Starting phenix.real_space_refine on Mon Dec 11 04:09:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/12_2023/7k36_22650_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/12_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_22650/12_2023/7k36_22650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/12_2023/7k36_22650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/12_2023/7k36_22650_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k36_22650/12_2023/7k36_22650_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians 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-1.21rc1-5172/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: 9.11, per 1000 atoms: 0.55 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: 7.11 Conformation dependent library (CDL) restraints added in 3.2 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: 3.21 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: 5.19 Time building geometry restraints manager: 7.45 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 - 24.53: 9446 24.53 - 49.06: 607 49.06 - 73.59: 77 73.59 - 98.12: 18 98.12 - 122.66: 3 Dihedral angle restraints: 10151 sinusoidal: 3752 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 10148 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 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: 10.440 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 49.120 Find NCS groups from input model: 0.570 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.740 ------------------------------------------------------------------------------- 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 : 16.339 122.656 5975 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 % Allowed : 17.16 % Favored : 75.58 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 69 HIS 0.007 0.001 HIS I 231 PHE 0.023 0.002 PHE A 538 TYR 0.017 0.001 TYR I 712 ARG 0.004 0.000 ARG B 446 *********************** 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 : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 74 residues processed: 329 average time/residue: 0.3414 time to fit residues: 160.0543 Evaluate side-chains 227 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 153 time to evaluate : 1.932 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 74 outliers final: 1 residues processed: 74 average time/residue: 0.1561 time to fit residues: 24.0967 ------------------------------------------------------------------------------- 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 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 I 629 ASN I 664 ASN I 720 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16932 Z= 0.183 Angle : 0.583 11.438 23004 Z= 0.288 Chirality : 0.040 0.270 2650 Planarity : 0.004 0.059 2938 Dihedral : 5.342 59.745 2366 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.40 % Allowed : 21.28 % Favored : 76.32 % 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: -0.17 (0.19), residues: 2121 helix: 0.92 (0.14), residues: 1380 sheet: -1.36 (0.37), residues: 183 loop : -2.22 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 423 HIS 0.005 0.001 HIS I 570 PHE 0.022 0.002 PHE A 538 TYR 0.017 0.001 TYR G 71 ARG 0.006 0.000 ARG A 527 *********************** 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 228 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 189 time to evaluate : 1.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 12 residues processed: 218 average time/residue: 0.3188 time to fit residues: 102.2339 Evaluate side-chains 171 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2269 time to fit residues: 6.8510 ------------------------------------------------------------------------------- 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: 2.9990 chunk 60 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 210 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 193 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 156 optimal weight: 0.0870 overall best weight: 1.1560 ------------------------------------------------------------------------------- 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** E 107 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 ASN I 664 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16932 Z= 0.182 Angle : 0.558 7.176 23004 Z= 0.280 Chirality : 0.039 0.222 2650 Planarity : 0.004 0.070 2938 Dihedral : 4.955 58.800 2366 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.52 % Allowed : 23.49 % Favored : 73.99 % 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: 0.62 (0.19), residues: 2121 helix: 1.57 (0.14), residues: 1382 sheet: -1.22 (0.37), residues: 190 loop : -1.97 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 423 HIS 0.008 0.001 HIS H 93 PHE 0.019 0.001 PHE A 538 TYR 0.015 0.001 TYR H 164 ARG 0.005 0.000 ARG I 441 *********************** 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 222 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 18 residues processed: 215 average time/residue: 0.3258 time to fit residues: 103.4611 Evaluate side-chains 180 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1555 time to fit residues: 7.7590 ------------------------------------------------------------------------------- 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: 0.9990 chunk 146 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 