Starting phenix.real_space_refine on Sun Dec 10 22:24:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uop_26652/12_2023/7uop_26652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uop_26652/12_2023/7uop_26652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uop_26652/12_2023/7uop_26652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uop_26652/12_2023/7uop_26652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uop_26652/12_2023/7uop_26652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uop_26652/12_2023/7uop_26652.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.142 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 90 5.16 5 C 9954 2.51 5 N 2562 2.21 5 O 3096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 16": "OE1" <-> "OE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15702 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "D" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "G" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3404 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain breaks: 1 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 965 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 965 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "E" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 965 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "F" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 809 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.53, per 1000 atoms: 0.54 Number of scatterers: 15702 At special positions: 0 Unit cell: (125.4, 128.7, 141.9, 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 90 16.00 O 3096 8.00 N 2562 7.00 C 9954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.02 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 67 " " NAG A 502 " - " ASN A 99 " " NAG A 503 " - " ASN A 414 " " NAG A 504 " - " ASN A 464 " " NAG D 501 " - " ASN D 67 " " NAG D 502 " - " ASN D 99 " " NAG D 503 " - " ASN D 414 " " NAG D 504 " - " ASN D 464 " " NAG G 501 " - " ASN G 67 " " NAG G 502 " - " ASN G 99 " " NAG G 503 " - " ASN G 414 " " NAG G 504 " - " ASN G 464 " Time building additional restraints: 5.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3756 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 33 sheets defined 30.0% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 removed outlier: 3.730A pdb=" N LYS A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 72 removed outlier: 3.978A pdb=" N SER A 69 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N CYS A 71 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 100 removed outlier: 3.688A pdb=" N ASN A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Proline residue: A 89 - end of helix removed outlier: 4.101A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.634A pdb=" N ALA A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.659A pdb=" N LYS A 146 " --> pdb=" O ASP A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.517A pdb=" N SER A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 removed outlier: 3.634A pdb=" N ILE A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.976A pdb=" N THR A 195 " --> pdb=" O PRO A 191 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 197 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 210 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.838A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 removed outlier: 3.538A pdb=" N THR A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.706A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 475 removed outlier: 3.855A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.742A pdb=" N LYS D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 removed outlier: 3.933A pdb=" N SER D 69 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N CYS D 71 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 100 removed outlier: 3.636A pdb=" N ASN D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 86 " --> pdb=" O ARG D 82 " (cutoff:3.500A) Proline residue: D 89 - end of helix removed outlier: 4.067A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.768A pdb=" N LYS D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 153 Processing helix chain 'D' and resid 175 through 182 removed outlier: 3.625A pdb=" N ILE D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 215 removed outlier: 4.021A pdb=" N THR D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.807A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 437 through 441 removed outlier: 3.806A pdb=" N GLU D 441 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 475 Processing helix chain 'G' and resid 29 through 37 removed outlier: 3.698A pdb=" N LYS G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 72 removed outlier: 3.936A pdb=" N SER G 69 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS G 71 " --> pdb=" O MET G 68 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR G 72 " --> pdb=" O SER G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 100 removed outlier: 3.576A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 4.100A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN G 100 " --> pdb=" O ILE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 121 Processing helix chain 'G' and resid 125 through 136 Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 182 removed outlier: 3.572A pdb=" N ILE G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 215 removed outlier: 3.698A pdb=" N THR G 195 " --> pdb=" O PRO G 191 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE G 214 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY G 215 " --> pdb=" O LEU G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.746A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 328 through 331 Processing helix chain 'G' and resid 349 through 357 Processing helix chain 'G' and resid 359 through 363 removed outlier: 3.694A pdb=" N LYS G 362 " --> pdb=" O SER G 359 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS G 363 " --> pdb=" O THR G 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 359 through 363' Processing helix chain 'G' and resid 437 through 441 removed outlier: 3.692A pdb=" N GLU G 441 " --> pdb=" O TYR G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 475 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.590A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 4.180A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.561A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 4.176A pdb=" N LYS B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.557A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 4.189A pdb=" N LYS C 64 " --> pdb=" O ASP C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 5.011A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N VAL A 338 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS A 45 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N CYS A 340 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS A 47 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.346A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 263 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL A 269 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR A 275 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE A 276 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL A 58 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 278 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASP A 56 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 280 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR A 54 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE A 282 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N GLU A 295 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR A 43 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE A 293 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LYS A 45 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ALA A 291 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A 315 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE A 326 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.619A pdb=" N SER G 428 " --> pdb=" O MET A 115 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN G 393 " --> pdb=" O VAL G 421 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 400 removed outlier: 3.520A pdb=" N ARG A 399 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN A 393 " --> pdb=" O VAL A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 removed outlier: 5.003A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL D 338 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LYS D 45 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N CYS D 340 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYS D 47 " --> pdb=" O CYS D 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.328A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE D 276 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL D 58 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL D 278 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP D 56 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 280 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR D 54 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N PHE D 282 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLU D 295 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR D 43 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 293 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LYS D 45 " --> pdb=" O ALA D 291 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA D 291 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE D 315 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE D 326 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 301 through 302 Processing sheet with id=AB2, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB3, first strand: chain 'D' and resid 399 through 400 removed outlier: 4.065A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 161 removed outlier: 5.002A pdb=" N TYR G 170 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL G 338 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS G 45 " --> pdb=" O VAL G 338 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N CYS G 340 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS G 47 " --> pdb=" O CYS G 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.332A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR G 263 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE G 277 " --> pdb=" O ILE G 267 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL G 269 " --> pdb=" O TYR G 275 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR G 275 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE G 276 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL G 58 " --> pdb=" O ILE G 276 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL G 278 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP G 56 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL G 280 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR G 54 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N PHE G 282 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N PHE G 315 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ILE G 326 " --> pdb=" O PHE G 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 301 through 302 Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.504A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.504A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AC2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.558A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N HIS L 37 " --> pdb=" O PRO L 46 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.558A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.679A pdb=" N LEU B 80 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.924A pdb=" N VAL B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP B 50 