0.8953 (tp) cc_final: 0.8584 (tp) REVERT: A 89 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7850 (mm110) REVERT: A 131 GLN cc_start: 0.7784 (mt0) cc_final: 0.7100 (mm-40) REVERT: A 282 LYS cc_start: 0.8682 (ptpp) cc_final: 0.8330 (ptpp) REVERT: A 306 TYR cc_start: 0.8578 (m-10) cc_final: 0.8376 (m-10) REVERT: A 349 ASP cc_start: 0.7441 (t0) cc_final: 0.7131 (t0) REVERT: A 367 THR cc_start: 0.8974 (p) cc_final: 0.8659 (t) REVERT: A 416 MET cc_start: 0.7361 (ttt) cc_final: 0.6110 (tpp) REVERT: A 422 MET cc_start: 0.8705 (tpp) cc_final: 0.8359 (tpp) REVERT: B 39 MET cc_start: 0.7680 (ptt) cc_final: 0.7361 (ptp) REVERT: D 15 MET cc_start: 0.7917 (mmm) cc_final: 0.7709 (mmm) REVERT: D 53 MET cc_start: 0.7932 (ptp) cc_final: 0.7723 (ptp) REVERT: D 73 ARG cc_start: 0.6942 (ttm170) cc_final: 0.6563 (ttm170) REVERT: D 108 PHE cc_start: 0.6910 (m-10) cc_final: 0.6382 (m-10) REVERT: D 195 SER cc_start: 0.8531 (p) cc_final: 0.8263 (p) REVERT: D 245 GLU cc_start: 0.8270 (tt0) cc_final: 0.8054 (tt0) REVERT: D 282 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8257 (mtmm) REVERT: D 289 HIS cc_start: 0.8305 (p-80) cc_final: 0.8071 (p-80) REVERT: D 349 ASP cc_start: 0.7889 (t0) cc_final: 0.7660 (t0) REVERT: D 425 LEU cc_start: 0.8798 (mm) cc_final: 0.8482 (mt) REVERT: D 461 MET cc_start: 0.6308 (mpp) cc_final: 0.5801 (mpp) REVERT: D 464 PHE cc_start: 0.7785 (m-10) cc_final: 0.7306 (m-80) REVERT: D 487 MET cc_start: 0.3787 (mpp) cc_final: 0.2914 (tmm) REVERT: E 39 MET cc_start: 0.5449 (mmm) cc_final: 0.5104 (mmm) REVERT: E 49 MET cc_start: 0.9523 (tpt) cc_final: 0.9250 (tpp) REVERT: E 68 TRP cc_start: 0.7715 (p90) cc_final: 0.7105 (p90) REVERT: G 42 ASP cc_start: 0.8480 (m-30) cc_final: 0.7967 (t0) REVERT: G 151 MET cc_start: 0.6079 (tpt) cc_final: 0.5529 (tpp) REVERT: G 207 MET cc_start: 0.9168 (tmm) cc_final: 0.8234 (tmm) REVERT: G 248 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7829 (pm20) REVERT: H 12 MET cc_start: 0.8127 (ptm) cc_final: 0.7507 (mpp) REVERT: H 36 ILE cc_start: 0.7845 (mt) cc_final: 0.7338 (mt) REVERT: H 37 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7550 (mp-120) REVERT: H 83 HIS cc_start: 0.7795 (m170) cc_final: 0.7323 (m-70) REVERT: H 88 GLU cc_start: 0.8841 (tp30) cc_final: 0.8577 (tp30) REVERT: I 127 GLU cc_start: 0.8868 (tp30) cc_final: 0.8485 (tp30) REVERT: C 161 LEU cc_start: 0.8595 (tp) cc_final: 0.8391 (tp) outliers start: 3 outliers final: 1 residues processed: 470 average time/residue: 0.2517 time to fit residues: 174.1738 Evaluate side-chains 390 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 389 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 37 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 46 optimal weight: 0.0170 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 131 GLN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS ** D 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS E 43 HIS E 83 HIS G 27 HIS ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15432 Z= 0.202 Angle : 0.709 19.097 20886 Z= 0.372 Chirality : 0.047 0.295 2319 Planarity : 0.004 0.042 2661 Dihedral : 5.817 82.395 2166 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.91 (0.19), residues: 1947 helix: 1.53 (0.27), residues: 411 sheet: -0.16 (0.20), residues: 627 loop : -1.99 (0.19), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 20 HIS 0.010 0.001 HIS A 27 PHE 0.018 0.001 PHE A 108 TYR 0.012 0.001 TYR D 61 ARG 0.010 0.000 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 488 time to evaluate : 1.784 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: A 37 ASN cc_start: 0.8411 (m-40) cc_final: 0.7848 (m-40) REVERT: A 67 GLU cc_start: 0.8589 (mt-10) cc_final: 0.7851 (mp0) REVERT: A 82 LEU cc_start: 0.8951 (tp) cc_final: 0.7898 (tp) REVERT: A 89 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7768 (mm110) REVERT: A 167 ARG cc_start: 0.7997 (mtp-110) cc_final: 0.7577 (mtt90) REVERT: A 282 LYS cc_start: 0.8708 (ptpp) cc_final: 0.8347 (ptpp) REVERT: A 304 MET cc_start: 0.8071 (ppp) cc_final: 0.7629 (ppp) REVERT: A 349 ASP cc_start: 0.7494 (t0) cc_final: 0.7292 (t0) REVERT: A 367 THR cc_start: 0.9034 (p) cc_final: 0.8196 (t) REVERT: A 416 MET cc_start: 0.7241 (ttt) cc_final: 0.5928 (tpp) REVERT: A 422 MET cc_start: 0.8646 (tpp) cc_final: 0.8250 (tpp) REVERT: B 49 MET cc_start: 0.9039 (tpp) cc_final: 0.8666 (tpp) REVERT: B 68 TRP cc_start: 0.8144 (p90) cc_final: 0.7580 (p90) REVERT: B 93 ARG cc_start: 0.8320 (ptm160) cc_final: 0.7995 (ptp90) REVERT: D 73 ARG cc_start: 0.6896 (ttm170) cc_final: 0.6476 (ttm170) REVERT: D 108 PHE cc_start: 0.6861 (m-10) cc_final: 0.6368 (m-10) REVERT: D 136 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7946 (mm-30) REVERT: D 180 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7474 (mm-30) REVERT: D 195 SER cc_start: 0.8501 (p) cc_final: 0.8225 (p) REVERT: D 245 GLU cc_start: 0.8269 (tt0) cc_final: 0.7996 (tt0) REVERT: D 487 MET cc_start: 0.4317 (mpp) cc_final: 0.3216 (tmm) REVERT: E 68 TRP cc_start: 0.7773 (p90) cc_final: 0.7192 (p90) REVERT: G 151 MET cc_start: 0.5975 (tpt) cc_final: 0.5170 (tpp) REVERT: G 207 MET cc_start: 0.9153 (tmm) cc_final: 0.8245 (tmm) REVERT: G 290 LEU cc_start: 0.8797 (tp) cc_final: 0.8572 (tp) REVERT: G 349 ASP cc_start: 0.8506 (t0) cc_final: 0.7872 (p0) REVERT: G 378 GLU cc_start: 0.8640 (tt0) cc_final: 0.8209 (tt0) REVERT: G 438 MET cc_start: 0.7512 (mmm) cc_final: 0.7140 (mmp) REVERT: H 36 ILE cc_start: 0.7963 (mt) cc_final: 0.7572 (mt) REVERT: H 37 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7473 (mp10) REVERT: H 83 HIS cc_start: 0.7892 (m170) cc_final: 0.7391 (m-70) REVERT: I 127 GLU cc_start: 0.9017 (tp30) cc_final: 0.8784 (tp30) REVERT: C 147 LEU cc_start: 0.7860 (mt) cc_final: 0.7494 (mt) outliers start: 1 outliers final: 0 residues processed: 489 average time/residue: 0.2582 time to fit residues: 185.2237 Evaluate side-chains 414 