Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 03:50:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/04_2023/7k36_22650_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/04_2023/7k36_22650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/04_2023/7k36_22650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/04_2023/7k36_22650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/04_2023/7k36_22650_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/04_2023/7k36_22650_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Mn 2 7.51 5 Zn 2 6.06 5 P 6 5.49 5 S 87 5.16 5 C 10561 2.51 5 N 2895 2.21 5 O 3060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 46": "NH1" <-> "NH2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 531": "OD1" <-> "OD2" Residue "A GLU 565": "OE1" <-> "OE2" Residue "B ARG 393": "NH1" <-> "NH2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 446": "NH1" <-> "NH2" Residue "B ASP 484": "OD1" <-> "OD2" Residue "B ASP 487": "OD1" <-> "OD2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B PHE 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 602": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 706": "OD1" <-> "OD2" Residue "B PHE 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C ASP 57": "OD1" <-> "OD2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 85": "OD1" <-> "OD2" Residue "C TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 175": "OD1" <-> "OD2" Residue "C GLU 192": "OE1" <-> "OE2" Residue "C ASP 204": "OD1" <-> "OD2" Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C ASP 279": "OD1" <-> "OD2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ASP 113": "OD1" <-> "OD2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E GLU 108": "OE1" <-> "OE2" Residue "E ASP 113": "OD1" <-> "OD2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "F TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "G TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 55": "OD1" <-> "OD2" Residue "H GLU 59": "OE1" <-> "OE2" Residue "H ASP 65": "OD1" <-> "OD2" Residue "H ARG 75": "NH1" <-> "NH2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H ASP 95": "OD1" <-> "OD2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ASP 130": "OD1" <-> "OD2" Residue "H PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H ARG 175": "NH1" <-> "NH2" Residue "H GLU 182": "OE1" <-> "OE2" Residue "I PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 71": "OE1" <-> "OE2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I ASP 131": "OD1" <-> "OD2" Residue "I ARG 138": "NH1" <-> "NH2" Residue "I ARG 170": "NH1" <-> "NH2" Residue "I GLU 235": "OE1" <-> "OE2" Residue "I GLU 310": "OE1" <-> "OE2" Residue "I ARG 329": "NH1" <-> "NH2" Residue "I ARG 429": "NH1" <-> "NH2" Residue "I GLU 434": "OE1" <-> "OE2" Residue "I PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 441": "NH1" <-> "NH2" Residue "I PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 491": "NH1" <-> "NH2" Residue "I ASP 547": "OD1" <-> "OD2" Residue "I ASP 566": "OD1" <-> "OD2" Residue "I ARG 569": "NH1" <-> "NH2" Residue "I TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 763": "OD1" <-> "OD2" Residue "I ARG 785": "NH1" <-> "NH2" Residue "I ASP 791": "OD1" <-> "OD2" Residue "I ASP 796": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16613 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 3515 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 245} Link IDs: {'PTRANS': 24, 'TRANS': 529} Chain breaks: 6 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 838 Unresolved non-hydrogen angles: 1057 Unresolved non-hydrogen dihedrals: 681 Unresolved non-hydrogen chiralities: 78 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 11, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 28, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 440 Chain: "B" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2296 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 281} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2360 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 281} 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: "D" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 563 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 510 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 457 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 58} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "H" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1422 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "I" Number of atoms: 4829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4829 Classifications: {'peptide': 599} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 22, 'TRANS': 576} Chain breaks: 9 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10922 SG CYS H 110 45.332 54.337 99.147 1.00140.34 S ATOM 10989 SG CYS H 119 43.054 56.546 98.471 1.00145.37 S ATOM 10851 SG CYS H 92 32.048 53.692 103.889 1.00171.12 S ATOM 10889 SG CYS H 97 30.821 55.981 106.236 1.00170.80 