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.878A pdb=" N CYS B 92 " --> pdb=" O TRP B 103 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TRP B 103 " --> pdb=" O CYS B 92 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ARG B 94 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 101 " --> pdb=" O ARG B 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 4 through 5 Processing sheet with id=AC8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.516A pdb=" N MET E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS E 37 " --> pdb=" O PRO E 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.516A pdb=" N MET E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.515A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.907A pdb=" N VAL C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 96 through 97 Processing sheet with id=AD4, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.457A pdb=" N MET F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N HIS F 37 " --> pdb=" O PRO F 46 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.457A pdb=" N MET F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) 646 hydrogen bonds defined for protein. 1698 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: 5.42 Time building geometry restraints manager: 5.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4987 1.34 - 1.46: 3694 1.46 - 1.58: 7180 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 15993 Sorted by residual: bond pdb=" N CYS F 88 " pdb=" CA CYS F 88 " ideal model delta sigma weight residual 1.456 1.502 -0.045 1.23e-02 6.61e+03 1.34e+01 bond pdb=" N CYS L 88 " pdb=" CA CYS L 88 " ideal model delta sigma weight residual 1.456 1.499 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" N TYR F 87 " pdb=" CA TYR F 87 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" N TYR E 86 " pdb=" CA TYR E 86 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.19e-02 7.06e+03 9.83e+00 bond pdb=" N GLN F 89 " pdb=" CA GLN F 89 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.27e-02 6.20e+03 9.80e+00 ... (remaining 15988 not shown) Histogram of bond angle deviations from ideal: 100.00 - 106.80: 398 106.80 - 113.60: 8940 113.60 - 120.40: 5705 120.40 - 127.20: 6552 127.20 - 134.00: 119 Bond angle restraints: 21714 Sorted by residual: angle pdb=" C CYS F 88 " pdb=" CA CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sigma weight residual 109.75 115.94 -6.19 1.65e+00 3.67e-01 1.41e+01 angle pdb=" CA ILE H 20 " pdb=" C ILE H 20 " pdb=" O ILE H 20 " ideal model delta sigma weight residual 121.93 117.85 4.08 1.12e+00 7.97e-01 1.33e+01 angle pdb=" CA SER B 25 " pdb=" C SER B 25 " pdb=" O SER B 25 " ideal model delta sigma weight residual 121.45 117.82 3.63 1.07e+00 8.73e-01 1.15e+01 angle pdb=" CA ASN B 82B" pdb=" C ASN B 82B" pdb=" O ASN B 82B" ideal model delta sigma weight residual 122.03 118.08 3.95 1.17e+00 7.31e-01 1.14e+01 angle pdb=" CA SER E 24 " pdb=" C SER E 24 " pdb=" O SER E 24 " ideal model delta sigma weight residual 121.89 118.01 3.88 1.17e+00 7.31e-01 1.10e+01 ... (remaining 21709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 9144 17.33 - 34.65: 519 34.65 - 51.98: 109 51.98 - 69.30: 34 69.30 - 86.63: 19 Dihedral angle restraints: 9825 sinusoidal: 3972 harmonic: 5853 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual -86.00 -159.81 73.81 1 1.00e+01 1.00e-02 6.92e+01 dihedral pdb=" CB CYS D 71 " pdb=" SG CYS D 71 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual -86.00 -152.35 66.35 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CB CYS A 71 " pdb=" SG CYS A 71 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual -86.00 -137.69 51.69 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 9822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2095 0.056 - 0.111: 376 0.111 - 0.167: 83 0.167 - 0.223: 11 0.223 - 0.278: 6 Chirality restraints: 2571 Sorted by residual: chirality pdb=" CA PHE B 91 " pdb=" N PHE B 91 " pdb=" C PHE B 91 " pdb=" CB PHE B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA ARG B 94 " pdb=" N ARG B 94 " pdb=" C ARG B 94 " pdb=" CB ARG B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA CYS H 92 " pdb=" N CYS H 92 " pdb=" C CYS H 92 " pdb=" CB CYS H 92 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2568 not shown) Planarity restraints: 2742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 86 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C TYR F 86 " 0.070 2.00e-02 2.50e+03 pdb=" O TYR F 86 " -0.026 2.00e-02 2.50e+03 pdb=" N TYR F 87 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 86 " -0.019 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C TYR L 86 " 0.064 2.00e-02 2.50e+03 pdb=" O TYR L 86 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR L 87 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY G 215 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.54e+00 pdb=" N PRO G 216 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 216 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 216 " 0.022 5.00e-02 4.00e+02 ... (remaining 2739 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 191 2.68 - 3.24: 13775 3.24 - 3.79: 21578 3.79 - 4.35: 29691 4.35 - 4.90: 51652 Nonbonded interactions: 116887 Sorted by model distance: nonbonded pdb=" OE2 GLU B 72 " pdb=" OG SER B 74 " model vdw 2.126 2.440 nonbonded pdb=" OG1 THR G 334 " pdb=" O SER G 337 " model vdw 2.209 2.440 nonbonded pdb=" OG1 THR A 334 " pdb=" O SER A 337 " model vdw 2.243 2.440 nonbonded pdb=" OG1 THR D 334 " pdb=" O SER D 337 " model vdw 2.253 2.440 nonbonded pdb=" OD1 ASN C 35 " pdb=" OG1 THR C 95 " model vdw 2.260 2.440 ... (remaining 116882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.830 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: 9.090 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 42.210 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15993 Z= 0.231 Angle : 0.587 7.239 21714 Z= 0.363 Chirality : 0.048 0.278 2571 Planarity : 0.004 0.040 2730 Dihedral : 12.278 86.626 5997 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.02 % Allowed : 0.80 % Favored : 98.18 % 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: 0.45 (0.19), residues: 1986 helix: 2.30 (0.28), residues: 393 sheet: 0.39 (0.20), residues: 678 loop : -0.63 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 103 HIS 0.001 0.000 HIS L 37 PHE 0.009 0.001 PHE A 376 TYR 0.010 0.001 TYR G 473 ARG 0.008 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 187 time to evaluate : 2.005 Fit side-chains outliers start: 18 outliers final: 2 residues processed: 201 average time/residue: 1.5948 time to fit residues: 348.2581 Evaluate side-chains 149 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.921 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.2577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 155 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 468 GLN G 290 GLN H 6 GLN B 6 GLN B 54 ASN B 82AASN C 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15993 Z= 0.222 Angle : 0.560 8.414 21714 Z= 0.303 Chirality : 0.047 0.168 2571 Planarity : 0.004 0.039 2730 Dihedral : 5.513 55.121 2397 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.93 % Allowed : 7.62 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1986 helix: 1.81 (0.26), residues: 459 sheet: 0.36 (0.21), residues: 651 loop : -0.87 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 308 HIS 0.003 0.001 HIS E 37 PHE 0.012 0.001 PHE C 91 TYR 0.022 0.002 TYR H 90 ARG 0.005 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 1.740 Fit side-chains outliers start: 34 outliers final: 14 residues processed: 168 average time/residue: 1.5235 time to fit residues: 279.5062 Evaluate side-chains 153 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 0.3908 time to fit residues: 5.5175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 149 optimal weight: 0.0050 chunk 122 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 160 optimal weight: 0.0470 chunk 178 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.7696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 468 GLN B 82AASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15993 Z= 0.164 Angle : 0.501 8.548 21714 Z= 0.268 Chirality : 0.045 0.160 2571 Planarity : 0.004 0.037 2730 Dihedral : 5.252 54.385 2397 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.33 % Allowed : 8.59 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1986 helix: 1.88 (0.27), residues: 462 sheet: 0.36 (0.21), residues: 648 loop : -0.91 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 308 HIS 0.002 0.001 HIS E 37 PHE 0.008 0.001 PHE H 91 TYR 0.013 0.001 TYR F 94 ARG 0.006 0.000 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 1.802 Fit side-chains outliers start: 41 outliers final: 25 residues processed: 164 average time/residue: 1.4795 time to fit residues: 265.6586 Evaluate side-chains 163 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.623 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 16 residues processed: 9 average time/residue: 0.3288 time to fit residues: 6.1534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.0770 chunk 135 optimal weight: 4.9990 chunk 93 optimal weight: 0.0010 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 171 optimal weight: 0.0030 chunk 51 optimal weight: 4.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82AASN C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15993 Z= 0.142 Angle : 0.477 8.987 21714 Z= 0.254 Chirality : 0.044 0.160 2571 Planarity : 0.004 0.036 2730 Dihedral : 5.065 54.056 2397 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.28 % Allowed : 9.33 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.20), residues: 1986 helix: 2.02 (0.27), residues: 462 sheet: 0.40 (0.21), residues: 681 loop : -0.88 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 308 HIS 0.002 0.000 HIS F 37 PHE 0.008 0.001 PHE G 376 TYR 0.010 0.001 TYR E 87 ARG 0.004 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 1.951 Fit side-chains outliers start: 40 outliers final: 27 residues processed: 159 average time/residue: 1.5023 time to fit residues: 262.1009 Evaluate side-chains 158 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 17 residues processed: 11 average time/residue: 0.5191 time to fit residues: 9.7163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN C 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 15993 Z= 0.426 Angle : 0.677 8.620 21714 Z= 0.363 Chirality : 0.051 0.211 2571 Planarity : 0.005 0.050 2730 Dihedral : 6.101 59.144 2397 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.45 % Allowed : 10.69 % Favored : 86.86 % 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: -0.01 (0.19), residues: 1986 helix: 1.82 (0.27), residues: 444 sheet: 0.27 (0.21), residues: 675 loop : -1.21 (0.20), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 308 HIS 0.005 0.002 HIS E 49 PHE 0.014 0.002 PHE G 282 TYR 0.024 0.002 TYR F 94 ARG 0.004 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.906 Fit side-chains outliers start: 43 outliers final: 24 residues processed: 170 average time/residue: 1.4905 time to fit residues: 277.9693 Evaluate side-chains 163 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 139 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 0.3221 time to fit residues: 6.0112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 191 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 15 optimal weight: 0.0040 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.0270 overall best weight: 0.4250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 468 GLN C 3 GLN C 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15993 Z= 0.138 Angle : 0.498 10.343 21714 Z= 0.264 Chirality : 0.044 0.156 2571 Planarity : 0.004 0.038 2730 Dihedral : 5.332 53.523 2397 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.65 % Allowed : 12.40 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1986 helix: 2.16 (0.27), residues: 441 sheet: 0.35 (0.21), residues: 693 loop : -1.06 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 103 HIS 0.002 0.001 HIS L 49 PHE 0.009 0.001 PHE G 376 TYR 0.013 0.001 TYR G 248 ARG 0.005 0.000 ARG B 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 2.040 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 148 average time/residue: 1.5115 time to fit residues: 245.0205 Evaluate side-chains 147 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.813 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 5 average time/residue: 0.2310 time to fit residues: 4.3148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 70 GLN H 6 GLN C 3 GLN C 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15993 Z= 0.385 Angle : 0.661 10.707 21714 Z= 0.351 Chirality : 0.050 0.221 2571 Planarity : 0.005 0.049 2730 Dihedral : 6.048 58.857 2397 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.33 % Allowed : 12.29 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1986 helix: 2.09 (0.27), residues: 426 sheet: 0.24 (0.21), residues: 672 loop : -1.34 (0.19), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 308 HIS 0.004 0.001 HIS F 37 PHE 0.014 0.002 PHE G 282 TYR 0.019 0.002 TYR G 275 ARG 0.006 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 1.798 Fit side-chains outliers start: 41 outliers final: 28 residues processed: 162 average time/residue: 1.4851 time to fit residues: 264.7645 Evaluate side-chains 166 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 2.030 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 19 residues processed: 10 average time/residue: 0.3328 time to fit residues: 7.0934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN C 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15993 Z= 0.215 Angle : 0.561 11.243 21714 Z= 0.295 Chirality : 0.046 0.168 2571 Planarity : 0.004 0.039 2730 Dihedral : 5.638 55.732 2397 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.05 % Allowed : 12.91 % Favored : 85.04 % 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: 0.08 (0.19), residues: 1986 helix: 2.19 (0.27), residues: 426 sheet: 0.32 (0.21), residues: 690 loop : -1.28 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 308 HIS 0.003 0.001 HIS E 49 PHE 0.010 0.001 PHE G 301 TYR 0.011 0.001 TYR H 90 ARG 0.006 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 134 time to evaluate : 2.055 Fit side-chains outliers start: 36 outliers final: 27 residues processed: 157 average time/residue: 1.4585 time to fit residues: 251.2785 Evaluate side-chains 160 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.802 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 18 residues processed: 10 average time/residue: 0.3582 time to fit residues: 7.1649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15993 Z= 0.265 Angle : 0.593 11.335 21714 Z= 0.312 Chirality : 0.047 0.188 2571 Planarity : 0.005 0.040 2730 Dihedral : 5.737 57.259 2397 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.65 % Allowed : 13.48 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 1986 helix: 2.17 (0.27), residues: 426 sheet: 0.27 (0.20), residues: 705 loop : -1.31 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 47 HIS 0.003 0.001 HIS F 37 PHE 0.010 0.001 PHE G 282 TYR 0.013 0.002 TYR G 275 ARG 0.006 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 1.642 Fit side-chains outliers start: 29 outliers final: 23 residues processed: 156 average time/residue: 1.6046 time to fit residues: 273.9190 Evaluate side-chains 159 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.866 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 17 residues processed: 6 average time/residue: 0.2964 time to fit residues: 5.1047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 181 optimal weight: 0.0020 chunk 157 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN C 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15993 Z= 0.187 Angle : 0.544 11.701 21714 Z= 0.284 Chirality : 0.045 0.167 2571 Planarity : 0.004 0.039 2730 Dihedral : 5.425 54.661 2397 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.25 % Allowed : 13.94 % Favored : 84.81 % 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: 0.13 (0.20), residues: 1986 helix: 2.26 (0.27), residues: 426 sheet: 0.36 (0.21), residues: 690 loop : -1.28 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 308 HIS 0.003 0.001 HIS E 49 PHE 0.011 0.001 PHE G 301 TYR 0.010 0.001 TYR H 90 ARG 0.006 0.000 ARG C 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3972 Ramachandran restraints generated. 1986 Oldfield, 0 Emsley, 1986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 135 time to evaluate : 1.810 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 152 average time/residue: 1.5492 time to fit residues: 258.0612 Evaluate side-chains 152 residues out of total 1758 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 0.2723 time to fit residues: 3.7248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 157 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS H 6 GLN L 49 HIS C 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.087569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.068675 restraints weight = 27744.961| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.54 r_work: 0.2788 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15993 Z= 0.325 Angle : 0.634 11.676 21714 Z= 0.333 Chirality : 0.049 0.213 2571 Planarity : 0.005 0.040 2730 Dihedral : 5.836 57.618 2397 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.54 % Allowed : 13.71 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.19), residues: 1986 helix: 2.14 (0.27), residues: 426 sheet: 0.23 (0.21), residues: 675 loop : -1.45 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 47 HIS 0.004 0.001 HIS E 37 PHE 0.013 0.002 PHE G 282 TYR 0.016 0.002 TYR G 275 ARG 0.007 0.001 ARG C 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5127.05 seconds wall clock time: 92 minutes 15.60 seconds (5535.60 seconds total)