Starting phenix.real_space_refine on Sun Jan 26 12:02:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aqq_11872/01_2025/7aqq_11872.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aqq_11872/01_2025/7aqq_11872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7aqq_11872/01_2025/7aqq_11872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aqq_11872/01_2025/7aqq_11872.map" model { file = "/net/cci-nas-00/data/ceres_data/7aqq_11872/01_2025/7aqq_11872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aqq_11872/01_2025/7aqq_11872.cif" } resolution = 3.06 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= 0.001 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 1 6.06 5 P 6 5.49 5 S 140 5.16 5 C 15301 2.51 5 N 3768 2.21 5 O 4064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 4.66s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 23281 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 779 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 2439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2439 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 18, 'TRANS': 292} Chain breaks: 1 Chain: "J" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "K" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 707 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain: "L" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 208 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "M" Number of atoms: 2126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2126 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 10, 'TRANS': 251} Chain: "N" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3820 Classifications: {'peptide': 488} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 471} Chain: "O" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 956 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "X" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "Z" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 798 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "a" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 469 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "b" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 295 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "d" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 592 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "e" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 557 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "f" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 763 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "i" Number of atoms: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 614 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 5, 'TRANS': 64} Chain: "u" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "v" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 226 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "x" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1659 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 14, 'TRANS': 199} Chain: "y" Number of atoms: 2032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2032 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "z" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 226} Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'PTY': 1, 'UQ9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1, 'UQ9:plan-7': 1, 'UQ9:plan-2': 1} Unresolved non-hydrogen planarities: 23 Chain: "M" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC7': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {' ZN': 1, 'PGT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "z" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'PSF': 1, 'T7X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11654 SG CYS O 91 63.732 76.570 110.681 1.00 80.80 S ATOM 11680 SG CYS O 95 62.372 75.072 114.020 1.00 85.61 S ATOM 12019 SG CYS O 135 64.767 77.787 114.320 1.00 86.20 S Time building chain proxies: 15.95, per 1000 atoms: 0.69 Number of scatterers: 23281 At special positions: 0 Unit cell: (135.594, 122.202, 174.096, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 S 140 16.00 P 6 15.00 O 4064 8.00 N 3768 7.00 C 15301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 336 " - pdb=" SG CYS N 420 " distance=2.03 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 34 " 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 Time building additional restraints: 6.52 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN y 301 " pdb="ZN ZN y 301 " - pdb=" NE2 HIS z 130 " pdb="ZN ZN y 301 " - pdb=" NE2 HIS y 135 " pdb="ZN ZN y 301 " - pdb=" NE2 HIS y 107 " 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 13 sheets defined 64.8% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 5 through 29 Proline residue: A 26 - end of helix removed outlier: 4.371A pdb=" N PHE A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 84 removed outlier: 3.783A pdb=" N SER A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 91 through 113 Processing helix chain 'H' and resid 4 through 35 Proline residue: H 15 - end of helix removed outlier: 3.684A pdb=" N ALA H 32 " --> pdb=" O ARG H 28 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN H 35 " --> pdb=" O MET H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 71 through 88 removed outlier: 3.618A pdb=" N ARG H 75 " --> pdb=" O PHE H 71 " (cutoff:3.500A) Proline residue: H 78 - end of helix removed outlier: 3.767A pdb=" N ALA H 88 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 105 through 116 Processing helix chain 'H' and resid 117 through 128 removed outlier: 4.680A pdb=" N ILE H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 163 removed outlier: 4.084A pdb=" N SER H 150 " --> pdb=" O SER H 146 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS H 161 " --> pdb=" O THR H 157 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.682A pdb=" N MET H 172 " --> pdb=" O SER H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 198 Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'H' and resid 222 through 247 Processing helix chain 'H' and resid 264 through 287 removed outlier: 3.847A pdb=" N TRP H 268 " --> pdb=" O PRO H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 302 removed outlier: 3.968A pdb=" N GLY H 297 " --> pdb=" O ASP H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 303 through 321 Processing helix chain 'J' and resid 2 through 19 removed outlier: 3.862A pdb=" N ALA J 10 " --> pdb=" O LEU J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 44 removed outlier: 3.749A pdb=" N PHE J 34 " --> pdb=" O PHE J 30 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY J 39 " --> pdb=" O CYS J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 57 Processing helix chain 'J' and resid 60 through 73 removed outlier: 3.869A pdb=" N PHE J 72 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N HIS J 73 " --> pdb=" O VAL J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 130 removed outlier: 3.519A pdb=" N GLY J 129 " --> pdb=" O VAL J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 145 removed outlier: 4.157A pdb=" N LEU J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR J 145 " --> pdb=" O GLY J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 170 removed outlier: 3.654A pdb=" N PHE J 152 " --> pdb=" O TYR J 148 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE J 167 " --> pdb=" O MET J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 24 Processing helix chain 'K' and resid 27 through 54 removed outlier: 3.849A pdb=" N MET K 31 " --> pdb=" O ASN K 27 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE K 35 " --> pdb=" O MET K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 88 removed outlier: 3.825A pdb=" N THR K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 68 " --> pdb=" O LEU K 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG K 87 " --> pdb=" O THR K 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 592 through 597 Processing helix chain 'L' and resid 602 through 605 Processing helix chain 'L' and resid 606 through 611 removed outlier: 3.596A pdb=" N GLU L 611 " --> pdb=" O ARG L 607 " (cutoff:3.500A) Processing helix chain 'L' and resid 612 through 615 Processing helix chain 'M' and resid 11 through 28 removed outlier: 3.695A pdb=" N LEU M 15 " --> pdb=" O ASN M 11 " (cutoff:3.500A) Proline residue: M 19 - end of helix removed outlier: 3.761A pdb=" N PHE M 28 " --> pdb=" O ILE M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 58 removed outlier: 3.503A pdb=" N GLN M 58 " --> pdb=" O VAL M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 108 removed outlier: 4.197A pdb=" N ILE M 101 " --> pdb=" O THR M 97 " (cutoff:3.500A) Proline residue: M 102 - end of helix removed outlier: 3.657A pdb=" N GLY M 108 " --> pdb=" O CYS M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 116 removed outlier: 3.767A pdb=" N TYR M 115 " --> pdb=" O GLY M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 136 removed outlier: 4.291A pdb=" N ILE M 120 " --> pdb=" O GLY M 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA M 132 " --> pdb=" O PHE M 128 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE M 134 " --> pdb=" O MET M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 138 through 147 Processing helix chain 'M' and resid 149 through 160 Processing helix chain 'M' and resid 165 through 196 removed outlier: 3.630A pdb=" N PHE M 183 " --> pdb=" O LEU M 179 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA M 187 " --> pdb=" O PHE M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 204 Processing helix chain 'M' and resid 209 through 228 removed outlier: 3.861A pdb=" N ILE M 214 " --> pdb=" O GLU M 210 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE M 215 " --> pdb=" O ARG M 211 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER M 223 " --> pdb=" O ALA M 219 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL M 226 " --> pdb=" O ALA M 222 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS M 227 " --> pdb=" O SER M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 235 through 243 removed outlier: 4.510A pdb=" N GLU M 239 " --> pdb=" O ILE M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 245 through 255 removed outlier: 3.575A pdb=" N VAL M 250 " --> pdb=" O THR M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 267 removed outlier: 4.545A pdb=" N THR M 261 " --> pdb=" O LEU M 257 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 18 removed outlier: 4.075A pdb=" N ALA N 18 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 41 removed outlier: 3.503A pdb=" N ILE N 25 " --> pdb=" O PRO N 21 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR N 41 " --> pdb=" O VAL N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 72 removed outlier: 3.619A pdb=" N VAL N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 78 removed outlier: 4.193A pdb=" N THR N 77 " --> pdb=" O PRO N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 111 Processing helix chain 'N' and resid 111 through 118 removed outlier: 3.710A pdb=" N PHE N 115 " --> pdb=" O CYS N 111 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP N 116 " --> pdb=" O PHE N 112 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU N 118 " --> pdb=" O PHE N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 141 removed outlier: 3.560A pdb=" N VAL N 127 " --> pdb=" O PHE N 123 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 164 removed outlier: 3.551A pdb=" N ILE N 162 " --> pdb=" O CYS N 158 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA N 164 " --> pdb=" O TYR N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 169 through 202 removed outlier: 3.550A pdb=" N THR N 173 " --> pdb=" O SER N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 212 Processing helix chain 'N' and resid 223 through 242 Processing helix chain 'N' and resid 249 through 257 Processing helix chain 'N' and resid 258 through 266 removed outlier: 3.518A pdb=" N PHE N 264 " --> pdb=" O PRO N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 285 removed outlier: 3.660A pdb=" N SER N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE N 273 " --> pdb=" O PRO N 269 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR N 283 " --> pdb=" O ARG N 279 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER N 285 " --> pdb=" O PHE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 288 through 310 removed outlier: 3.562A pdb=" N GLN N 292 " --> pdb=" O ALA N 288 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET N 310 " --> pdb=" O ALA N 306 " (cutoff:3.500A) Processing helix chain 'N' and resid 314 through 336 removed outlier: 4.106A pdb=" N GLY N 333 " --> pdb=" O TYR N 329 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE N 334 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 367 Processing helix chain 'N' and resid 368 through 370 No H-bonds generated for 'chain 'N' and resid 368 through 370' Processing helix chain 'N' and resid 373 through 378 Processing helix chain 'N' and resid 379 through 384 Processing helix chain 'N' and resid 386 through 400 Processing helix chain 'N' and resid 405 through 420 removed outlier: 4.032A pdb=" N SER N 409 " --> pdb=" O ALA N 405 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS N 410 " --> pdb=" O