21 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 195 optimal weight: 0.7980 chunk 206 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 694 HIS ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16932 Z= 0.154 Angle : 0.543 8.417 23004 Z= 0.271 Chirality : 0.039 0.217 2650 Planarity : 0.004 0.066 2938 Dihedral : 4.793 59.559 2366 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.28 % Allowed : 23.68 % Favored : 74.05 % 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: 1.03 (0.19), residues: 2121 helix: 1.85 (0.15), residues: 1383 sheet: -0.76 (0.40), residues: 177 loop : -1.86 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 423 HIS 0.006 0.001 HIS H 113 PHE 0.018 0.001 PHE B 555 TYR 0.015 0.001 TYR H 164 ARG 0.006 0.000 ARG F 83 *********************** 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: 37 poor density : 183 time to evaluate : 1.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 13 residues processed: 215 average time/residue: 0.3019 time to fit residues: 96.1778 Evaluate side-chains 169 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 156 time to evaluate : 1.947 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2359 time to fit residues: 7.4545 ------------------------------------------------------------------------------- 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: 0.0770 chunk 117 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 154 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 142 optimal weight: 0.4980 chunk 0 optimal weight: 40.0000 chunk 105 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 ASN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16932 Z= 0.174 Angle : 0.558 9.733 23004 Z= 0.276 Chirality : 0.040 0.269 2650 Planarity : 0.004 0.065 2938 Dihedral : 4.765 59.850 2366 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.17 % Allowed : 24.97 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 2121 helix: 2.00 (0.15), residues: 1382 sheet: -0.75 (0.39), residues: 179 loop : -1.76 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 476 HIS 0.006 0.001 HIS H 113 PHE 0.016 0.001 PHE A 538 TYR 0.015 0.001 TYR H 164 ARG 0.010 0.000 ARG F 116 *********************** 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 195 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 176 time to evaluate : 2.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 188 average time/residue: 0.3320 time to fit residues: 92.2949 Evaluate side-chains 169 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1551 time to fit residues: 5.2092 ------------------------------------------------------------------------------- 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: 10.0000 chunk 186 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 50.0000 chunk 68 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 GLN H 199 ASN I 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16932 Z= 0.273 Angle : 0.591 9.003 23004 Z= 0.295 Chirality : 0.041 0.249 2650 Planarity : 0.004 0.063 2938 Dihedral : 4.812 59.857 2366 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.78 % Allowed : 25.28 % Favored : 72.94 % 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: 1.28 (0.20), residues: 2121 helix: 2.02 (0.15), residues: 1383 sheet: -0.67 (0.38), residues: 193 loop : -1.70 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 86 HIS 0.006 0.001 HIS H 113 PHE 0.023 0.002 PHE B 555 TYR 0.015 0.001 TYR I 712 ARG 0.005 0.000 ARG A 527 *********************** 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 197 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 8 residues processed: 188 average time/residue: 0.3283 time to fit residues: 90.6467 Evaluate side-chains 162 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 1.909 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2260 time to fit residues: 5.4537 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 206 optimal weight: 0.0870 chunk 129 optimal weight: 9.9990 chunk 125 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16932 Z= 0.242 Angle : 0.597 10.546 23004 Z= 0.296 Chirality : 0.040 0.240 2650 Planarity : 0.004 0.061 2938 Dihedral : 4.819 59.907 2366 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.35 % Allowed : 25.83 % Favored : 72.82 % 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: 1.35 (0.20), residues: 2121 helix: 2.06 (0.14), residues: 1379 sheet: -0.53 (0.40), residues: 182 loop : -1.64 (0.27), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 476 HIS 0.005 0.001 HIS H 113 PHE 0.025 0.002 PHE B 623 TYR 0.017 0.001 TYR H 198 ARG 0.006 0.000 ARG A 527 *********************** 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 187 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 180 average time/residue: 0.3111 time to fit residues: 83.7997 Evaluate side-chains 166 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 2.066 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1654 time to fit residues: 6.2749 ------------------------------------------------------------------------------- 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: 2.9990 chunk 123 optimal weight: 4.9990 chunk 62 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 40.0000 chunk 162 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** D 73 GLN H 139 ASN H 