Starting phenix.real_space_refine on Wed Jan 22 06:37:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw8_41662/01_2025/8tw8_41662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw8_41662/01_2025/8tw8_41662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tw8_41662/01_2025/8tw8_41662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw8_41662/01_2025/8tw8_41662.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw8_41662/01_2025/8tw8_41662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw8_41662/01_2025/8tw8_41662.cif" } resolution = 3.5 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= 0.008 sd= 0.057 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 3 5.21 5 S 83 5.16 5 C 11632 2.51 5 N 3112 2.21 5 O 3578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18419 Number of models: 1 Model: "" Number of chains: 12 Chain: "4" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2457 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 309} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "3" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2563 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 314} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "2" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2675 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 327} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2613 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "1" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2015 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 247} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2003 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2007 Classifications: {'peptide': 258} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 249} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 1963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1963 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 8, 'TRANS': 245} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "4" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.46, per 1000 atoms: 0.62 Number of scatterers: 18419 At special positions: 0 Unit cell: (108.468, 127.512, 133.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 83 16.00 P 11 15.00 Mg 3 11.99 O 3578 8.00 N 3112 7.00 C 11632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 5.50 Conformation dependent library (CDL) restraints added in 2.7 seconds 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4490 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 14 sheets defined 53.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain '4' and resid 10 through 15 Processing helix chain '4' and resid 19 through 23 removed outlier: 3.599A pdb=" N ILE 4 23 " --> pdb=" O LEU 4 20 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 40 Processing helix chain '4' and resid 55 through 68 Processing helix chain '4' and resid 70 through 74 Processing helix chain '4' and resid 85 through 99 removed outlier: 4.072A pdb=" N ILE 4 93 " --> pdb=" O VAL 4 89 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS 4 94 " --> pdb=" O ARG 4 90 " (cutoff:3.500A) Processing helix chain '4' and resid 116 through 119 Processing helix chain '4' and resid 120 through 134 removed outlier: 3.781A pdb=" N ARG 4 128 " --> pdb=" O GLN 4 124 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG 4 129 " --> pdb=" O GLN 4 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR 4 130 " --> pdb=" O ALA 4 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR 4 134 " --> pdb=" O THR 4 130 " (cutoff:3.500A) Processing helix chain '4' and resid 146 through 150 Processing helix chain '4' and resid 151 through 157 removed outlier: 3.677A pdb=" N ARG 4 157 " --> pdb=" O PRO 4 153 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 183 Processing helix chain '4' and resid 187 through 199 Processing helix chain '4' and resid 201 through 217 Processing helix chain '4' and resid 220 through 228 Processing helix chain '4' and resid 231 through 241 removed outlier: 3.754A pdb=" N ILE 4 235 " --> pdb=" O PRO 4 231 " (cutoff:3.500A) Processing helix chain '4' and resid 244 through 255 Processing helix chain '4' and resid 262 through 276 Processing helix chain '4' and resid 281 through 301 Processing helix chain '4' and resid 305 through 321 removed outlier: 3.725A pdb=" N LEU 4 309 " --> pdb=" O THR 4 305 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 13 Processing helix chain '3' and resid 14 through 19 Processing helix chain '3' and resid 23 through 27 removed outlier: 3.734A pdb=" N VAL 3 27 " --> pdb=" O LEU 3 24 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 44 removed outlier: 3.518A pdb=" N THR 3 36 " --> pdb=" O GLU 3 32 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 72 Processing helix chain '3' and resid 74 through 78 removed outlier: 3.513A pdb=" N MET 3 78 " --> pdb=" O ASN 3 74 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 74 through 78' Processing helix chain '3' and resid 89 through 103 removed outlier: 4.013A pdb=" N LYS 3 98 " --> pdb=" O ARG 3 94 " (cutoff:3.500A) Processing helix chain '3' and resid 118 through 122 removed outlier: 3.549A pdb=" N ALA 3 121 " --> pdb=" O GLU 3 118 " (cutoff:3.500A) Processing