GLY N 406 " (cutoff:3.500A) Processing helix chain 'N' and resid 422 through 449 removed outlier: 3.719A pdb=" N ALA N 426 " --> pdb=" O ALA N 422 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU N 443 " --> pdb=" O TYR N 439 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL N 444 " --> pdb=" O TYR N 440 " (cutoff:3.500A) Processing helix chain 'N' and resid 462 through 478 Processing helix chain 'N' and resid 483 through 497 Processing helix chain 'O' and resid 40 through 43 Processing helix chain 'O' and resid 67 through 76 removed outlier: 4.268A pdb=" N THR O 75 " --> pdb=" O ALA O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 121 removed outlier: 3.625A pdb=" N SER O 121 " --> pdb=" O VAL O 117 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 137 No H-bonds generated for 'chain 'O' and resid 135 through 137' Processing helix chain 'O' and resid 140 through 144 removed outlier: 3.854A pdb=" N GLN O 144 " --> pdb=" O GLN O 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 21 Processing helix chain 'X' and resid 21 through 29 removed outlier: 3.789A pdb=" N MET X 27 " --> pdb=" O LYS X 23 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 43 Processing helix chain 'X' and resid 45 through 48 Processing helix chain 'X' and resid 49 through 71 removed outlier: 3.634A pdb=" N LEU X 63 " --> pdb=" O CYS X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 85 removed outlier: 3.520A pdb=" N ASP X 77 " --> pdb=" O LYS X 73 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 93 through 103 removed outlier: 3.687A pdb=" N VAL X 102 " --> pdb=" O ALA X 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 81 removed outlier: 3.552A pdb=" N MET Z 61 " --> pdb=" O PHE Z 57 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 112 removed outlier: 3.545A pdb=" N LEU Z 89 " --> pdb=" O ILE Z 85 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET Z 112 " --> pdb=" O GLU Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 139 through 143 removed outlier: 4.047A pdb=" N VAL Z 142 " --> pdb=" O ARG Z 139 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TRP Z 143 " --> pdb=" O PRO Z 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 139 through 143' Processing helix chain 'a' and resid 4 through 7 removed outlier: 4.099A pdb=" N GLU a 7 " --> pdb=" O VAL a 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 4 through 7' Processing helix chain 'a' and resid 8 through 29 removed outlier: 4.128A pdb=" N LEU a 12 " --> pdb=" O ALA a 8 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN a 26 " --> pdb=" O MET a 22 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR a 27 " --> pdb=" O GLY a 23 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR a 28 " --> pdb=" O ASN a 24 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE a 29 " --> pdb=" O SER a 25 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 35 Processing helix chain 'a' and resid 43 through 60 Processing helix chain 'b' and resid 5 through 14 Processing helix chain 'b' and resid 14 through 41 Proline residue: b 31 - end of helix removed outlier: 4.728A pdb=" N ARG b 35 " --> pdb=" O PRO b 31 " (cutoff:3.500A) Proline residue: b 36 - end of helix removed outlier: 3.882A pdb=" N LEU b 41 " --> pdb=" O ILE b 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 24 Processing helix chain 'd' and resid 31 through 73 removed outlier: 3.636A pdb=" N HIS d 35 " --> pdb=" O HIS d 31 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS d 55 " --> pdb=" O LYS d 51 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 76 No H-bonds generated for 'chain 'd' and resid 74 through 76' Processing helix chain 'e' and resid 14 through 26 Processing helix chain 'e' and resid 34 through 47 removed outlier: 3.561A pdb=" N HIS e 46 " --> pdb=" O LEU e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 47 through 66 Processing helix chain 'f' and resid 21 through 27 Processing helix chain 'f' and resid 30 through 52 Processing helix chain 'f' and resid 57 through 86 removed outlier: 3.717A pdb=" N SER f 61 " --> pdb=" O ILE f 57 " (cutoff:3.500A) Processing helix chain 'f' and resid 91 through 100 removed outlier: 3.649A pdb=" N ALA f 96 " --> pdb=" O ASP f 92 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS f 100 " --> pdb=" O ALA f 96 " (cutoff:3.500A) Processing helix chain 'i' and resid 18 through 45 Processing helix chain 'i' and resid 52 through 56 Processing helix chain 'i' and resid 61 through 66 Processing helix chain 'i' and resid 77 through 82 removed outlier: 3.951A pdb=" N ASP i 81 " --> pdb=" O ASP i 77 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU i 82 " --> pdb=" O PRO i 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 77 through 82' Processing helix chain 'u' and resid 2 through 26 removed outlier: 3.620A pdb=" N UNK u 21 " --> pdb=" O UNK u 17 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N UNK u 26 " --> pdb=" O UNK u 22 " (cutoff:3.500A) Processing helix chain 'v' and resid 79 through 103 Processing helix chain 'x' and resid 210 through 233 Proline residue: x 218 - end of helix removed outlier: 3.695A pdb=" N ALA x 221 " --> pdb=" O ILE x 217 " (cutoff:3.500A) Processing helix chain 'x' and resid 240 through 252 removed outlier: 4.156A pdb=" N GLU x 244 " --> pdb=" O THR x 240 " (cutoff:3.500A) Processing helix chain 'y' and resid 3 through 30 Processing helix chain 'y' and resid 193 through 219 removed outlier: 4.059A pdb=" N GLN y 212 " --> pdb=" O ILE y 208 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ILE y 213 " --> pdb=" O ASN y 209 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS y 214 " --> pdb=" O LEU y 210 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER y 219 " --> pdb=" O ALA y 215 " (cutoff:3.500A) Processing helix chain 'y' and resid 221 through 235 Processing helix chain 'y' and resid 239 through 247 Processing helix chain 'y' and resid 253 through 257 Processing helix chain 'z' and resid 3 through 30 Processing helix chain 'z' and resid 33 through 37 Processing helix chain 'z' and resid 193 through 219 removed outlier: 3.596A pdb=" N ALA z 204 " --> pdb=" O ILE z 200 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR z 205 " --> pdb=" O SER z 201 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN z 212 " --> pdb=" O SER z 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA z 213 " --> pdb=" O ASN z 209 " (cutoff:3.500A) Processing helix chain 'z' and resid 223 through 232 removed outlier: 3.614A pdb=" N PHE z 227 " --> pdb=" O ASN z 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 67 through 73 removed outlier: 5.515A pdb=" N PHE M 68 " --> pdb=" O ILE M 86 