S Time building chain proxies: 8.66, per 1000 atoms: 0.52 Number of scatterers: 16613 At special positions: 0 Unit cell: (212.48, 98.77, 141.93, 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 2 29.99 Mn 2 24.99 S 87 16.00 P 6 15.00 O 3060 8.00 N 2895 7.00 C 10561 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.82 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 127 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 113 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 110 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 119 " pdb=" ZN H 302 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 169 " pdb="ZN ZN H 302 " - pdb=" NE2 HIS H 174 " pdb="ZN ZN H 302 " - pdb=" SG CYS H 97 " pdb="ZN ZN H 302 " - pdb=" SG CYS H 92 " Number of angles added : 4 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 9 sheets defined 60.4% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.546A pdb=" N LEU A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.841A pdb=" N LEU A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 83 through 97 removed outlier: 5.647A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 102 through 115 Processing helix chain 'A' and resid 122 through 138 Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 142 through 158 removed outlier: 3.503A pdb=" N VAL A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 163 through 174 Processing helix chain 'A' and resid 179 through 192 removed outlier: 7.246A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 214 Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 240 through 252 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 258 through 271 removed outlier: 4.061A pdb=" N LYS A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLU A 269 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 298 through 316 removed outlier: 3.958A pdb=" N GLU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 334 removed outlier: 4.339A pdb=" N SER A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 342 through 355 Proline residue: A 354 - end of helix Processing helix chain 'A' and resid 360 through 375 Proline residue: A 367 - end of helix removed outlier: 3.533A pdb=" N ASP A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 394 removed outlier: 4.539A pdb=" N ASP A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS A 390 " --> pdb=" O SER A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 removed outlier: 4.053A pdb=" N LEU A 405 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 417 through 433 Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 456 through 489 removed outlier: 6.710A pdb=" N LYS A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 9.247A pdb=" N GLU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Proline residue: A 484 - end of helix Processing helix chain 'A' and resid 495 through 512 removed outlier: 4.833A pdb=" N THR A 500 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 509 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 510 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS A 512 " --> pdb=" O SER A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 530 removed outlier: 5.026A pdb=" N LEU A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix removed outlier: 4.280A pdb=" N GLY A 530 " --> pdb=" O LEU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 548 Processing helix chain 'A' and resid 553 through 568 removed outlier: 4.760A pdb=" N LYS A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 573 through 586 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'C' and resid 4 through 19 removed outlier: 3.961A pdb=" N GLU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 4.308A pdb=" N LYS C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 129 through 137 Processing helix chain 'C' and resid 141 through 152 removed outlier: 4.733A pdb=" N TYR C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 195 through 198 No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'D' and resid 65 through 134 Processing helix chain 'E' and resid 65 through 126 Processing helix chain 'F' and resid 65 through 122 Processing helix chain 'G' and resid 65 through 120 Processing helix chain 'H' and resid 20 through 24 Processing helix chain 'H' and resid 38 through 49 Processing helix chain 'H' and resid 54 through 58 Processing helix chain 'H' and resid 67 through 91 removed outlier: 4.182A pdb=" N GLY H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU H 84 " --> pdb=" O GLU H 80 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU H 91 " --> pdb=" O LYS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 136 Processing helix chain 'H' and resid 153 through 173 removed outlier: 3.944A pdb=" N GLY H 157 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG H 165 " --> pdb=" O ARG H 161 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 166 " --> pdb=" O ARG H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 184 Processing helix chain 'H' and resid 187 through 198 