helix chain '3' and resid 123 through 137 removed outlier: 4.380A pdb=" N ARG 3 132 " --> pdb=" O ASN 3 128 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL 3 133 " --> pdb=" O ALA 3 129 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU 3 135 " --> pdb=" O ARG 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 160 removed outlier: 3.550A pdb=" N ARG 3 160 " --> pdb=" O ALA 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 170 through 185 Processing helix chain '3' and resid 190 through 200 Processing helix chain '3' and resid 204 through 219 Processing helix chain '3' and resid 228 through 237 Processing helix chain '3' and resid 240 through 253 Processing helix chain '3' and resid 255 through 270 removed outlier: 3.801A pdb=" N LYS 3 270 " --> pdb=" O VAL 3 266 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 286 Processing helix chain '3' and resid 293 through 311 Processing helix chain '3' and resid 315 through 332 Processing helix chain '2' and resid 15 through 24 Processing helix chain '2' and resid 26 through 31 Processing helix chain '2' and resid 42 through 55 removed outlier: 3.620A pdb=" N VAL 2 46 " --> pdb=" O GLN 2 42 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL 2 48 " --> pdb=" O HIS 2 44 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 88 Proline residue: 2 85 - end of helix Processing helix chain '2' and resid 102 through 116 removed outlier: 3.894A pdb=" N VAL 2 110 " --> pdb=" O VAL 2 106 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 2 111 " --> pdb=" O ARG 2 107 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 129 removed outlier: 3.634A pdb=" N LEU 2 126 " --> pdb=" O SER 2 122 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN 2 128 " --> pdb=" O HIS 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 141 through 145 removed outlier: 3.634A pdb=" N SER 2 144 " --> pdb=" O GLU 2 141 " (cutoff:3.500A) Processing helix chain '2' and resid 146 through 160 removed outlier: 3.557A pdb=" N LEU 2 153 " --> pdb=" O ALA 2 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG 2 154 " --> pdb=" O GLN 2 150 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ARG 2 155 " --> pdb=" O SER 2 151 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR 2 156 " --> pdb=" O ALA 2 152 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR 2 160 " --> pdb=" O THR 2 156 " (cutoff:3.500A) Processing helix chain '2' and resid 172 through 176 Processing helix chain '2' and resid 177 through 184 Processing helix chain '2' and resid 193 through 208 removed outlier: 5.160A pdb=" N ASP 2 199 " --> pdb=" O SER 2 195 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG 2 200 " --> pdb=" O ASN 2 196 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 225 Processing helix chain '2' and resid 227 through 246 removed outlier: 3.639A pdb=" N LEU 2 245 " --> pdb=" O GLY 2 241 " (cutoff:3.500A) Processing helix chain '2' and resid 252 through 260 removed outlier: 3.580A pdb=" N LEU 2 259 " --> pdb=" O GLN 2 255 " (cutoff:3.500A) Processing helix chain '2' and resid 264 through 277 Processing helix chain '2' and resid 279 through 291 Processing helix chain '2' and resid 296 through 311 Processing helix chain '2' and resid 315 through 334 removed outlier: 3.504A pdb=" N GLN 2 321 " --> pdb=" O ASN 2 317 " (cutoff:3.500A) Processing helix chain '2' and resid 338 through 352 Processing helix chain '5' and resid 19 through 32 removed outlier: 4.417A pdb=" N GLN 5 32 " --> pdb=" O SER 5 28 " (cutoff:3.500A) Processing helix chain '5' and resid 48 through 61 Processing helix chain '5' and resid 62 through 66 removed outlier: 3.516A pdb=" N VAL 5 65 " --> pdb=" O GLY 5 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR 5 66 " --> pdb=" O PRO 5 63 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 62 through 66' Processing helix chain '5' and resid 97 through 101 removed outlier: 3.964A pdb=" N MET 5 101 " --> pdb=" O PRO 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 104 through 117 removed outlier: 3.692A pdb=" N VAL 5 108 " --> pdb=" O ASN 5 104 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 146 Processing helix chain '5' and resid 147 through 161 removed outlier: 4.059A pdb=" N ARG 5 156 " --> pdb=" O ALA 5 152 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 5 157 " --> pdb=" O ALA 5 153 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU 5 159 " --> pdb=" O ARG 5 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR 5 161 " --> pdb=" O THR 5 157 " (cutoff:3.500A) Processing helix chain '5' and resid 178 through 185 Processing helix chain '5' and resid 194 through 209 Processing helix chain '5' and resid 216 through 227 removed outlier: 4.021A pdb=" N LYS 5 220 " --> pdb=" O LYS 5 216 " (cutoff:3.500A) Processing helix chain '5' and resid 229 through 244 removed outlier: 3.529A pdb=" N ASN 5 243 " --> pdb=" O SER 5 239 " (cutoff:3.500A) Processing helix chain '5' and resid 257 through 273 Processing helix chain '5' and resid 275 through 291 removed outlier: 3.655A pdb=" N GLU 5 281 " --> pdb=" O ASN 5 277 " (cutoff:3.500A) Processing helix chain '5' and resid 295 through 309 Processing helix chain '5' and resid 314 through 335 Processing helix