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE M 86 " --> pdb=" O PHE M 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 57 through 63 removed outlier: 10.155A pdb=" N MET O 146 " --> pdb=" O ILE O 45 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LYS O 47 " --> pdb=" O MET O 146 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N VAL O 148 " --> pdb=" O LYS O 47 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER O 49 " --> pdb=" O VAL O 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 62 through 63 removed outlier: 6.731A pdb=" N VAL x 83 " --> pdb=" O LEU x 102 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY x 104 " --> pdb=" O VAL x 83 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA x 85 " --> pdb=" O GLY x 104 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU x 106 " --> pdb=" O ALA x 85 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLN x 87 " --> pdb=" O LEU x 106 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS x 108 " --> pdb=" O GLN x 87 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR x 89 " --> pdb=" O LYS x 108 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR x 110 " --> pdb=" O THR x 89 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL x 101 " --> pdb=" O VAL x 123 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU x 150 " --> pdb=" O LEU x 168 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE x 167 " --> pdb=" O LEU x 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'x' and resid 71 through 72 removed outlier: 6.434A pdb=" N LYS x 71 " --> pdb=" O VAL x 90 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL x 83 " --> pdb=" O LEU x 102 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY x 104 " --> pdb=" O VAL x 83 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA x 85 " --> pdb=" O GLY x 104 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU x 106 " --> pdb=" O ALA x 85 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLN x 87 " --> pdb=" O LEU x 106 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS x 108 " --> pdb=" O GLN x 87 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR x 89 " --> pdb=" O LYS x 108 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR x 110 " --> pdb=" O THR x 89 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU x 138 " --> pdb=" O ILE x 156 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR x 155 " --> pdb=" O VAL x 174 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU x 173 " --> pdb=" O ILE x 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'x' and resid 77 through 78 removed outlier: 6.442A pdb=" N TYR x 77 " --> pdb=" O VAL x 96 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER x 95 " --> pdb=" O VAL x 117 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN x 116 " --> pdb=" O VAL x 145 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR x 144 " --> pdb=" O ILE x 162 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE x 161 " --> pdb=" O LEU x 180 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE x 179 " --> pdb=" O TRP x 198 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU x 197 " --> pdb=" O ILE x 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'y' and resid 45 through 46 removed outlier: 6.429A pdb=" N MET y 46 " --> pdb=" O GLY y 69 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL y 71 " --> pdb=" O MET y 46 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER y 66 " --> pdb=" O LEU y 85 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY y 87 " --> pdb=" O SER y 66 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE y 68 " --> pdb=" O GLY y 87 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL y 89 " --> pdb=" O ILE y 68 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP y 70 " --> pdb=" O VAL y 89 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN y 91 " --> pdb=" O ASP y 70 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLN y 72 " --> pdb=" O ASN y 91 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER y 93 " --> pdb=" O GLN y 72 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'y' and resid 45 through 46 removed outlier: 6.429A pdb=" N MET y 46 " --> pdb=" O GLY y 69 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N VAL y 71 " --> pdb=" O MET y 46 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N SER y 66 " --> pdb=" O LEU y 85 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY y 87 " --> pdb=" O SER y 66 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE y 68 " --> pdb=" O GLY y 87 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL y 89 " --> pdb=" O ILE y 68 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP y 70 " --> pdb=" O VAL y 89 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN y 91 " --> pdb=" O ASP y 70 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N GLN y 72 " --> pdb=" O ASN y 91 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER y 93 " --> pdb=" O GLN y 72 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL y 84 " --> pdb=" O VAL y 106 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU y 105 " --> pdb=" O ILE y 134 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL y 133 " --> pdb=" O LEU y 151 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR y 150 " --> pdb=" O VAL y 169 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'y' and resid 60 through 61 removed outlier: 6.074A pdb=" N PHE y 60 " --> pdb=" O ILE y 79 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER y 78 " --> pdb=" O ILE y 100 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN y 99 " --> pdb=" O VAL y 128 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR y 127 " --> pdb=" O VAL y 145 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE y 144 " --> pdb=" O VAL y 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'y' and resid 156 through 157 removed outlier: 6.758A pdb=" N VAL y 156 " --> pdb=" O ILE y 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'z' and resid 45 through 46 removed outlier: 16.146A pdb=" N SER z 66 " --> pdb=" O ASP z 88 " (cutoff:3.500A) removed outlier: 13.977A pdb=" N ASN z 90 " --> pdb=" O SER z 66 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N ILE z 68 " --> pdb=" O ASN z 90 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL z 92 " --> pdb=" O ILE z 68 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP z 70 " --> pdb=" O VAL z 92 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL z 94 " --> pdb=" O ASP z 70 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS z 72 " --> pdb=" O VAL z 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'z' and resid 54 through 55 removed outlier: 