Processing helix chain 'I' and resid 78 through 84 Processing helix chain 'I' and resid 93 through 108 removed outlier: 4.290A pdb=" N GLU I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 134 removed outlier: 4.222A pdb=" N GLU I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 153 Processing helix chain 'I' and resid 162 through 179 Processing helix chain 'I' and resid 181 through 193 Processing helix chain 'I' and resid 211 through 213 No H-bonds generated for 'chain 'I' and resid 211 through 213' Processing helix chain 'I' and resid 215 through 232 Processing helix chain 'I' and resid 242 through 252 Processing helix chain 'I' and resid 262 through 274 Processing helix chain 'I' and resid 283 through 298 Processing helix chain 'I' and resid 301 through 314 Processing helix chain 'I' and resid 324 through 329 Processing helix chain 'I' and resid 430 through 444 Processing helix chain 'I' and resid 461 through 472 removed outlier: 3.739A pdb=" N SER I 466 " --> pdb=" O PRO I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 491 Processing helix chain 'I' and resid 505 through 531 Proline residue: I 515 - end of helix Proline residue: I 518 - end of helix Processing helix chain 'I' and resid 544 through 547 removed outlier: 3.877A pdb=" N ASP I 547 " --> pdb=" O ILE I 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 544 through 547' Processing helix chain 'I' and resid 557 through 592 Processing helix chain 'I' and resid 594 through 606 removed outlier: 3.620A pdb=" N HIS I 603 " --> pdb=" O TYR I 599 " (cutoff:3.500A) Processing helix chain 'I' and resid 609 through 617 Processing helix chain 'I' and resid 621 through 625 Processing helix chain 'I' and resid 662 through 678 Processing helix chain 'I' and resid 683 through 691 Processing helix chain 'I' and resid 695 through 703 removed outlier: 3.584A pdb=" N ARG I 700 " --> pdb=" O PRO I 696 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS I 703 " --> pdb=" O LYS I 699 " (cutoff:3.500A) Processing helix chain 'I' and resid 707 through 720 removed outlier: 3.840A pdb=" N LEU I 716 " --> pdb=" O TYR I 712 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL I 719 " --> pdb=" O LYS I 715 " (cutoff:3.500A) Processing helix chain 'I' and resid 722 through 731 removed outlier: 3.867A pdb=" N GLY I 725 " --> pdb=" O LYS I 722 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG I 726 " --> pdb=" O TYR I 723 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN I 727 " --> pdb=" O LEU I 724 " (cutoff:3.500A) Processing helix chain 'I' and resid 734 through 742 Processing helix chain 'I' and resid 764 through 783 removed outlier: 3.524A pdb=" N ALA I 773 " --> pdb=" O CYS I 769 " (cutoff:3.500A) Processing helix chain 'I' and resid 815 through 822 removed outlier: 4.455A pdb=" N TRP I 820 " --> pdb=" O ASN I 816 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 401 through 404 removed outlier: 6.524A pdb=" N ASN B 424 " --> pdb=" O PRO B 441 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 454 through 457 removed outlier: 7.108A pdb=" N ASN B 477 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 494 " --> pdb=" O ASN B 477 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 539 through 541 Processing sheet with id= D, first strand: chain 'B' and resid 553 through 555 removed outlier: 3.708A pdb=" N VAL B 584 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 603 through 605 removed outlier: 3.932A pdb=" N HIS B 633 " --> pdb=" O PHE B 623 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 675 through 677 Processing sheet with id= G, first strand: chain 'B' and resid 690 through 693 removed outlier: 3.809A pdb=" N ALA B 709 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 713 " --> pdb=" O PRO B 388 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.987A pdb=" N THR C 156 " --> pdb=" O GLN C 46 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL C 48 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 158 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 236 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N LEU C 166 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N SER C 238 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.510A pdb=" N TYR C 80 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) 981 hydrogen bonds defined for protein. 2802 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.11 Time building geometry restraints manager: 8.