chain '5' and resid 337 through 353 removed outlier: 3.736A pdb=" N HIS 5 341 " --> pdb=" O LYS 5 337 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY 5 344 " --> pdb=" O PHE 5 340 " (cutoff:3.500A) Processing helix chain '1' and resid 388 through 395 Processing helix chain '1' and resid 398 through 407 Processing helix chain '1' and resid 414 through 430 removed outlier: 3.638A pdb=" N GLY 1 430 " --> pdb=" O VAL 1 426 " (cutoff:3.500A) Processing helix chain '1' and resid 431 through 443 Processing helix chain '1' and resid 453 through 476 removed outlier: 4.087A pdb=" N ALA 1 457 " --> pdb=" O ILE 1 453 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP 1 461 " --> pdb=" O ALA 1 457 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR 1 474 " --> pdb=" O TYR 1 470 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA 1 475 " --> pdb=" O GLN 1 471 " (cutoff:3.500A) Processing helix chain '1' and resid 477 through 479 No H-bonds generated for 'chain '1' and resid 477 through 479' Processing helix chain '1' and resid 480 through 485 removed outlier: 3.859A pdb=" N SER 1 484 " --> pdb=" O LEU 1 480 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA 1 485 " --> pdb=" O LEU 1 481 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 480 through 485' Processing helix chain '1' and resid 485 through 496 removed outlier: 3.873A pdb=" N LEU 1 489 " --> pdb=" O ALA 1 485 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE 1 491 " --> pdb=" O VAL 1 487 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE 1 492 " --> pdb=" O PRO 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 508 through 534 removed outlier: 3.656A pdb=" N GLU 1 512 " --> pdb=" O ASN 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 537 through 542 removed outlier: 3.766A pdb=" N PHE 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 543 through 550 Processing helix chain '1' and resid 550 through 561 removed outlier: 3.558A pdb=" N TYR 1 554 " --> pdb=" O GLU 1 550 " (cutoff:3.500A) Processing helix chain '1' and resid 562 through 566 Processing helix chain '1' and resid 568 through 586 Processing helix chain '1' and resid 610 through 615 Processing helix chain '1' and resid 617 through 643 removed outlier: 3.675A pdb=" N ASN 1 622 " --> pdb=" O PRO 1 618 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU 1 623 " --> pdb=" O LYS 1 619 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN 1 630 " --> pdb=" O HIS 1 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 20 removed outlier: 4.310A pdb=" N PHE A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 141 through 153 removed outlier: 4.110A pdb=" N GLN A 153 " --> pdb=" O ARG A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 72 through 79 Processing helix chain 'B' and resid 141 through 153 removed outlier: 4.107A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 194 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 217 through 221 Processing helix chain 'C' and resid 8 through 20 removed outlier: 4.309A pdb=" N PHE C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 57 No H-bonds generated for 'chain 'C' and resid 55 through 57' Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 141 through 153 removed outlier: 4.106A pdb=" N GLN C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 221 Processing sheet with id=AA1, first strand: chain '4' and resid 75 through 78 removed outlier: 6.286A pdb=" N LYS 4 109 " --> pdb=" O ARG 4 139 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ALA 4 141 " --> pdb=" O LYS 4 109 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL 4 111 " --> pdb=" O ALA 4 141 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA 4 143 " --> pdb=" O VAL 4 111 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU 4 113 " --> pdb=" O ALA 4 143 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE 4 46 " --> pdb=" O LEU 4 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '4' and resid 185 through 186 removed outlier: 7.490A pdb=" N LYS 4 185 " --> pdb=" O VAL 4 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '3' and resid 79 through 82 removed outlier: 6.604A pdb=" N LEU 3 49 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ALA 3 147 " --> pdb=" O LEU 3 49 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE 3 51 " --> pdb=" O ALA 3 147 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU 3 50 " --> pdb=" O PHE 3 164 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 92 through 95 removed outlier: 6.221A pdb=" N LEU 2 62 " --> pdb=" O PHE 2 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 69 through 76 removed outlier: 6.875A pdb=" N LEU 5 94 " --> pdb=" O ILE 5 139 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN 5 141 " --> pdb=" O LEU 5 94 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ILE 5 96 " --> pdb=" O ASN 5 141 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS 5 136 " --> pdb=" O ARG 5 166 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE 5 168 " --> pdb=" O LYS 5 136 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL 5 138 " --> pdb=" O ILE 5 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL 5 170 " --> pdb=" O VAL 5 138 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE 5 140 " --> pdb=" O VAL 5 170 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU 5 40 " --> pdb=" O ILE 5 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 212 through 213 removed outlier: 5.834A pdb=" N GLN 5 212 " --> pdb=" O LEU 5 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '1' and resid 589 through 592 Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.523A pdb=" N GLU A 59 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 66 through 71 removed outlier: 5.538A pdb=" N LEU A 25 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 40 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ASP A 240 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG A 224 " --> pdb=" O ASP A 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 203 through 208 removed outlier: 6.289A pdb=" N SER A 157 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP A 172 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER A 177 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE A 181 " --> pdb=" O ILE C 111 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 111 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 59 " --> pdb=" O LYS C 5 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 59 through 60 removed outlier: 3.523A pdb=" N GLU B 59 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C 172 " --> pdb=" O SER C 157 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER C 157 " --> pdb=" O ASP C 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 66 through 71 removed outlier: 5.539A pdb=" N LEU B 25 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 40 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 244 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP B 240 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG B 224 " --> pdb=" O ASP B 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 177 through 182 removed outlier: 4.663A pdb=" N ASP B 172 " --> pdb=" O SER B 157 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER B 157 " --> pdb=" O ASP B 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 66 through 71 removed outlier: 5.539A pdb=" N LEU C 25 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL C 40 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY C 244 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP C 240 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG C 224 " --> pdb=" O ASP C 240 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3015 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: 6.34 Time building geometry restraints manager: 6.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.26: 3150 1.26 - 1.43: 4482 1.43 - 1.61: 10947 1.61 - 1.78: 11 1.78 - 1.95: 119 Bond restraints: 18709 Sorted by residual: bond pdb=" C GLU B 258 " pdb=" OXT GLU B 258 " ideal model delta sigma weight residual 1.231 1.091 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C GLU B 258 " pdb=" O GLU B 258 " ideal model delta sigma weight residual 1.231 1.371 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C GLU A 258 " pdb=" OXT GLU A 258 " ideal model delta sigma weight residual 1.231 1.091 0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C GLU A 258 " pdb=" O GLU A 258 " ideal model delta sigma weight residual 1.231 1.369 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" C4 ADP 5 401 " pdb=" C5 ADP 5 401 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 18704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 24492 3.06 - 6.13: 756 6.13 - 9.19: 67 9.19 - 12.26: 10 12.26 - 15.32: 7 Bond angle restraints: 25332 Sorted by residual: angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" C GLU A 257 " ideal model delta sigma weight residual 110.41 122.91 -12.50 1.18e+00 7.18e-01 1.12e+02 angle pdb=" N GLU B 257 " pdb=" CA GLU B 257 " pdb=" C GLU B 257 " ideal model delta sigma weight residual 110.41 122.90 -12.49 1.18e+00 7.18e-01 1.12e+02 angle pdb=" N ASP B 97 " pdb=" CA ASP B 97 " pdb=" C ASP B 97 " ideal model delta sigma weight residual 113.72 104.47 9.25 1.30e+00 5.92e-01 5.06e+01 angle pdb=" N ASP C 97 " pdb=" CA ASP C 97 " pdb=" C ASP C 97 " ideal model delta sigma weight residual 113.72 104.62 9.10 1.30e+00 5.92e-01 4.90e+01 angle pdb=" N ASP A 97 " pdb=" CA ASP A 97 " pdb=" C ASP A 97 " ideal model delta sigma weight residual 113.72 104.67 9.05 1.30e+00 5.92e-01 4.85e+01 ... (remaining 25327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.42: 10960 25.42 - 50.85: 448 50.85 - 76.27: 82 76.27 - 101.69: 22 101.69 - 127.11: 3 Dihedral angle restraints: 11515 sinusoidal: 4629 harmonic: 6886 Sorted by residual: dihedral pdb=" O2A ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PA ADP 5 401 " pdb=" PB ADP 5 401 " ideal model delta sinusoidal sigma weight residual -60.00 60.69 -120.69 1 2.00e+01 2.50e-03 3.63e+01 dihedral pdb=" O1B ADP 5 401 " pdb=" O3A ADP 5 401 " pdb=" PB ADP 5 401 " pdb=" PA ADP 5 401 " ideal model delta sinusoidal sigma weight residual -60.00 48.55 -108.55 1 2.00e+01 2.50e-03 3.16e+01 dihedral pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CA GLU B 257 " pdb=" CB GLU B 257 " ideal model delta harmonic sigma weight residual 122.80 134.76 -11.96 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 