16.146A pdb=" N SER z 66 " --> pdb=" O ASP z 88 " (cutoff:3.500A) removed outlier: 13.977A pdb=" N ASN z 90 " --> pdb=" O SER z 66 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N ILE z 68 " --> pdb=" O ASN z 90 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL z 92 " --> pdb=" O ILE z 68 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP z 70 " --> pdb=" O VAL z 92 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL z 94 " --> pdb=" O ASP z 70 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N HIS z 72 " --> pdb=" O VAL z 94 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL z 84 " --> pdb=" O VAL z 106 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU z 105 " --> pdb=" O LEU z 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'z' and resid 60 through 61 removed outlier: 6.434A pdb=" N PHE z 60 " --> pdb=" O ILE z 79 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER z 78 " --> pdb=" O ILE z 100 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE z 128 " --> pdb=" O ASN z 99 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR z 127 " --> pdb=" O ILE z 145 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE z 144 " --> pdb=" O VAL z 163 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET z 162 " --> pdb=" O TRP z 181 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG z 190 " --> pdb=" O VAL z 180 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLY z 182 " --> pdb=" O PHE z 188 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N PHE z 188 " --> pdb=" O GLY z 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'z' and resid 138 through 139 removed outlier: 7.077A pdb=" N THR z 138 " --> pdb=" O VAL z 157 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL z 156 " --> pdb=" O ILE z 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 1312 hydrogen bonds defined for protein. 3855 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: 8.73 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3572 1.31 - 1.43: 6469 1.43 - 1.56: 13520 1.56 - 1.69: 26 1.69 - 1.82: 231 Bond restraints: 23818 Sorted by residual: bond pdb=" C3 UQ9 H 401 " pdb=" C4 UQ9 H 401 " ideal model delta sigma weight residual 1.340 1.534 -0.194 2.00e-02 2.50e+03 9.43e+01 bond pdb=" C1 UQ9 H 401 " pdb=" C6 UQ9 H 401 " ideal model delta sigma weight residual 1.345 1.529 -0.184 2.00e-02 2.50e+03 8.42e+01 bond pdb=" C1 LMN M 501 " pdb=" O5 LMN M 501 " ideal model delta sigma weight residual 1.403 1.533 -0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" CBS LMN M 501 " pdb=" CCM LMN M 501 " ideal model delta sigma weight residual 1.529 1.627 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C4 LMN M 501 " pdb=" O4 LMN M 501 " ideal model delta sigma weight residual 1.409 1.506 -0.097 2.00e-02 2.50e+03 2.37e+01 ... (remaining 23813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.35: 31891 3.35 - 6.70: 293 6.70 - 10.05: 34 10.05 - 13.40: 6 13.40 - 16.75: 5 Bond angle restraints: 32229 Sorted by residual: angle pdb=" N MET H 223 " pdb=" CA MET H 223 " pdb=" C MET H 223 " ideal model delta sigma weight residual 111.28 118.51 -7.23 1.09e+00 8.42e-01 4.40e+01 angle pdb=" O3P PGT y 302 " pdb=" P PGT y 302 " pdb=" O4P PGT y 302 " ideal model delta sigma weight residual 92.82 109.57 -16.75 3.00e+00 1.11e-01 3.12e+01 angle pdb=" O11 PTY N 501 " pdb=" P1 PTY N 501 " pdb=" O14 PTY N 501 " ideal model delta sigma weight residual 92.90 109.37 -16.47 3.00e+00 1.11e-01 3.01e+01 angle pdb=" O11 PTY H 402 " pdb=" P1 PTY H 402 " pdb=" O14 PTY H 402 " ideal model delta sigma weight residual 92.90 109.28 -16.38 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O3P PC7 v 201 " pdb=" P PC7 v 201 " pdb=" O4P PC7 v 201 " ideal model delta sigma weight residual 93.18 109.21 -16.03 3.00e+00 1.11e-01 2.86e+01 ... (remaining 32224 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.51: 13710 33.51 - 67.02: 392 67.02 - 100.52: 59 100.52 - 134.03: 22 134.03 - 167.54: 4 Dihedral angle restraints: 14187 sinusoidal: 5796 harmonic: 8391 Sorted by residual: dihedral pdb=" CB PSF z 301 " pdb=" O1 PSF z 301 " pdb=" P PSF z 301 " pdb=" O3 PSF z 301 " ideal model delta sinusoidal sigma weight residual -29.12 138.42 -167.54 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3 PTY N 501 " pdb=" O11 PTY N 501 " pdb=" P1 PTY N 501 " pdb=" O12 PTY N 501 " ideal model delta sinusoidal sigma weight residual -59.77 95.63 -155.40 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C20 UQ9 H 401 " pdb=" C19 UQ9 H 401 " pdb=" C21 UQ9 H 401 " pdb=" C22 UQ9 H 401 " ideal model delta sinusoidal sigma weight residual -67.82 83.76 -151.58 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 14184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.971: 3672 0.971 - 1.942: 0 1.942 - 2.913: 0 2.913 - 3.884: 0 3.884 - 4.855: 1 Chirality restraints: 3673 Sorted by residual: chirality pdb=" C1 T7X z 302 " pdb=" C2 T7X z 302 " pdb=" C6 T7X z 302 " pdb=" O1 T7X z 302 " both_signs ideal model delta sigma weight residual False -2.42 2.44 -4.85 2.00e-01 2.50e+01 5.89e+02 chirality pdb=" CA MET H 223 " pdb=" N MET H 223 " pdb=" C MET H 223 " pdb=" CB MET H 223 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA SER H 222 " pdb=" N SER H 222 " pdb=" C SER H 222 " pdb=" CB SER H 222 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3670 not shown) Planarity restraints: 3960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP Z 141 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C ASP Z 141 " 0.032 2.00e-02 2.50e+03 pdb=" O ASP Z 141 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL Z 142 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP Z 141 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" CG ASP Z 141 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASP Z 141 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP Z 141 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE M 269 " 0.029 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO M 270 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO M 270 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO M 270 " 0.026 5.00e-02 4.00e+02 ... (remaining 3957 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 147 2.57 - 3.16: 19012 3.16 - 3.74: 36827 3.74 - 4.32: 51209 4.32 - 4.90: 86931 Nonbonded interactions: 194126 Sorted by model distance: nonbonded pdb=" OE2 GLU K 36 " pdb=" OG SER K 73 " model vdw 1.992 3.040 nonbonded pdb=" OH TYR x 148 " pdb=" O ASN z 103 " model vdw 2.061 3.040 nonbonded pdb=" NE2 HIS O 83 " pdb="FE FE O 200 " model vdw 2.085 2.340 nonbonded pdb=" OG1 THR z 143 " pdb=" O GLY z 161 " model vdw 2.133 3.040 nonbonded pdb=" O PHE A 77 " pdb=" OH TYR J 145 " model vdw 2.162 3.040 ... (remaining 194121 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 38.