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16932 Z= 0.227 Angle : 0.600 11.450 23004 Z= 0.297 Chirality : 0.040 0.274 2650 Planarity : 0.004 0.060 2938 Dihedral : 4.816 59.772 2366 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.11 % Allowed : 25.95 % Favored : 72.94 % 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: 1.41 (0.20), residues: 2121 helix: 2.10 (0.15), residues: 1381 sheet: -0.51 (0.40), residues: 182 loop : -1.60 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 476 HIS 0.005 0.001 HIS H 73 PHE 0.025 0.001 PHE B 555 TYR 0.016 0.001 TYR B 541 ARG 0.006 0.000 ARG A 527 *********************** 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 184 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 166 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 178 average time/residue: 0.3146 time to fit residues: 83.2548 Evaluate side-chains 163 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 1.940 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2917 time to fit residues: 7.2963 ------------------------------------------------------------------------------- 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: 1.9990 chunk 180 optimal weight: 0.9980 chunk 192 optimal weight: 0.4980 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 191 optimal weight: 0.0270 chunk 126 optimal weight: 0.5980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 667 ASN ** C 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16932 Z= 0.171 Angle : 0.610 11.588 23004 Z= 0.299 Chirality : 0.039 0.244 2650 Planarity : 0.004 0.059 2938 Dihedral : 4.764 59.043 2366 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.43 % Allowed : 26.20 % Favored : 73.37 % 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: 1.50 (0.20), residues: 2121 helix: 2.14 (0.15), residues: 1384 sheet: -0.16 (0.43), residues: 163 loop : -1.58 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 86 HIS 0.004 0.001 HIS B 501 PHE 0.021 0.001 PHE B 623 TYR 0.019 0.001 TYR B 541 ARG 0.007 0.000 ARG D 116 *********************** 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 177 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 170 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 175 average time/residue: 0.3210 time to fit residues: 84.3184 Evaluate side-chains 159 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 156 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1500 time to fit residues: 3.4974 ------------------------------------------------------------------------------- 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: 0.9980 chunk 124 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 213 optimal weight: 0.1980 chunk 196 optimal weight: 0.1980 chunk 169 optimal weight: 0.3980 chunk 17 optimal weight: 50.0000 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 0.0870 chunk 134 optimal weight: 5.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- 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 107 GLN H 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16932 Z= 0.159 Angle : 0.623 12.105 23004 Z= 0.310 Chirality : 0.040 0.225 2650 Planarity : 0.004 0.059 2938 Dihedral : 4.712 58.454 2366 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.12 % Allowed : 27.12 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 2121 helix: 2.15 (0.15), residues: 1384 sheet: -0.12 (0.43), residues: 163 loop : -1.58 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 475 HIS 0.004 0.001 HIS H 127 PHE 0.020 0.001 PHE B 623 TYR 0.060 0.001 TYR B 510 ARG 0.007 0.000 ARG A 527 ********************** 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 179 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 177 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 179 average time/residue: 0.3169 time to fit residues: 84.8871 Evaluate side-chains 157 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.992 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6985 ------------------------------------------------------------------------------- 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: 0.9990 chunk 52 optimal weight: 0.0020 chunk 156 optimal weight: 0.9990 chunk 25 optimal weight: 0.0170 chunk 47 optimal weight: 0.8980 chunk 170 optimal weight: 0.0020 chunk 71 optimal weight: 20.0000 chunk 174 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 overall best weight: 0.2834 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.083255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.059415 restraints weight = 69815.996| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.29 r_work: 0.3071 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16932 Z= 0.156 Angle : 0.628 11.739 23004 Z= 0.311 Chirality : 0.039 0.223 2650 Planarity : 0.004 0.059 2938 Dihedral : 4.663 59.131 2366 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.18 % Allowed : 27.43 % Favored : 72.39 % 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: 1.56 (0.19), residues: 2121 helix: 2.15 (0.14), residues: 1385 sheet: -0.02 (0.43), residues: 163 loop : -1.50 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 476 HIS 0.005 0.001 HIS B 606 PHE 0.025 0.001 PHE A 76 TYR 0.054 0.001 TYR B 510 ARG 0.008 0.000 ARG E 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3578.72 seconds wall clock time: 65 minutes 47.15 seconds (3947.15 seconds total)