11512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2594 0.119 - 0.238: 301 0.238 - 0.356: 61 0.356 - 0.475: 12 0.475 - 0.594: 5 Chirality restraints: 2973 Sorted by residual: chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.81e+00 chirality pdb=" CA GLU B 257 " pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CB GLU B 257 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.79e+00 chirality pdb=" CA CYS C 22 " pdb=" N CYS C 22 " pdb=" C CYS C 22 " pdb=" CB CYS C 22 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 2970 not shown) Planarity restraints: 3239 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 258 " 0.037 2.00e-02 2.50e+03 8.20e-02 6.72e+01 pdb=" C GLU A 258 " -0.141 2.00e-02 2.50e+03 pdb=" O GLU A 258 " 0.042 2.00e-02 2.50e+03 pdb=" OXT GLU A 258 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 258 " 0.037 2.00e-02 2.50e+03 8.14e-02 6.63e+01 pdb=" C GLU B 258 " -0.140 2.00e-02 2.50e+03 pdb=" O GLU B 258 " 0.042 2.00e-02 2.50e+03 pdb=" OXT GLU B 258 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 1 563 " -0.087 2.00e-02 2.50e+03 5.81e-02 5.92e+01 pdb=" CG PHE 1 563 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE 1 563 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 PHE 1 563 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE 1 563 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE 1 563 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE 1 563 " -0.081 2.00e-02 2.50e+03 ... (remaining 3236 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 32 2.40 - 3.02: 10571 3.02 - 3.65: 26983 3.65 - 4.27: 41786 4.27 - 4.90: 69871 Nonbonded interactions: 149243 Sorted by model distance: nonbonded pdb=" O ASP A 109 " pdb=" O ILE B 181 " model vdw 1.772 3.040 nonbonded pdb=" OD2 ASP 4 265 " pdb=" OH TYR 3 52 " model vdw 2.049 3.040 nonbonded pdb=" O3G AGS 3 401 " pdb="MG MG 3 402 " model vdw 2.104 2.170 nonbonded pdb=" OG1 THR 4 56 " pdb="MG MG 4 402 " model vdw 2.122 2.170 nonbonded pdb=" OD1 ASP 3 229 " pdb=" OD1 ASP 3 230 " model vdw 2.123 3.040 ... (remaining 149238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 43 or (resid 44 and (name N or name CA or name C \ or name O or name CB )) or resid 45 through 69 or (resid 70 and (name N or name \ CA or name C or name O or name CB )) or resid 71 through 83 or (resid 84 and (n \ ame N or name CA or name C or name O or name CB )) or resid 85 or (resid 86 and \ (name N or name CA or name C or name O or name CB )) or resid 87 through 96 or ( \ resid 97 and (name N or name CA or name C or name O or name CB )) or resid 98 th \ rough 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) \ or resid 118 or (resid 119 and (name N or name CA or name C or name O or name C \ B )) or resid 120 through 125 or (resid 126 and (name N or name CA or name C or \ name O or name CB )) or resid 127 through 173 or (resid 174 and (name N or name \ CA or name C or name O or name CB )) or resid 175 through 235 or (resid 236 and \ (name N or name CA or name C or name O or name CB )) or resid 237 through 254)) selection = (chain 'B' and (resid 1 through 19 or (resid 20 and (name N or name CA or name C \ or name O or name CB )) or resid 21 through 43 or (resid 44 and (name N or name \ CA or name C or name O or name CB )) or resid 45 through 67 or (resid 68 and (n \ ame N or name CA or name C or name O or name CB )) or resid 69 through 78 or (re \ sid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 thro \ ugh 85 or (resid 86 and (name N or name CA or name C or name O or name CB )) or \ resid 87 through 109 or (resid 110 and (name N or name CA or name C or name O or \ name CB )) or resid 111 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 173 or (resid 174 and (name N o \ r name CA or name C or name O or name CB )) or resid 175 through 235 or (resid 2 \ 36 and (name N or name CA or name C or name O or name CB )) or resid 237 through \ 254)) selection = (chain 'C' and (resid 1 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB )) or resid 69 or (resid 70 and (name N or name CA or name \ C or name O or name CB )) or resid 71 or (resid 72 and (name N or name CA or na \ me C or name O or name CB )) or resid 73 through 78 or (resid 79 and (name N or \ name CA or name C or name O or name CB )) or resid 80 through 109 or (resid 110 \ and (name N or name CA or name C or name O or name CB )) or resid 111 through 11 \ 8 or (resid 119 and (name N or name CA or name C or name O or name CB )) or resi \ d 120 through 252 or (resid 253 and (name N or name CA or name C or name O or na \ me CB )) or resid 254)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 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: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.950 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 : 0.009 0.140 18709 Z= 0.553 Angle : 1.199 15.323 25332 Z= 0.775 Chirality : 0.088 0.594 2973 Planarity : 0.010 0.184 3239 Dihedral : 14.614 127.113 7025 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.86 % Allowed : 3.26 % Favored : 95.88 % Rotamer: Outliers : 0.54 % Allowed : 6.76 % Favored : 92.69 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.23 % 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: -1.23 (0.16), residues: 2331 helix: -0.49 (0.14), residues: 1103 sheet: 0.11 (0.22), residues: 505 loop : -1.80 (0.21), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP 1 399 HIS 0.007 0.001 HIS 1 466 PHE 0.087 0.009 PHE 1 563 TYR 0.078 0.006 TYR C 133 ARG 0.028 0.002 ARG C 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 489 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 7 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7265 (pp) REVERT: 2 20 GLN cc_start: 0.7888 (mm-40) cc_final: 0.6958 (tp40) REVERT: 2 118 VAL cc_start: 0.7166 (m) cc_final: 0.6562 (m) REVERT: 2 140 ASP cc_start: 0.8211 (t0) cc_final: 0.8005 (t0) REVERT: 2 169 ILE cc_start: 0.7648 (mt) cc_final: 0.7274 (mt) REVERT: 5 159 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7241 (mt-10) REVERT: A 150 ASP cc_start: 0.7200 (m-30) cc_final: 0.6990 (m-30) REVERT: C 119 MET cc_start: 0.7574 (OUTLIER) cc_final: 0.7327 (mtt) REVERT: C 198 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8334 (mt-10) outliers start: 11 outliers final: 2 residues processed: 494 average time/residue: 0.3403 time to fit residues: 245.4035 Evaluate side-chains 262 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 257 time to evaluate : 2.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain C residue 119 MET Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 18 GLN 4 60 HIS 4 92 GLN 4 177 GLN 4 220 ASN 4 244 ASN 4 320 ASN 3 180 ASN 3 213 GLN 3 317 GLN 2 60 HIS 2 96 ASN 2 150 GLN 2 303 GLN 2 340 HIS 2 352 GLN ** 5 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 80 ASN 5 86 ASN 5 244 ASN 1 425 GLN A 64 HIS A 159 ASN A 247 GLN B 159 ASN C 24 GLN C 64 HIS C 83 ASN C 94 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.132232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.113169 restraints weight = 45401.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.112181 restraints weight = 32575.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.112792 restraints weight = 25351.728| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18709 Z= 0.293 Angle : 0.644 9.749 25332 Z= 0.333 Chirality : 0.044 0.221 2973 Planarity : 0.005 0.087 3239 Dihedral : 8.028 118.882 2586 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.73 % Allowed : 13.52 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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 (0.17), residues: 2331 helix: 0.77 (0.15), residues: 1110 sheet: 0.48 (0.22), residues: 506 loop : -1.37 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 1 399 HIS 0.008 0.001 HIS 5 38 PHE 0.026 0.002 PHE 5 345 TYR 0.030 0.002 TYR 1 483 ARG 0.012 0.001 ARG C 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 2.037 Fit side-chains revert: symmetry clash REVERT: 4 7 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7301 (pp) REVERT: 4 50 MET cc_start: 0.7548 (mpp) cc_final: 0.7113 (mtt) REVERT: 3 21 PRO cc_start: 0.7916 (Cg_exo) cc_final: 0.7709 (Cg_endo) REVERT: 2 140 ASP cc_start: 0.8516 (t0) cc_final: 0.7979 (m-30) REVERT: 5 101 MET cc_start: 0.7815 (ptp) cc_final: 0.7564 (ptp) REVERT: 5 184 ARG cc_start: 0.7106 (mtt90) cc_final: 0.6769 (mtt90) REVERT: 1 413 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7574 (mtp180) REVERT: 1 417 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6394 (tm-30) REVERT: 1 621 ILE cc_start: 0.8108 (mt) cc_final: 0.7875 (tt) REVERT: 1 631 ASN cc_start: 0.5777 (m110) cc_final: 0.5569 (m110) REVERT: A 161 MET cc_start: 0.8380 (ttt) cc_final: 0.8165 (ttp) REVERT: B 156 ASP cc_start: 0.7421 (t0) cc_final: 0.7155 (t0) REVERT: B 199 MET cc_start: 0.7090 (ttm) cc_final: 0.6759 (ttm) REVERT: B 211 TYR cc_start: 0.7707 (m-80) cc_final: 0.7368 (m-80) outliers start: 35 outliers final: 21 residues processed: 289 average time/residue: 0.3008 time to fit residues: 133.6018 Evaluate side-chains 243 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 221 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 113 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 231 VAL Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 92 ILE Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 5 residue 134 ARG Chi-restraints excluded: chain 5 residue 342 LEU Chi-restraints excluded: chain 1 residue 570 LYS Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 177 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 40 optimal weight: 0.0170 chunk 109 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 70 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 213 GLN 2 150 GLN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 19 ASN 5 244 ASN A 29 GLN C 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.133888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.115263 restraints weight = 44831.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.114117 restraints weight = 32147.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.115130 restraints weight = 24166.236| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 18709 Z= 0.149 Angle : 0.532 8.565 25332 Z= 0.273 Chirality : 0.040 0.205 2973 Planarity : 0.003 0.056 3239 Dihedral : 7.573 118.473 2578 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.33 % Allowed : 14.56 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 0.56 (0.17), residues: 2331 helix: 1.28 (0.16), residues: 1104 sheet: 0.48 (0.22), residues: 504 loop : -1.07 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 4 11 HIS 0.007 0.001 HIS 2 340 PHE 0.025 0.001 PHE 5 345 TYR 0.014 0.001 TYR A 211 ARG 0.003 0.000 ARG 1 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 237 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 7 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7179 (pp) REVERT: 4 50 MET cc_start: 0.7502 (mpp) cc_final: 0.7014 (mtt) REVERT: 4 202 MET cc_start: 0.5901 (tpt) cc_final: 0.5255 (tpp) REVERT: 4 271 PHE cc_start: 0.7785 (t80) cc_final: 0.7267 (t80) REVERT: 2 140 ASP cc_start: 0.8447 (t0) cc_final: 0.8027 (t0) REVERT: 1 413 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7516 (mtp180) REVERT: 1 417 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6519 (tm-30) REVERT: 1 631 ASN cc_start: 0.5506 (m110) cc_final: 0.5282 (m110) REVERT: A 117 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7538 (tptm) REVERT: A 119 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.6507 (mpp) REVERT: B 156 ASP cc_start: 0.7573 (t0) cc_final: 0.7247 (t0) outliers start: 27 outliers final: 12 residues processed: 252 average time/residue: 0.3265 time to fit residues: 125.3500 Evaluate side-chains 227 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 4 residue 82 ASP Chi-restraints excluded: chain 3 residue 49 LEU Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 131 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 31 optimal weight: 0.0170 chunk 50 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 183 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 317 HIS 3 213 GLN 2 25 GLN 2 124 HIS 1 508 ASN ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 617 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.124159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.103085 restraints weight = 44941.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.102762 restraints weight = 32117.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.103583 restraints weight = 25078.889| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18709 Z= 0.335 Angle : 0.649 7.381 25332 Z= 0.332 Chirality : 0.044 0.164 2973 Planarity : 0.005 0.058 3239 Dihedral : 7.694 116.848 2578 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.67 % Allowed : 15.30 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 0.33 (0.17), residues: 2331 helix: 1.13 (0.16), residues: 1089 sheet: 0.34 (0.22), residues: 502 loop : -1.19 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP 2 295 HIS 0.018 0.002 HIS 2 340 PHE 0.044 0.002 PHE 5 305 TYR 0.020 0.002 TYR 3 288 ARG 0.011 0.001 ARG 3 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 2.163 Fit side-chains revert: symmetry clash REVERT: 4 7 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7416 (pp) REVERT: 4 50 MET cc_start: 0.7608 (mpp) cc_final: 0.7218 (mtt) REVERT: 4 119 MET cc_start: 0.5823 (OUTLIER) cc_final: 0.5536 (mtm) REVERT: 4 186 TYR cc_start: 0.9020 (p90) cc_final: 0.8595 (p90) REVERT: 4 202 MET cc_start: 0.6001 (tpt) cc_final: 0.5449 (tpp) REVERT: 4 271 PHE cc_start: 0.7895 (t80) cc_final: 0.7331 (t80) REVERT: 3 88 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8335 (mtm180) REVERT: 5 184 ARG cc_start: 0.7459 (tpp80) cc_final: 0.7156 (ttm110) REVERT: 5 299 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6499 (mt) REVERT: 1 413 ARG cc_start: 0.7852 (ttm-80) cc_final: 0.7506 (mtp180) REVERT: 1 417 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6758 (tm-30) REVERT: 1 514 ARG cc_start: 0.5815 (ttt180) cc_final: 0.3405 (mtm110) REVERT: A 117 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7656 (tmtp) REVERT: B 24 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 49 SER cc_start: 0.8601 (m) cc_final: 0.8258 (t) REVERT: B 256 ASP cc_start: 0.7591 (m-30) cc_final: 0.7132 (p0) REVERT: C 7 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7470 (tp30) REVERT: C 51 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7752 (tt0) outliers start: 54 outliers final: 28 residues processed: 250 average time/residue: 0.3546 time to fit residues: 131.4897 Evaluate side-chains 225 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 119 MET Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 88 ARG Chi-restraints excluded: chain 3 residue 113 LEU Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 231 VAL Chi-restraints excluded: chain 3 residue 252 LEU Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 146 THR Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 173 VAL Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 201 LEU Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 2 residue 353 LEU Chi-restraints excluded: chain 5 residue 215 THR Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 114 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 196 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 145 ASN ** 2 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 341 HIS 1 418 GLN ** 1 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.125515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.104444 restraints weight = 45249.