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 56.470 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.100 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 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 : 0.005 0.194 23818 Z= 0.362 Angle : 0.754 16.754 32229 Z= 0.341 Chirality : 0.091 4.855 3673 Planarity : 0.004 0.045 3960 Dihedral : 17.171 167.541 8789 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.13 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.16), residues: 2841 helix: 1.66 (0.13), residues: 1705 sheet: -0.97 (0.54), residues: 96 loop : -0.64 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.007 0.001 HIS z 214 PHE 0.026 0.002 PHE N 20 TYR 0.025 0.001 TYR N 439 ARG 0.008 0.000 ARG d 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 2.742 Fit side-chains REVERT: H 301 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8714 (mttt) REVERT: a 5 TRP cc_start: 0.8572 (p-90) cc_final: 0.4683 (t-100) REVERT: f 86 MET cc_start: 0.8794 (mtp) cc_final: 0.8589 (mtm) REVERT: y 110 LYS cc_start: 0.7317 (tptp) cc_final: 0.6900 (mttp) outliers start: 0 outliers final: 0 residues processed: 439 average time/residue: 0.4013 time to fit residues: 263.5441 Evaluate side-chains 385 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 0.7980 chunk 215 optimal weight: 0.0970 chunk 119 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 257 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 294 GLN M 31 ASN M 58 GLN N 53 ASN N 368 GLN X 45 ASN X 72 GLN a 42 HIS ** x 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 209 ASN ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 212 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096581 restraints weight = 35056.679| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.83 r_work: 0.3130 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23818 Z= 0.249 Angle : 0.584 9.729 32229 Z= 0.286 Chirality : 0.043 0.264 3673 Planarity : 0.004 0.049 3960 Dihedral : 15.061 171.561 3545 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 0.73 % Allowed : 7.72 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.16), residues: 2841 helix: 1.85 (0.13), residues: 1727 sheet: -1.78 (0.50), residues: 94 loop : -0.46 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 111 HIS 0.005 0.001 HIS z 214 PHE 0.021 0.002 PHE J 72 TYR 0.023 0.001 TYR N 439 ARG 0.006 0.000 ARG e 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 425 time to evaluate : 2.399 Fit side-chains REVERT: M 115 TYR cc_start: 0.9100 (m-80) cc_final: 0.8839 (m-80) REVERT: N 438 PHE cc_start: 0.8298 (t80) cc_final: 0.7982 (t80) REVERT: O 120 ARG cc_start: 0.7650 (mtm110) cc_final: 0.6423 (mmm160) REVERT: X 47 GLU cc_start: 0.7751 (mp0) cc_final: 0.7540 (mp0) REVERT: X 74 GLU cc_start: 0.8793 (mp0) cc_final: 0.8534 (mp0) REVERT: Z 141 ASP cc_start: 0.8363 (p0) cc_final: 0.8117 (p0) REVERT: a 5 TRP cc_start: 0.8872 (p-90) cc_final: 0.4615 (t-100) REVERT: a 7 GLU cc_start: 0.8311 (mp0) cc_final: 0.7524 (mt-10) REVERT: d 72 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7409 (mt-10) REVERT: y 110 LYS cc_start: 0.7488 (tptp) cc_final: 0.6904 (mttp) outliers start: 18 outliers final: 14 residues processed: 434 average time/residue: 0.4159 time to fit residues: 267.1122 Evaluate side-chains 410 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 396 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 220 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain d residue 7 MET Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain y residue 216 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 181 optimal weight: 0.9990 chunk 216 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 154 optimal weight: 0.0050 chunk 95 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.0000 chunk 283 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 368 GLN a 26 GLN a 42 HIS ** x 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 202 GLN z 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.096782 restraints weight = 34743.740| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.85 r_work: 0.3130 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23818 Z= 0.194 Angle : 0.547 12.212 32229 Z= 0.265 Chirality : 0.042 0.321 3673 Planarity : 0.004 0.049 3960 Dihedral : 13.468 176.879 3545 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.99 % Favored : 96.90 % Rotamer: Outliers : 1.55 % Allowed : 10.17 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.16), residues: 2841 helix: 1.94 (0.12), residues: 1733 sheet: -1.81 (0.49), residues: 99 loop : -0.36 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 111 HIS 0.004 0.001 HIS N 35 PHE 0.020 0.001 PHE J 30 TYR 0.023 0.001 TYR N 439 ARG 0.006 0.000 ARG O 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 415 time to evaluate : 2.838 Fit side-chains REVERT: J 145 TYR cc_start: 0.9088 (m-80) cc_final: 0.8727 (m-80) REVERT: M 115 TYR cc_start: 0.9082 (m-80) cc_final: 0.8845 (m-80) REVERT: M 214 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8200 (mp) REVERT: N 438 PHE cc_start: 0.8299 (t80) cc_final: 0.7954 (t80) REVERT: O 120 ARG cc_start: 0.7613 (mtm110) cc_final: 0.6513 (mmm160) REVERT: X 74 GLU cc_start: 0.8689 (mp0) cc_final: 0.8384 (mp0) REVERT: Z 141 ASP cc_start: 0.8205 (p0) cc_final: 0.7878 (p0) REVERT: a 5 TRP cc_start: 0.8847 (p-90) cc_final: 0.4686 (t-100) REVERT: a 7 GLU cc_start: 0.8307 (mp0) cc_final: 0.7526 (mt-10) REVERT: a 55 LYS cc_start: 0.8594 (mttp) cc_final: 0.8247 (mptt) REVERT: d 72 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7437 (mt-10) REVERT: e 32 LYS cc_start: 0.8800 (mppt) cc_final: 0.8553 (mptt) REVERT: y 110 LYS cc_start: 0.7404 (tptp) cc_final: 0.6887 (tttt) outliers start: 38 outliers final: 23 residues processed: 436 average time/residue: 0.4087 time to fit residues: 265.9202 Evaluate side-chains 423 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 399 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain N residue 244 VAL Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 398 TYR Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain e residue 62 GLN Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain i residue 43 MET Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain y residue 141 ASP Chi-restraints excluded: chain y residue 216 SER Chi-restraints excluded: chain y residue 261 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 173 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 88 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 58 GLN N 368 