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 414 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 187 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 HIS A 448 GLN D 144 HIS D 400 HIS D 448 GLN E 43 HIS E 83 HIS G 236 HIS G 324 HIS G 448 GLN I 128 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.6623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 15432 Z= 0.388 Angle : 0.805 20.197 20886 Z= 0.425 Chirality : 0.050 0.344 2319 Planarity : 0.005 0.053 2661 Dihedral : 6.142 83.056 2166 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.06 % Allowed : 2.11 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.13 (0.19), residues: 1947 helix: 1.35 (0.27), residues: 411 sheet: -0.41 (0.20), residues: 657 loop : -2.08 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 129 HIS 0.011 0.002 HIS D 27 PHE 0.025 0.002 PHE A 219 TYR 0.023 0.002 TYR G 203 ARG 0.006 0.001 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 1.765 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: A 37 ASN cc_start: 0.8291 (m-40) cc_final: 0.7872 (m-40) REVERT: A 82 LEU cc_start: 0.9153 (tp) cc_final: 0.8639 (tp) REVERT: A 126 THR cc_start: 0.9009 (p) cc_final: 0.8776 (p) REVERT: A 167 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7223 (mtt90) REVERT: A 282 LYS cc_start: 0.8916 (ptpp) cc_final: 0.8591 (ptpp) REVERT: A 349 ASP cc_start: 0.7409 (t0) cc_final: 0.7122 (t0) REVERT: A 416 MET cc_start: 0.7362 (ttt) cc_final: 0.6093 (tpp) REVERT: A 422 MET cc_start: 0.8758 (tpp) cc_final: 0.8439 (tpp) REVERT: A 438 MET cc_start: 0.8570 (tpt) cc_final: 0.7066 (mpp) REVERT: B 39 MET cc_start: 0.7939 (ptt) cc_final: 0.7292 (ptp) REVERT: B 49 MET cc_start: 0.9199 (tpp) cc_final: 0.8854 (tpp) REVERT: D 73 ARG cc_start: 0.6912 (ttm170) cc_final: 0.6427 (ttm170) REVERT: D 195 SER cc_start: 0.8727 (p) cc_final: 0.8410 (p) REVERT: D 245 GLU cc_start: 0.8243 (tt0) cc_final: 0.8003 (tt0) REVERT: D 466 GLN cc_start: 0.7001 (mp10) cc_final: 0.6687 (mp10) REVERT: D 487 MET cc_start: 0.4367 (mpp) cc_final: 0.3495 (tmm) REVERT: E 88 GLU cc_start: 0.7614 (mp0) cc_final: 0.7383 (mp0) REVERT: G 151 MET cc_start: 0.6184 (tpt) cc_final: 0.5497 (tpp) REVERT: G 170 ILE cc_start: 0.8766 (tp) cc_final: 0.8457 (tp) REVERT: G 201 ASP cc_start: 0.7913 (t0) cc_final: 0.7632 (t0) REVERT: G 207 MET cc_start: 0.9107 (tmm) cc_final: 0.8227 (tmm) REVERT: G 248 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7972 (pm20) REVERT: G 287 SER cc_start: 0.8821 (t) cc_final: 0.8598 (m) REVERT: G 301 LEU cc_start: 0.9096 (tp) cc_final: 0.8861 (tt) REVERT: H 36 ILE cc_start: 0.7481 (mt) cc_final: 0.7057 (mt) REVERT: H 37 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7365 (mp10) REVERT: H 83 HIS cc_start: 0.7925 (m170) cc_final: 0.7401 (m-70) REVERT: I 125 LYS cc_start: 0.9452 (mtpt) cc_final: 0.9079 (mtmt) REVERT: I 127 GLU cc_start: 0.9199 (tp30) cc_final: 0.8905 (tp30) REVERT: I 161 LEU cc_start: 0.6312 (mm) cc_final: 0.5938 (tp) REVERT: C 134 PRO cc_start: 0.7076 (Cg_endo) cc_final: 0.6840 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.2491 time to fit residues: 166.2578 Evaluate side-chains 396 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 128 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 chunk 170 optimal weight: 9.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 400 HIS E 43 HIS E 83 HIS ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.6790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 15432 Z= 0.323 Angle : 0.787 22.520 20886 Z= 0.413 Chirality : 0.050 0.347 2319 Planarity : 0.004 0.040 2661 Dihedral : 6.058 81.919 2166 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.06 % Allowed : 1.43 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.21 (0.19), residues: 1947 helix: 1.46 (0.27), residues: 408 sheet: -0.53 (0.20), residues: 645 loop : -2.14 (0.19), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 129 HIS 0.009 0.001 HIS A 27 PHE 0.020 0.002 PHE A 445 TYR 0.017 0.002 TYR A 61 ARG 0.006 0.001 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 1.701 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: A 37 ASN cc_start: 0.8168 (m-40) cc_final: 0.7780 (m-40) REVERT: A 67 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7832 (mp0) REVERT: A 82 LEU cc_start: 0.9132 (tp) cc_final: 0.8688 (tp) REVERT: A 282 LYS cc_start: 0.8935 (ptpp) cc_final: 0.8597 (ptpp) REVERT: A 349 ASP cc_start: 0.7590 (t0) cc_final: 0.7356 (t0) REVERT: A 416 MET cc_start: 0.7318 (ttt) cc_final: 0.5942 (tpp) REVERT: A 422 MET cc_start: 0.8732 (tpp) cc_final: 0.8498 (tpp) REVERT: A 438 MET cc_start: 0.8489 (tpt) cc_final: 0.7231 (mpp) REVERT: A 476 MET cc_start: 0.8628 (tmm) cc_final: 0.8387 (tmm) REVERT: B 39 MET cc_start: 0.7960 (ptt) cc_final: 0.7248 (ptp) REVERT: B 49 MET cc_start: 0.9195 (tpp) cc_final: 0.8933 (tpp) REVERT: D 2 ARG cc_start: 0.7582 (tpt90) cc_final: 0.7347 (tpt90) REVERT: D 73 ARG cc_start: 0.7042 (ttm170) cc_final: 0.6512 (ttm170) REVERT: D 178 GLU cc_start: 0.6724 (tm-30) cc_final: 0.5950 (tm-30) REVERT: D 195 SER cc_start: 0.8765 (p) cc_final: 0.8509 (p) REVERT: D 245 GLU cc_start: 0.8213 (tt0) cc_final: 0.8003 (tt0) REVERT: D 282 LYS cc_start: 0.8349 (mtmm) cc_final: 0.8103 (mttm) REVERT: D 289 HIS cc_start: 0.8154 (p-80) cc_final: 0.7797 (p-80) REVERT: D 349 ASP cc_start: 0.7646 (t0) cc_final: 0.7333 (t0) REVERT: D 466 GLN cc_start: 0.7041 (mp10) cc_final: 0.6775 (mp10) REVERT: D 487 MET cc_start: 0.4709 (mpp) cc_final: 0.3659 (tmm) REVERT: E 49 MET cc_start: 0.8691 (ttt) cc_final: 0.8408 (tpp) REVERT: E 51 TYR cc_start: 0.7890 (p90) cc_final: 0.7397 (p90) REVERT: E 88 GLU cc_start: 0.7614 (mp0) cc_final: 0.7237 (mp0) REVERT: G 68 MET cc_start: 0.8635 (mtt) cc_final: 0.8240 (mtp) REVERT: G 140 LEU cc_start: 0.8557 (mp) cc_final: 0.8169 (mp) REVERT: G 151 MET cc_start: 0.6139 (tpt) cc_final: 0.5479 (tpp) REVERT: G 201 ASP cc_start: 0.7960 (t0) cc_final: 0.7617 (t0) REVERT: G 203 TYR cc_start: 0.8723 (m-80) cc_final: 0.8463 (m-80) REVERT: G 207 MET cc_start: 0.9062 (tmm) cc_final: 0.8213 (tmm) REVERT: G 301 LEU cc_start: 0.9116 (tp) cc_final: 0.8915 (tt) REVERT: G 422 MET cc_start: 0.8764 (tpp) cc_final: 0.8535 (mmm) REVERT: H 36 ILE cc_start: 0.7497 (mt) cc_final: 0.7096 (mt) REVERT: H 37 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7678 (mp10) REVERT: H 83 HIS cc_start: 0.7890 (m170) cc_final: 0.7314 (m-70) REVERT: I 161 LEU cc_start: 0.6322 (mm) cc_final: 0.5853 (tp) REVERT: F 132 ARG cc_start: 0.8635 (ttp-110) cc_final: 0.8358 (ttm110) REVERT: C 134 PRO cc_start: 0.7110 (Cg_endo) cc_final: 0.6786 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.2696 time to fit residues: 180.5708 Evaluate side-chains 393 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 174 optimal weight: 0.0470 chunk 115 optimal weight: 5.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN D 144 HIS D 400 HIS E 43 HIS ** G 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15432 Z= 0.175 Angle : 0.744 23.538 20886 Z= 0.384 Chirality : 0.048 0.331 2319 Planarity : 0.004 0.042 2661 Dihedral : 5.662 81.401 2166 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.89 (0.19), residues: 1947 helix: 1.70 (0.28), residues: 411 sheet: -0.21 (0.21), residues: 621 loop : -2.01 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 129 HIS 0.009 0.001 HIS D 27 PHE 0.018 0.001 PHE G 454 TYR 0.020 0.001 TYR C 122 ARG 0.007 0.000 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 466 time to evaluate : 1.618 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: A 37 ASN cc_start: 0.8080 (m-40) cc_final: 0.7696 (m-40) REVERT: A 67 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7582 (mp0) REVERT: A 82 LEU cc_start: 0.9045 (tp) cc_final: 0.8531 (tp) REVERT: A 207 MET cc_start: 0.8566 (tmm) cc_final: 0.7624 (ptm) REVERT: A 282 LYS cc_start: 0.8906 (ptpp) cc_final: 0.8617 (ptpp) REVERT: A 367 THR cc_start: 0.8820 (p) cc_final: 0.8109 (p) REVERT: A 416 MET cc_start: 0.7418 (ttt) cc_final: 0.6280 (tpp) REVERT: A 422 MET cc_start: 0.8630 (tpp) cc_final: 0.8235 (tpp) REVERT: A 438 MET cc_start: 0.8285 (tpt) cc_final: 0.6938 (mpp) REVERT: D 2 ARG cc_start: 0.7248 (tpt90) cc_final: 0.6992 (tpt90) REVERT: D 73 ARG cc_start: 0.6795 (ttm170) cc_final: 0.6261 (ttm170) REVERT: D 136 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8091 (mm-30) REVERT: D 178 GLU cc_start: 0.6136 (tm-30) cc_final: 0.5768 (tm-30) REVERT: D 195 SER cc_start: 0.8738 (p) cc_final: 0.8418 (p) REVERT: D 201 ASP cc_start: 0.8621 (m-30) cc_final: 0.8245 (m-30) REVERT: D 282 LYS cc_start: 0.8117 (mtmm) cc_final: 0.7814 (mttm) REVERT: D 289 HIS cc_start: 0.8121 (p-80) cc_final: 0.7860 (p-80) REVERT: D 349 ASP cc_start: 0.7421 (t0) cc_final: 0.7145 (t0) REVERT: D 400 HIS cc_start: 0.7960 (t70) cc_final: 0.7755 (t-90) REVERT: D 476 MET cc_start: 0.7756 (tmm) cc_final: 0.7469 (tmm) REVERT: D 487 MET cc_start: 0.5181 (mpp) cc_final: 0.3904 (tmm) REVERT: E 4 THR cc_start: 0.7727 (t) cc_final: 0.7473 (t) REVERT: E 49 MET cc_start: 0.8692 (ttt) cc_final: 0.8062 (tmm) REVERT: E 51 TYR cc_start: 0.8317 (p90) cc_final: 0.6279 (p90) REVERT: E 88 GLU cc_start: 0.7572 (mp0) cc_final: 0.7329 (mp0) REVERT: G 34 MET cc_start: 0.7982 (ptp) cc_final: 0.7737 (ptt) REVERT: G 68 MET cc_start: 0.8541 (mtt) cc_final: 0.8186 (mtt) REVERT: G 140 LEU cc_start: 0.8359 (mp) cc_final: 0.8123 (mm) REVERT: G 151 MET cc_start: 0.5751 (tpt) cc_final: 0.5251 (tpp) REVERT: G 201 ASP cc_start: 0.7603 (t0) cc_final: 0.7232 (t0) REVERT: G 203 TYR cc_start: 0.8625 (m-80) cc_final: 0.8356 (m-80) REVERT: G 207 MET cc_start: 0.9048 (tmm) cc_final: 0.8237 (tmm) REVERT: G 349 ASP cc_start: 0.8515 (t0) cc_final: 0.7949 (p0) REVERT: G 378 GLU cc_start: 0.8582 (tt0) cc_final: 0.8032 (tt0) REVERT: G 422 MET cc_start: 0.8770 (tpp) cc_final: 0.8481 (mmm) REVERT: H 36 ILE cc_start: 0.7980 (mt) cc_final: 0.7679 (mt) REVERT: H 37 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7980 (mp10) REVERT: H 83 HIS cc_start: 0.7674 (m170) cc_final: 0.7072 (m-70) REVERT: I 161 LEU cc_start: 0.6234 (mm) cc_final: 0.5922 (tp) outliers start: 1 outliers final: 0 residues processed: 467 average time/residue: 0.2554 time to fit residues: 175.6166 Evaluate side-chains 407 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 178 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN E 43 HIS E 83 HIS G 37 ASN ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.6845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15432 Z= 0.233 Angle : 0.766 24.511 20886 Z= 0.396 Chirality : 0.048 0.341 2319 Planarity : 0.004 0.038 2661 Dihedral : 5.697 81.913 2166 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.91 (0.19), residues: 1947 helix: 1.67 (0.27), residues: 411 sheet: -0.23 (0.21), residues: 621 loop : -2.00 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 129 HIS 0.006 0.001 HIS G 27 PHE 0.023 0.002 PHE F 157 TYR 0.014 0.002 TYR G 204 ARG 0.005 0.000 ARG A 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 449 time to evaluate : 1.761 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: A 37 ASN cc_start: 0.8124 (m-40) cc_final: 0.7738 (m-40) REVERT: A 67 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7592 (mp0) REVERT: A 82 LEU cc_start: 0.9083 (tp) cc_final: 0.8553 (tp) REVERT: A 116 CYS cc_start: 0.5683 (p) cc_final: 0.5471 (p) REVERT: A 207 MET cc_start: 0.8531 (tmm) cc_final: 0.7800 (ptm) REVERT: A 282 LYS cc_start: 0.8955 (ptpp) cc_final: 0.8616 (ptpp) REVERT: A 353 MET cc_start: 0.8063 (mpp) cc_final: 0.7644 (mpp) REVERT: A 416 MET cc_start: 0.7436 (ttt) cc_final: 0.6032 (tpp) REVERT: A 438 MET cc_start: 0.8306 (tpt) cc_final: 0.7032 (mpp) REVERT: A 476 MET cc_start: 0.8512 (tmm) cc_final: 0.7594 (tpt) REVERT: D 73 ARG cc_start: 0.6766 (ttm170) cc_final: 0.6281 (ttm170) REVERT: D 195 SER cc_start: 0.8738 (p) cc_final: 0.8496 (p) REVERT: D 282 LYS cc_start: 0.8142 (mtmm) cc_final: 0.7827 (mttm) REVERT: D 289 HIS cc_start: 0.8192 (p-80) cc_final: 0.7790 (p-80) REVERT: D 349 ASP cc_start: 0.7388 (t0) cc_final: 0.7055 (t0) REVERT: D 461 MET cc_start: 0.5853 (mpp) cc_final: 0.5337 (mmt) REVERT: D 476 MET cc_start: 0.7726 (tmm) cc_final: 0.7429 (tmm) REVERT: D 487 MET cc_start: 0.4922 (mpp) cc_final: 0.3993 (tmm) REVERT: E 12 MET cc_start: 0.8082 (ppp) cc_final: 0.7702 (ppp) REVERT: G 2 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7860 (ttt-90) REVERT: G 68 MET cc_start: 0.8561 (mtt) cc_final: 0.8103 (mtp) REVERT: G 151 MET cc_start: 0.5875 (tpt) cc_final: 0.5313 (tpp) REVERT: G 160 HIS cc_start: 0.6867 (m90) cc_final: 0.6510 (m90) REVERT: G 201 ASP cc_start: 0.7879 (t0) cc_final: 0.7460 (t0) REVERT: G 203 TYR cc_start: 0.8618 (m-80) cc_final: 0.8317 (m-80) REVERT: G 207 MET cc_start: 0.9063 (tmm) cc_final: 0.8267 (tmm) REVERT: G 306 TYR cc_start: 0.7958 (m-10) cc_final: 0.7740 (m-10) REVERT: G 349 ASP cc_start: 0.8433 (t0) cc_final: 0.7867 (p0) REVERT: G 378 GLU cc_start: 0.8577 (tt0) cc_final: 0.8116 (tt0) REVERT: G 403 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7949 (ttp80) REVERT: G 422 MET cc_start: 0.8927 (tpp) cc_final: 0.8712 (mmm) REVERT: H 36 ILE cc_start: 0.7862 (mt) cc_final: 0.7492 (mt) REVERT: H 37 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8006 (mp10) REVERT: H 83 HIS cc_start: 0.7658 (m170) cc_final: 0.7054 (m-70) REVERT: I 125 LYS cc_start: 0.9520 (mtpt) cc_final: 0.9095 (mtmt) REVERT: I 161 LEU cc_start: 0.6233 (mm) cc_final: 0.5884 (tp) outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.2526 time to fit residues: 167.5277 Evaluate side-chains 400 residues out of total 1611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 22 optimal weight: 0.0030 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 HIS D 400 HIS E 43 HIS E 83 HIS ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119375 restraints weight = 29916.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123131 restraints weight = 18597.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124256 restraints weight = 11831.270| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.6923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15432 Z= 0.227 Angle : 0.764 22.731 20886 Z= 0.396 Chirality : 0.048 0.331 2319 Planarity : 0.004 0.039 2661 Dihedral : 5.706 82.775 2166 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.06 % Allowed : 0.43 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.90 (0.19), residues: 1947 helix: 1.70 (0.27), residues: 408 sheet: -0.21 (0.21), residues: 621 loop : -2.00 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 129 HIS 0.010 0.001 HIS D 27 PHE 0.032 0.002 PHE F 157 TYR 0.023 0.002 TYR C 122 ARG 0.006 0.001 ARG G 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3714.90 seconds wall clock time: 66 minutes 52.17 seconds (4012.17 seconds total)