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5497 1.34 - 1.46: 3685 1.46 - 1.58: 7609 1.58 - 1.70: 6 1.70 - 1.82: 135 Bond restraints: 16932 Sorted by residual: bond pdb=" C GLY I 253 " pdb=" N SER I 254 " ideal model delta sigma weight residual 1.331 1.280 0.051 2.07e-02 2.33e+03 6.05e+00 bond pdb=" O12 IHP I 901 " pdb=" P2 IHP I 901 " ideal model delta sigma weight residual 1.675 1.626 0.049 2.00e-02 2.50e+03 5.88e+00 bond pdb=" O15 IHP I 901 " pdb=" P5 IHP I 901 " ideal model delta sigma weight residual 1.675 1.635 0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" O32 IHP I 901 " pdb=" P2 IHP I 901 " ideal model delta sigma weight residual 1.537 1.499 0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" O14 IHP I 901 " pdb=" P4 IHP I 901 " ideal model delta sigma weight residual 1.671 1.633 0.038 2.00e-02 2.50e+03 3.55e+00 ... (remaining 16927 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.56: 437 106.56 - 113.49: 9672 113.49 - 120.42: 6441 120.42 - 127.35: 6250 127.35 - 134.28: 204 Bond angle restraints: 23004 Sorted by residual: angle pdb=" N PRO A 354 " pdb=" CA PRO A 354 " pdb=" CB PRO A 354 " ideal model delta sigma weight residual 103.52 110.43 -6.91 9.50e-01 1.11e+00 5.29e+01 angle pdb=" N PRO A 121 " pdb=" CA PRO A 121 " pdb=" CB PRO A 121 " ideal model delta sigma weight residual 103.00 110.45 -7.45 1.10e+00 8.26e-01 4.59e+01 angle pdb=" N PRO A 130 " pdb=" CA PRO A 130 " pdb=" CB PRO A 130 " ideal model delta sigma weight residual 103.39 110.32 -6.93 1.08e+00 8.57e-01 4.12e+01 angle pdb=" N PRO A 328 " pdb=" CA PRO A 328 " pdb=" CB PRO A 328 " ideal model delta sigma weight residual 103.23 110.07 -6.84 1.07e+00 8.73e-01 4.08e+01 angle pdb=" N PRO A 207 " pdb=" CA PRO A 207 " pdb=" CB PRO A 207 " ideal model delta sigma weight residual 103.39 110.14 -6.75 1.08e+00 8.57e-01 3.90e+01 ... (remaining 22999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 8995 18.12 - 36.24: 855 36.24 - 54.36: 211 54.36 - 72.48: 37 72.48 - 90.60: 17 Dihedral angle restraints: 10115 sinusoidal: 3716 harmonic: 6399 Sorted by residual: dihedral pdb=" CA VAL C 87 " pdb=" C VAL C 87 " pdb=" N ASP C 88 " pdb=" CA ASP C 88 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA THR H 17 " pdb=" C THR H 17 " pdb=" N LYS H 18 " pdb=" CA LYS H 18 " ideal model delta harmonic sigma weight residual -180.00 -159.35 -20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG C 49 " pdb=" C ARG C 49 " pdb=" N CYS C 50 " pdb=" CA CYS C 50 " ideal model delta harmonic sigma weight residual -180.00 -159.39 -20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 10112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.954: 2646 0.954 - 1.909: 0 1.909 - 2.863: 0 2.863 - 3.817: 0 3.817 - 4.771: 4 Chirality restraints: 2650 Sorted by residual: chirality pdb=" C2 IHP I 901 " pdb=" C1 IHP I 901 " pdb=" C3 IHP I 901 " pdb=" O12 IHP I 901 " both_signs ideal model delta sigma weight residual False -2.52 2.25 -4.77 2.00e-01 2.50e+01 5.69e+02 chirality pdb=" C3 IHP I 901 " pdb=" C2 IHP I 901 " pdb=" C4 IHP I 901 " pdb=" O13 IHP I 901 " both_signs ideal model delta sigma weight residual False -2.34 2.26 -4.60 2.00e-01 2.50e+01 5.28e+02 chirality pdb=" C5 IHP I 901 " pdb=" C4 IHP I 901 " pdb=" C6 IHP I 901 " pdb=" O15 IHP I 901 " both_signs ideal model delta sigma weight residual False -2.42 2.10 -4.52 2.00e-01 2.50e+01 5.10e+02 ... (remaining 2647 not shown) Planarity restraints: 2938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS H 93 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO H 94 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 94 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 94 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 225 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C LEU I 225 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU I 225 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE I 226 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 606 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 607 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 607 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 607 " 0.025 5.00e-02 4.00e+02 ... (remaining 2935 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 2 1.82 - 2.59: 267 2.59 - 3.36: 24212 3.36 - 4.13: 40841 4.13 - 4.90: 74513 Nonbonded interactions: 139835 Sorted by model distance: nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 401 " model vdw 1.054 2.320 nonbonded pdb=" OD1 ASN C 117 " pdb=" NE2 HIS C 167 " model vdw 1.487 2.520 nonbonded pdb=" CG ASP C 85 " pdb="MN MN C 401 " model vdw 1.860 2.550 nonbonded pdb=" OD1 ASP C 85 " pdb=" ND2 ASN C 117 " model vdw 2.059 2.520 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 402 " model vdw 2.076 2.320 ... (remaining 139830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 62 through 125 or (resid 126 through 127 and (name N or na \ me CA or name C or name O or name CB )))) selection = chain 'E' } ncs_group { reference = (chain 'F' and (resid 62 through 100 or (resid 101 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 102 through 105 and (name N or name CA or \ name C or name O or name CB )) or (resid 106 through 113 and (name N or name CA \ or name C or name O or name CB )) or resid 114 through 115 or (resid 116 through \ 117 and (name N or name CA or name C or name O or name CB )) or resid 118 throu \ gh 119 or (resid 120 and (name N or name CA or name C or name O or name CB )) or \ resid 121)) selection = chain 'G' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 11.220 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 47.540 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.007 0.052 16932 Z= 0.454 Angle : 0.741 12.780 23004 Z= 0.422 Chirality : 0.184 4.771 2650 Planarity : 0.004 0.050 2938 Dihedral : 15.823 90.598 5939 Min Nonbonded Distance : 1.054 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.97 % Rotamer Outliers : 7.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.17), residues: 2121 helix: -0.87 (0.13), residues: 1371 sheet: -1.90 (0.37), residues: 186 loop : -2.84 (0.25), residues: 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 221 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 74 residues processed: 329 average time/residue: 0.3395 time to fit residues: 157.7368 Evaluate side-chains 227 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 153 time to evaluate : 1.951 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 74 outliers final: 1 residues processed: 74 average time/residue: 0.1521 time to fit residues: 23.3098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 124 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 539 ASN B 477 ASN B 501 HIS B 562 HIS B 568 ASN B 599 HIS ** B 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN D 70 HIS F 74 HIS G 70 HIS ** H 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN H 173 HIS ** I 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 629 ASN I 664 ASN I 720 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16932 Z= 0.183 Angle : 0.583 10.130 23004 Z= 0.287 Chirality : 0.040 0.304 2650 Planarity : 0.004 0.060 2938 Dihedral : 4.596 57.303 2330 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.19), residues: 2121 helix: 0.95 (0.14), residues: 1380 sheet: -1.35 (0.37), residues: 183 loop : -2.21 (0.26), residues: 558 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 191 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 12 residues processed: 220 average time/residue: 0.3168 time to fit residues: 102.9432 Evaluate side-chains 170 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2250 time to fit residues: 7.0425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 chunk 194 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 173 optimal weight: 0.0010 chunk 193 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 156 optimal weight: 0.2980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 HIS ** B 694 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN F 94 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 ASN I 664 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 16932 Z= 0.153 Angle : 0.553 7.881 23004 Z= 0.276 Chirality : 0.039 0.236 2650 Planarity : 0.004 0.070 2938 Dihedral : 4.399 51.413 2330 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 2121 helix: 1.62 (0.14), residues: 1383 sheet: -1.04 (0.38), residues: 181 loop : -2.02 (0.27), residues: 557 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 17 residues processed: 223 average time/residue: 0.3232 time to fit residues: 107.3763 Evaluate side-chains 182 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1645 time to fit residues: 8.1466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 130 optimal weight: 20.0000 chunk 195 optimal weight: 0.6980 chunk 206 optimal weight: 0.1980 chunk 102 optimal weight: 0.9980 chunk 185 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 ASN B 694 HIS ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 ASN I 570 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 16932 Z= 0.149 Angle : 0.534 7.903 23004 Z= 0.267 Chirality : 0.039 0.253 2650 Planarity : 0.004 0.065 2938 Dihedral : 4.235 46.785 2330 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 2.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2121 helix: 1.91 (0.15), residues: 1385 sheet: -0.85 (0.38), residues: 187 loop : -1.87 (0.27), residues: 549 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 10 residues processed: 212 average time/residue: 0.3147 time to fit residues: 99.0910 Evaluate side-chains 169 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 159 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2074 time to fit residues: 6.2576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 154 optimal weight: 0.0070 chunk 85 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 105 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 ASN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 ASN I 620 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16932 Z= 0.206 Angle : 0.562 9.659 23004 Z= 0.279 Chirality : 0.040 0.269 2650 Planarity : 0.004 0.064 2938 Dihedral : 4.232 45.784 2330 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 2121 helix: 2.00 (0.15), residues: 1385 sheet: -0.73 (0.40), residues: 177 loop : -1.71 (0.27), residues: 559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 15 residues processed: 188 average time/residue: 0.3324 time to fit residues: 91.9606 Evaluate side-chains 174 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 2.203 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1850 time to fit residues: 7.5910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 50.0000 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16932 Z= 0.214 Angle : 0.565 9.545 23004 Z= 0.282 Chirality : 0.040 0.229 2650 Planarity : 0.004 0.061 2938 Dihedral : 4.239 45.653 2330 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.20), residues: 2121 helix: 2.10 (0.15), residues: 1381 sheet: -0.68 (0.40), residues: 179 loop : -1.64 (0.27), residues: 561 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 189 average time/residue: 0.3146 time to fit residues: 88.0023 Evaluate side-chains 160 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2219 time to fit residues: 5.0539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 206 optimal weight: 0.0770 chunk 129 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 ASN H 205 ASN I 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 16932 Z= 0.241 Angle : 0.588 10.357 23004 Z= 0.293 Chirality : 0.040 0.248 2650 Planarity : 0.004 0.060 2938 Dihedral : 4.280 45.423 2330 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 2121 helix: 2.07 (0.15), residues: 1382 sheet: -0.45 (0.40), residues: 180 loop : -1.63 (0.27), residues: 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 182 average time/residue: 0.3171 time to fit residues: 85.6539 Evaluate side-chains 165 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1853 time to fit residues: 6.5815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 62 optimal weight: 30.0000 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 50.0000 chunk 162 optimal weight: 2.9990 chunk 187 optimal weight: 0.0370 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 16932 Z= 0.229 Angle : 0.598 9.856 23004 Z= 0.296 Chirality : 0.040 0.230 2650 Planarity : 0.004 0.058 2938 Dihedral : 4.273 46.360 2330 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.20), residues: 2121 helix: 2.10 (0.15), residues: 1382 sheet: -0.32 (0.41), residues: 173 loop : -1.55 (0.27), residues: 566 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 170 average time/residue: 0.3223 time to fit residues: 81.2992 Evaluate side-chains 155 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 152 time to evaluate : 2.163 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3461 time to fit residues: 4.2371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 0.7980 chunk 180 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 126 optimal weight: 0.0870 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16932 Z= 0.186 Angle : 0.608 13.211 23004 Z= 0.296 Chirality : 0.039 0.208 2650 Planarity : 0.003 0.058 2938 Dihedral : 4.254 49.350 2330 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 2121 helix: 2.16 (0.15), residues: 1381 sheet: -0.36 (0.41), residues: 173 loop : -1.49 (0.27), residues: 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 173 average time/residue: 0.3366 time to fit residues: 87.2144 Evaluate side-chains 156 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 2.262 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1540 time to fit residues: 3.8311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 196 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 17 optimal weight: 50.0000 chunk 131 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 16932 Z= 0.168 Angle : 0.624 11.726 23004 Z= 0.307 Chirality : 0.040 0.198 2650 Planarity : 0.004 0.058 2938 Dihedral : 4.238 51.023 2330 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.20), residues: 2121 helix: 2.15 (0.15), residues: 1384 sheet: -0.14 (0.43), residues: 163 loop : -1.52 (0.27), residues: 574 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4242 Ramachandran restraints generated. 2121 Oldfield, 0 Emsley, 2121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 174 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 175 average time/residue: 0.3290 time to fit residues: 86.7064 Evaluate side-chains 161 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 2.140 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4795 time to fit residues: 3.4633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 156 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 149 optimal weight: 0.0270 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.082899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.056610 restraints weight = 69597.542| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.03 r_work: 0.3068 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 16932 Z= 0.159 Angle : 0.622 13.345 23004 Z= 0.306 Chirality : 0.039 0.185 2650 Planarity : 0.003 0.057 2938 Dihedral : 4.193 52.632 2330 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.20), residues: 2121 helix: 2.19 (0.15), residues: 1382 sheet: -0.05 (0.45), residues: 153 loop : -1.49 (0.26), residues: 586 =============================================================================== Job complete usr+sys time: 3498.67 seconds wall clock time: 64 minutes 18.10 seconds (3858.10 seconds total)