GLN a 42 HIS ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 116 ASN ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 202 GLN z 212 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094461 restraints weight = 35304.767| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.86 r_work: 0.3096 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23818 Z= 0.320 Angle : 0.582 9.982 32229 Z= 0.285 Chirality : 0.044 0.429 3673 Planarity : 0.004 0.049 3960 Dihedral : 12.844 178.557 3545 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.34 % Favored : 96.55 % Rotamer: Outliers : 1.84 % Allowed : 12.58 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.16), residues: 2841 helix: 1.87 (0.12), residues: 1739 sheet: -1.03 (0.53), residues: 97 loop : -0.51 (0.20), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 111 HIS 0.005 0.001 HIS z 130 PHE 0.021 0.002 PHE J 30 TYR 0.020 0.001 TYR N 439 ARG 0.009 0.000 ARG e 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 402 time to evaluate : 2.505 Fit side-chains REVERT: H 31 MET cc_start: 0.8465 (tpp) cc_final: 0.8241 (tpp) REVERT: H 83 MET cc_start: 0.7917 (mmm) cc_final: 0.7548 (mtt) REVERT: K 36 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8315 (mm-30) REVERT: M 210 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7681 (tm-30) REVERT: M 214 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8298 (mp) REVERT: N 43 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8563 (mptt) REVERT: N 438 PHE cc_start: 0.8397 (t80) cc_final: 0.7961 (t80) REVERT: X 47 GLU cc_start: 0.7817 (mp0) cc_final: 0.7612 (mp0) REVERT: Z 141 ASP cc_start: 0.8208 (p0) cc_final: 0.7812 (p0) REVERT: a 7 GLU cc_start: 0.8306 (mp0) cc_final: 0.7527 (mt-10) REVERT: d 72 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7429 (mt-10) REVERT: x 216 GLU cc_start: 0.8523 (pp20) cc_final: 0.8196 (pp20) REVERT: y 110 LYS cc_start: 0.7465 (tptp) cc_final: 0.6974 (tttt) REVERT: y 224 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8535 (tp40) outliers start: 45 outliers final: 36 residues processed: 428 average time/residue: 0.4132 time to fit residues: 262.9939 Evaluate side-chains 430 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 393 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 220 TYR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 58 GLN Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 261 THR Chi-restraints excluded: chain N residue 244 VAL Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 398 TYR Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain i residue 43 MET Chi-restraints excluded: chain x residue 75 ASP Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain y residue 141 ASP Chi-restraints excluded: chain y residue 156 VAL Chi-restraints excluded: chain y residue 216 SER Chi-restraints excluded: chain y residue 261 ASN Chi-restraints excluded: chain z residue 138 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 268 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 200 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 58 GLN N 368 GLN a 26 GLN a 42 HIS ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 202 GLN z 212 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094592 restraints weight = 35183.674| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.86 r_work: 0.3098 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23818 Z= 0.290 Angle : 0.571 9.993 32229 Z= 0.281 Chirality : 0.043 0.416 3673 Planarity : 0.004 0.050 3960 Dihedral : 12.430 168.145 3545 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 2.12 % Allowed : 13.07 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 2841 helix: 1.91 (0.12), residues: 1730 sheet: -0.93 (0.54), residues: 92 loop : -0.51 (0.20), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.013 0.001 HIS a 42 PHE 0.020 0.002 PHE J 30 TYR 0.020 0.001 TYR N 439 ARG 0.009 0.000 ARG e 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 405 time to evaluate : 2.702 Fit side-chains REVERT: H 31 MET cc_start: 0.8529 (tpp) cc_final: 0.8276 (tpp) REVERT: H 83 MET cc_start: 0.7976 (mmm) cc_final: 0.7719 (mtt) REVERT: M 115 TYR cc_start: 0.9106 (m-80) cc_final: 0.8834 (m-80) REVERT: M 210 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7742 (tm-30) REVERT: M 214 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8265 (mp) REVERT: N 438 PHE cc_start: 0.8383 (t80) cc_final: 0.7943 (t80) REVERT: X 47 GLU cc_start: 0.7854 (mp0) cc_final: 0.7636 (mp0) REVERT: X 74 GLU cc_start: 0.8787 (mp0) cc_final: 0.8457 (mp0) REVERT: Z 141 ASP cc_start: 0.8166 (p0) cc_final: 0.7739 (p0) REVERT: a 7 GLU cc_start: 0.8297 (mp0) cc_final: 0.7547 (mt-10) REVERT: d 72 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7474 (mt-10) REVERT: i 31 TYR cc_start: 0.8015 (t80) cc_final: 0.7412 (m-80) REVERT: x 216 GLU cc_start: 0.8518 (pp20) cc_final: 0.8193 (pp20) REVERT: y 110 LYS cc_start: 0.7449 (tptp) cc_final: 0.6954 (tttt) outliers start: 52 outliers final: 40 residues processed: 438 average time/residue: 0.4359 time to fit residues: 287.1068 Evaluate side-chains 430 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 389 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 260 PHE Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain N residue 244 VAL Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 398 TYR Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 113 LYS Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 6 LYS Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain i residue 43 MET Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain y residue 141 ASP Chi-restraints excluded: chain y residue 156 VAL Chi-restraints excluded: chain y residue 216 SER Chi-restraints excluded: chain y residue 261 ASN Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 143 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 34 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 266 optimal weight: 0.4980 chunk 83 optimal weight: 0.5980 chunk 130 optimal weight: 0.6980 chunk 221 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 246 optimal weight: 0.0040 chunk 212 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 31 ASN N 368 GLN a 42 HIS ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 202 GLN z 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096279 restraints weight = 35122.603| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.90 r_work: 0.3120 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23818 Z= 0.207 Angle : 0.538 9.981 32229 Z= 0.266 Chirality : 0.042 0.348 3673 Planarity : 0.004 0.052 3960 Dihedral : 11.962 157.075 3545 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 