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104755 restraints weight = 30291.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105529 restraints weight = 22632.436| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18709 Z= 0.212 Angle : 0.551 10.378 25332 Z= 0.282 Chirality : 0.041 0.158 2973 Planarity : 0.004 0.058 3239 Dihedral : 7.511 117.655 2578 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.02 % Allowed : 17.08 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.23 % 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: 0.49 (0.17), residues: 2331 helix: 1.31 (0.16), residues: 1088 sheet: 0.21 (0.22), residues: 515 loop : -1.02 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 4 11 HIS 0.004 0.001 HIS 5 93 PHE 0.036 0.001 PHE 5 345 TYR 0.013 0.001 TYR B 114 ARG 0.005 0.000 ARG 3 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4662 Ramachandran restraints generated. 2331 Oldfield, 0 Emsley, 2331 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 213 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 7 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7435 (pp) REVERT: 4 202 MET cc_start: 0.6025 (tpt) cc_final: 0.5613 (tpp) REVERT: 4 271 PHE cc_start: 0.7877 (t80) cc_final: 0.7365 (t80) REVERT: 5 299 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6450 (mt) REVERT: 1 417 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6814 (tm-30) REVERT: 1 514 ARG cc_start: 0.5784 (ttt180) cc_final: 0.3310 (mtm110) REVERT: A 175 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7622 (mt) REVERT: B 24 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7259 (tm-30) REVERT: B 49 SER cc_start: 0.8480 (m) cc_final: 0.8170 (t) REVERT: B 211 TYR cc_start: 0.7751 (m-80) cc_final: 0.7201 (m-80) REVERT: C 51 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7574 (tt0) outliers start: 41 outliers final: 26 residues processed: 244 average time/residue: 0.3253 time to fit residues: 120.0310 Evaluate side-chains 223 residues out of total 2107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 7 LEU Chi-restraints excluded: chain 4 residue 30 ILE Chi-restraints excluded: chain 3 residue 115 ILE Chi-restraints excluded: chain 3 residue 158 LEU Chi-restraints excluded: chain 3 residue 171 GLN Chi-restraints excluded: chain 3 residue 252 LEU Chi-restraints excluded: chain 3 residue 295 THR Chi-restraints excluded: chain 3 residue 316 ASP Chi-restraints excluded: chain 3 residue 323 VAL Chi-restraints excluded: chain 2 residue 144 SER Chi-restraints excluded: chain 2 residue 146 THR Chi-restraints excluded: chain 2 residue 161 SER Chi-restraints excluded: chain 2 residue 174 THR Chi-restraints excluded: chain 2 residue 178 ASP Chi-restraints excluded: chain 2 residue 305 HIS Chi-restraints excluded: chain 2 residue 353 LEU Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 270 ILE Chi-restraints excluded: chain 5 residue 299 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain C residue 7 GLU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 198 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.3465 > 50: distance: 65 - 68: 20.655 distance: 68 - 69: 21.359 distance: 69 - 70: 16.450 distance: 69 - 72: 12.979 distance: 70 - 71: 29.094 distance: 70 - 76: 19.240 distance: 72 - 73: 6.330 distance: 73 - 74: 15.564 distance: 73 - 75: 19.268 distance: 76 - 77: 10.657 distance: 77 - 78: 40.501 distance: 77 - 80: 18.008 distance: 78 - 79: 57.453 distance: 78 - 85: 47.966 distance: 80 - 81: 30.141 distance: 81 - 82: 15.888 distance: 82 - 83: 3.942 distance: 83 - 84: 10.626 distance: 85 - 86: 48.032 distance: 86 - 87: 32.290 distance: 86 - 89: 38.671 distance: 87 - 88: 33.353 distance: 87 - 91: 8.931 distance: 89 - 90: 44.064 distance: 91 - 92: 11.309 distance: 92 - 93: 15.880 distance: 92 - 95: 11.561 distance: 93 - 94: 21.649 distance: 93 - 97: 33.213 distance: 95 - 96: 8.605 distance: 97 - 98: 22.412 distance: 98 - 99: 7.933 distance: 98 - 101: 18.466 distance: 99 - 100: 10.222 distance: 99 - 103: 11.844 distance: 101 - 102: 19.704 distance: 103 - 104: 7.582 distance: 103 - 109: 13.234 distance: 104 - 105: 9.426 distance: 104 - 107: 6.943 distance: 105 - 106: 16.638 distance: 105 - 110: 6.752 distance: 107 - 108: 9.647 distance: 108 - 109: 8.477 distance: 110 - 111: 11.734 distance: 111 - 112: 12.597 distance: 111 - 114: 10.855 distance: 112 - 113: 17.991 distance: 112 - 118: 11.155 distance: 114 - 115: 15.145 distance: 114 - 116: 8.913 distance: 115 - 117: 7.754 distance: 118 - 119: 14.637 distance: 119 - 120: 18.372 distance: 119 - 122: 17.240 distance: 120 - 121: 17.879 distance: 120 - 126: 12.283 distance: 122 - 123: 20.590 distance: 122 - 124: 29.795 distance: 123 - 125: 32.724 distance: 126 - 127: 21.236 distance: 127 - 128: 11.770 distance: 127 - 130: 32.336 distance: 128 - 129: 15.972 distance: 128 - 135: 25.231 distance: 130 - 131: 9.618 distance: 131 - 132: 16.251 distance: 132 - 133: 14.109 distance: 133 - 134: 11.796 distance: 135 - 136: 8.985 distance: 135 - 141: 23.067 distance: 136 - 137: 30.011 distance: 136 - 139: 18.673 distance: 137 - 138: 22.999 distance: 137 - 142: 16.828 distance: 138 - 167: 27.254 distance: 139 - 140: 19.288 distance: 140 - 141: 28.458