1.92 % Allowed : 14.25 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.16), residues: 2841 helix: 2.05 (0.13), residues: 1717 sheet: -0.90 (0.55), residues: 92 loop : -0.40 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.008 0.001 HIS a 42 PHE 0.020 0.001 PHE H 71 TYR 0.022 0.001 TYR N 439 ARG 0.011 0.000 ARG e 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 392 time to evaluate : 2.510 Fit side-chains REVERT: H 83 MET cc_start: 0.7971 (mmm) cc_final: 0.7763 (mtt) REVERT: J 72 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7499 (t80) REVERT: K 36 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8248 (mm-30) REVERT: M 115 TYR cc_start: 0.9107 (m-80) cc_final: 0.8817 (m-80) REVERT: M 210 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7748 (tm-30) REVERT: M 214 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8181 (mp) REVERT: N 438 PHE cc_start: 0.8378 (t80) cc_final: 0.7980 (t80) REVERT: X 47 GLU cc_start: 0.7840 (mp0) cc_final: 0.7611 (mp0) REVERT: Z 141 ASP cc_start: 0.8166 (p0) cc_final: 0.7735 (p0) REVERT: a 7 GLU cc_start: 0.8273 (mp0) cc_final: 0.7508 (mt-10) REVERT: a 55 LYS cc_start: 0.8605 (mttp) cc_final: 0.8272 (mptt) REVERT: d 72 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7474 (mt-10) REVERT: i 31 TYR cc_start: 0.7962 (t80) cc_final: 0.7413 (m-10) REVERT: x 216 GLU cc_start: 0.8484 (pp20) cc_final: 0.8155 (pp20) REVERT: y 110 LYS cc_start: 0.7409 (tptp) cc_final: 0.6956 (tttt) outliers start: 47 outliers final: 38 residues processed: 418 average time/residue: 0.4109 time to fit residues: 256.8125 Evaluate side-chains 423 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 383 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 220 TYR Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 72 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain N residue 244 VAL Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 310 MET Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 398 TYR Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain Z residue 113 LYS Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain i residue 43 MET Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain y residue 141 ASP Chi-restraints excluded: chain y residue 156 VAL Chi-restraints excluded: chain y residue 216 SER Chi-restraints excluded: chain y residue 261 ASN Chi-restraints excluded: chain z residue 143 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 241 optimal weight: 0.0970 chunk 165 optimal weight: 0.4980 chunk 134 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 237 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 137 optimal weight: 0.0670 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 31 ASN N 368 GLN a 42 HIS ** d 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 202 GLN z 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.095716 restraints weight = 34891.524| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.82 r_work: 0.3130 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23818 Z= 0.203 Angle : 0.535 9.968 32229 Z= 0.264 Chirality : 0.042 0.303 3673 Planarity : 0.004 0.052 3960 Dihedral : 11.683 154.855 3545 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.20 % Favored : 96.69 % Rotamer: Outliers : 2.08 % Allowed : 14.78 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.16), residues: 2841 helix: 2.09 (0.12), residues: 1717 sheet: -1.03 (0.38), residues: 161 loop : -0.45 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 111 HIS 0.009 0.001 HIS a 42 PHE 0.020 0.001 PHE J 30 TYR 0.021 0.001 TYR N 439 ARG 0.009 0.000 ARG e 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 395 time to evaluate : 2.672 Fit side-chains REVERT: J 72 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7489 (t80) REVERT: J 145 TYR cc_start: 0.9084 (m-80) cc_final: 0.8791 (m-80) REVERT: K 36 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8142 (mm-30) REVERT: M 115 TYR cc_start: 0.9083 (m-80) cc_final: 0.8808 (m-80) REVERT: M 210 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7762 (tm-30) REVERT: M 214 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8149 (mp) REVERT: N 438 PHE cc_start: 0.8336 (t80) cc_final: 0.7928 (t80) REVERT: O 120 ARG cc_start: 0.7642 (mtm110) cc_final: 0.6728 (tpt90) REVERT: X 47 GLU cc_start: 0.7837 (mp0) cc_final: 0.7567 (mp0) REVERT: Z 141 ASP cc_start: 0.8170 (p0) cc_final: 0.7727 (p0) REVERT: a 7 GLU cc_start: 0.8258 (mp0) cc_final: 0.7507 (mt-10) REVERT: d 72 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7443 (mt-10) REVERT: i 31 TYR cc_start: 0.7925 (t80) cc_final: 0.7391 (m-10) REVERT: x 216 GLU cc_start: 0.8432 (pp20) cc_final: 0.8096 (pp20) REVERT: y 110 LYS cc_start: 0.7383 (tptp) cc_final: 0.6929 (tttt) outliers start: 51 outliers final: 42 residues processed: 423 average time/residue: 0.4456 time to fit residues: 282.7517 Evaluate side-chains 427 residues out of total 2450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 383 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 279 LEU Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 72 PHE Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 146 THR Chi-restraints excluded: chain J residue 174 THR Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain M residue 214 ILE Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 244 VAL Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 310 MET Chi-restraints excluded: chain N residue 377 LEU Chi-restraints excluded: chain N residue 398 TYR Chi-restraints excluded: chain N residue 411 PHE Chi-restraints excluded: chain N residue 471 MET Chi-restraints excluded: chain O residue 73 THR Chi-restraints excluded: chain O residue 148 VAL Chi-restraints excluded: chain X residue 61 LEU Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain Z residue 74 LEU Chi-restraints excluded: chain Z residue 106 GLU Chi-restraints excluded: chain Z residue 113 LYS Chi-restraints excluded: chain a residue 4 VAL Chi-restraints excluded: chain a residue 18 MET Chi-restraints excluded: chain a residue 42 HIS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain d residue 7 MET Chi-restraints excluded: chain d residue 11 LEU Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain i residue 43 MET Chi-restraints excluded: chain y residue 52 SER Chi-restraints excluded: chain y residue 141 ASP Chi-restraints excluded: chain y residue 156 VAL Chi-restraints excluded: chain y residue 216 SER Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 143 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 201 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 261 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: