Starting phenix.real_space_refine on Tue Dec 12 08:04:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/12_2023/7n5d_24186_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/12_2023/7n5d_24186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/12_2023/7n5d_24186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/12_2023/7n5d_24186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/12_2023/7n5d_24186_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5d_24186/12_2023/7n5d_24186_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 13516 2.51 5 N 3419 2.21 5 O 3574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 598": "OD1" <-> "OD2" Residue "C PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 625": "OE1" <-> "OE2" Residue "D TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 746": "OE1" <-> "OE2" Residue "E PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 611": "OE1" <-> "OE2" Residue "G PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 695": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20593 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3019 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 378} Chain breaks: 5 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 177 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "D" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.62, per 1000 atoms: 0.52 Number of scatterers: 20593 At special positions: 0 Unit cell: (147.29, 144.2, 140.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3574 8.00 N 3419 7.00 C 13516 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: 8.33 Conformation dependent library (CDL) restraints added in 3.7 seconds 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5066 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 14 sheets defined 60.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.59 Creating SS restraints... Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 191 through 201 Processing helix chain 'A' and resid 223 through 243 removed outlier: 4.232A pdb=" N LEU A 226 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU A 234 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 282 removed outlier: 5.237A pdb=" N THR A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N SER A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 332 removed outlier: 4.266A pdb=" N HIS A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 352 Processing helix chain 'A' and resid 504 through 551 Processing helix chain 'A' and resid 557 through 573 removed outlier: 3.585A pdb=" N PHE A 572 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 589 Processing helix chain 'A' and resid 631 through 636 removed outlier: 4.907A pdb=" N THR A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 678 Processing helix chain 'A' and resid 715 through 736 Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 223 through 231 Processing helix chain 'B' and resid 236 through 240 Processing helix chain 'B' and resid 265 through 284 Processing helix chain 'B' and resid 296 through 330 removed outlier: 3.906A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE B 330 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 removed outlier: 5.032A pdb=" N ASP B 337 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 349 " --> pdb=" O HIS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 551 removed outlier: 4.134A pdb=" N ASN B 525 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 526 " --> pdb=" O LEU B 522 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N VAL B 529 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 589 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 636 removed outlier: 4.664A pdb=" N THR B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 677 Processing helix chain 'B' and resid 715 through 735 Processing helix chain 'C' and resid 187 through 202 Processing helix chain 'C' and resid 223 through 231 Processing helix chain 'C' and resid 235 through 241 Processing helix chain 'C' and resid 265 through 284 Processing helix chain 'C' and resid 296 through 330 removed outlier: 3.892A pdb=" N SER C 329 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 351 removed outlier: 5.010A pdb=" N ASP C 337 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 551 removed outlier: 4.129A pdb=" N ASN C 525 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS C 526 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 527 " --> pdb=" O ASN C 523 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA C 528 " --> pdb=" O ASP C 524 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL C 529 " --> pdb=" O ASN C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 589 removed outlier: 5.551A pdb=" N ASN C 576 " --> pdb=" O PHE C 572 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 4.970A pdb=" N THR C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 677 Processing helix chain 'C' and resid 715 through 736 Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 223 through 231 Processing helix chain 'D' and resid 235 through 241 Processing helix chain 'D' and resid 265 through 284 Processing helix chain 'D' and resid 296 through 330 removed outlier: 3.709A pdb=" N SER D 328 " --> pdb=" O LYS D 324 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER D 329 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 351 removed outlier: 5.086A pdb=" N ASP D 337 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 551 removed outlier: 4.146A pdb=" N ASN D 525 " --> pdb=" O ALA D 521 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS D 526 " --> pdb=" O LEU D 522 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR D 527 " --> pdb=" O ASN D 523 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA D 528 " --> pdb=" O ASP D 524 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL D 529 " --> pdb=" O ASN D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 589 removed outlier: 5.586A pdb=" N ASN D 576 " --> pdb=" O PHE D 572 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N THR D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 636 removed outlier: 5.031A pdb=" N THR D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 679 Processing helix chain 'D' and resid 715 through 736 Processing helix chain 'E' and resid 187 through 202 Processing helix chain 'E' and resid 223 through 231 Processing helix chain 'E' and resid 235 through 241 Processing helix chain 'E' and resid 265 through 284 Processing helix chain 'E' and resid 296 through 330 removed outlier: 3.648A pdb=" N SER E 328 " --> pdb=" O LYS E 324 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER E 329 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 351 removed outlier: 5.103A pdb=" N ASP E 337 " --> pdb=" O ARG E 334 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU E 341 " --> pdb=" O ARG E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 523 Processing helix chain 'E' and resid 527 through 551 Processing helix chain 'E' and resid 557 through 589 removed outlier: 5.669A pdb=" N ASN E 576 " --> pdb=" O PHE E 572 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR E 577 " --> pdb=" O ILE E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 631 through 636 removed outlier: 4.850A pdb=" N THR E 636 " --> pdb=" O SER E 632 " (cutoff:3.500A) Processing helix chain 'E' and resid 662 through 677 Processing helix chain 'E' and resid 715 through 735 Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 223 through 231 Processing helix chain 'F' and resid 236 through 240 Processing helix chain 'F' and resid 265 through 284 Processing helix chain 'F' and resid 296 through 330 removed outlier: 3.985A pdb=" N SER F 329 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE F 330 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 351 removed outlier: 5.041A pdb=" N ASP F 337 " --> pdb=" O ARG F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 525 removed outlier: 4.147A pdb=" N ASN F 525 " --> pdb=" O ALA F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 551 Processing helix chain 'F' and resid 557 through 589 removed outlier: 5.688A pdb=" N ASN F 576 " --> pdb=" O PHE F 572 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 636 removed outlier: 5.218A pdb=" N THR F 636 " --> pdb=" O SER F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 678 Processing helix chain 'F' and resid 715 through 736 Processing helix chain 'G' and resid 187 through 202 Processing helix chain 'G' and resid 223 through 230 Processing helix chain 'G' and resid 236 through 241 Processing helix chain 'G' and resid 265 through 284 Processing helix chain 'G' and resid 296 through 330 removed outlier: 3.906A pdb=" N SER G 329 " --> pdb=" O ILE G 325 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE G 330 " --> pdb=" O LEU G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 351 removed outlier: 5.016A pdb=" N ASP G 337 " --> pdb=" O ARG G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 525 removed outlier: 4.328A pdb=" N ASN G 525 " --> pdb=" O ALA G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 551 Processing helix chain 'G' and resid 557 through 589 removed outlier: 5.688A pdb=" N ASN G 576 " --> pdb=" O PHE G 572 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N THR G 577 " --> pdb=" O ILE G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 631 through 636 removed outlier: 5.129A pdb=" N THR G 636 " --> pdb=" O SER G 632 " (cutoff:3.500A) Processing helix chain 'G' and resid 662 through 678 Processing helix chain 'G' and resid 715 through 735 Processing sheet with id= A, first strand: chain 'A' and resid 639 through 641 removed outlier: 6.640A pdb=" N VAL A 618 " --> pdb=" O GLU A 610 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N MET A 612 " --> pdb=" O THR A 616 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N THR A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 649 through 657 removed outlier: 6.783A pdb=" N ALA A 703 " --> pdb=" O VAL A 691 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL A 691 " --> pdb=" O ALA A 703 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 705 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N MET A 689 " --> pdb=" O PHE A 705 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN A 707 " --> pdb=" O HIS A 687 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N HIS A 687 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 639 through 641 removed outlier: 6.843A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.749A pdb=" N ALA B 703 " --> pdb=" O VAL B 691 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 691 " --> pdb=" O ALA B 703 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE B 705 " --> pdb=" O MET B 689 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N MET B 689 " --> pdb=" O PHE B 705 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 639 through 641 removed outlier: 6.833A pdb=" N VAL C 618 " --> pdb=" O GLU C 610 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N MET C 612 " --> pdb=" O THR C 616 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR C 616 " --> pdb=" O MET C 612 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 649 through 657 removed outlier: 6.743A pdb=" N ALA C 703 " --> pdb=" O VAL C 691 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL C 691 " --> pdb=" O ALA C 703 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE C 705 " --> pdb=" O MET C 689 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N MET C 689 " --> pdb=" O PHE C 705 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASN C 707 " --> pdb=" O HIS C 687 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N HIS C 687 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 639 through 641 removed outlier: 6.513A pdb=" N VAL D 618 " --> pdb=" O GLU D 610 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N MET D 612 " --> pdb=" O THR D 616 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR D 616 " --> pdb=" O MET D 612 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 649 through 657 removed outlier: 6.772A pdb=" N ALA D 703 " --> pdb=" O VAL D 691 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL D 691 " --> pdb=" O ALA D 703 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N PHE D 705 " --> pdb=" O MET D 689 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N MET D 689 " --> pdb=" O PHE D 705 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 639 through 641 removed outlier: 6.665A pdb=" N VAL E 618 " --> pdb=" O GLU E 610 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET E 612 " --> pdb=" O THR E 616 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N THR E 616 " --> pdb=" O MET E 612 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 649 through 657 removed outlier: 6.774A pdb=" N ALA E 703 " --> pdb=" O VAL E 691 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL E 691 " --> pdb=" O ALA E 703 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE E 705 " --> pdb=" O MET E 689 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N MET E 689 " --> pdb=" O PHE E 705 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 639 through 641 removed outlier: 6.799A pdb=" N VAL F 618 " --> pdb=" O GLU F 610 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 649 through 657 removed outlier: 6.713A pdb=" N ALA F 703 " --> pdb=" O VAL F 691 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL F 691 " --> pdb=" O ALA F 703 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE F 705 " --> pdb=" O MET F 689 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N MET F 689 " --> pdb=" O PHE F 705 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN F 707 " --> pdb=" O HIS F 687 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N HIS F 687 " --> pdb=" O ASN F 707 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 599 through 602 removed outlier: 6.667A pdb=" N VAL G 618 " --> pdb=" O GLU G 610 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N MET G 612 " --> pdb=" O THR G 616 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR G 616 " --> pdb=" O MET G 612 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 649 through 657 removed outlier: 6.782A pdb=" N ALA G 703 " --> pdb=" O VAL G 691 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL G 691 " --> pdb=" O ALA G 703 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE G 705 " --> pdb=" O MET G 689 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N MET G 689 " --> pdb=" O PHE G 705 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN G 707 " --> pdb=" O HIS G 687 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS G 687 " --> pdb=" O ASN G 707 " (cutoff:3.500A) 1386 hydrogen bonds defined for protein. 3771 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.16 Time building geometry restraints manager: 8.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3829 1.31 - 1.44: 5375 1.44 - 1.56: 11510 1.56 - 1.69: 113 1.69 - 1.82: 147 Bond restraints: 20974 Sorted by residual: bond pdb=" CB ILE E 285 " pdb=" CG1 ILE E 285 " ideal model delta sigma weight residual 1.530 1.672 -0.142 2.00e-02 2.50e+03 5.01e+01 bond pdb=" CB ILE F 285 " pdb=" CG1 ILE F 285 " ideal model delta sigma weight residual 1.530 1.671 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" CB ILE G 285 " pdb=" CG1 ILE G 285 " ideal model delta sigma weight residual 1.530 1.667 -0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" CB HIS A 331 " pdb=" CG HIS A 331 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.47e+01 bond pdb=" CD2 TRP D 507 " pdb=" CE3 TRP D 507 " ideal model delta sigma weight residual 1.398 1.505 -0.107 1.60e-02 3.91e+03 4.46e+01 ... (remaining 20969 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.71: 335 105.71 - 112.90: 11316 112.90 - 120.09: 8686 120.09 - 127.27: 7847 127.27 - 134.46: 240 Bond angle restraints: 28424 Sorted by residual: angle pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " pdb=" CG PHE A 335 " ideal model delta sigma weight residual 113.80 122.08 -8.28 1.00e+00 1.00e+00 6.86e+01 angle pdb=" C GLN G 291 " pdb=" N PRO G 292 " pdb=" CA PRO G 292 " ideal model delta sigma weight residual 119.47 128.27 -8.80 1.16e+00 7.43e-01 5.76e+01 angle pdb=" C GLN C 291 " pdb=" N PRO C 292 " pdb=" CA PRO C 292 " ideal model delta sigma weight residual 119.56 127.00 -7.44 1.02e+00 9.61e-01 5.32e+01 angle pdb=" N THR C 557 " pdb=" CA THR C 557 " pdb=" C THR C 557 " ideal model delta sigma weight residual 112.89 121.73 -8.84 1.24e+00 6.50e-01 5.08e+01 angle pdb=" C HIS E 592 " pdb=" N PRO E 593 " pdb=" CA PRO E 593 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.01e+00 9.80e-01 5.02e+01 ... (remaining 28419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 12108 17.71 - 35.42: 257 35.42 - 53.13: 50 53.13 - 70.84: 30 70.84 - 88.54: 12 Dihedral angle restraints: 12457 sinusoidal: 4779 harmonic: 7678 Sorted by residual: dihedral pdb=" N PHE A 335 " pdb=" C PHE A 335 " pdb=" CA PHE A 335 " pdb=" CB PHE A 335 " ideal model delta harmonic sigma weight residual 122.80 130.99 -8.19 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" N ARG A 296 " pdb=" C ARG A 296 " pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB GLU A 611 " pdb=" CG GLU A 611 " pdb=" CD GLU A 611 " pdb=" OE1 GLU A 611 " ideal model delta sinusoidal sigma weight residual 0.00 -88.54 88.54 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 12454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 2784 0.110 - 0.220: 601 0.220 - 0.330: 46 0.330 - 0.440: 9 0.440 - 0.550: 12 Chirality restraints: 3452 Sorted by residual: chirality pdb=" CG LEU C 264 " pdb=" CB LEU C 264 " pdb=" CD1 LEU C 264 " pdb=" CD2 LEU C 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.14 0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" CB ILE A 285 " pdb=" CA ILE A 285 " pdb=" CG1 ILE A 285 " pdb=" CG2 ILE A 285 " both_signs ideal model delta sigma weight residual False 2.64 3.18 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CG LEU A 258 " pdb=" CB LEU A 258 " pdb=" CD1 LEU A 258 " pdb=" CD2 LEU A 258 " both_signs ideal model delta sigma weight residual False -2.59 -3.12 0.53 2.00e-01 2.50e+01 7.03e+00 ... (remaining 3449 not shown) Planarity restraints: 3469 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 335 " -0.059 2.00e-02 2.50e+03 3.66e-02 2.35e+01 pdb=" CG PHE A 335 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE A 335 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 335 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 335 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 335 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 335 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 291 " 0.022 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C GLN E 291 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN E 291 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO E 292 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 675 " 0.044 2.00e-02 2.50e+03 2.53e-02 1.28e+01 pdb=" CG TYR E 675 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR E 675 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 675 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR E 675 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR E 675 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR E 675 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 675 " 0.042 2.00e-02 2.50e+03 ... (remaining 3466 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 7802 2.88 - 3.39: 21299 3.39 - 3.89: 34724 3.89 - 4.40: 40068 4.40 - 4.90: 62902 Nonbonded interactions: 166795 Sorted by model distance: nonbonded pdb=" OD1 ASP F 737 " pdb=" NZ LYS F 739 " model vdw 2.378 2.520 nonbonded pdb=" OD1 ASP G 737 " pdb=" NZ LYS G 739 " model vdw 2.385 2.520 nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 2.520 nonbonded pdb=" OD1 ASP D 737 " pdb=" NZ LYS D 739 " model vdw 2.399 2.520 nonbonded pdb=" OD1 ASP E 737 " pdb=" NZ LYS E 739 " model vdw 2.399 2.520 ... (remaining 166790 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 186 through 203 or resid 222 through 242 or resid 264 thro \ ugh 354 or resid 507 through 751 or resid 801)) selection = (chain 'B' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'C' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'D' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'E' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'F' and (resid 186 through 285 or resid 294 through 751 or resid 801)) selection = (chain 'G' and (resid 186 through 285 or resid 294 through 751 or resid 801)) } 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.660 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 54.180 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 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 : 0.023 0.142 20974 Z= 1.478 Angle : 1.521 8.842 28424 Z= 1.044 Chirality : 0.093 0.550 3452 Planarity : 0.008 0.043 3469 Dihedral : 9.909 88.544 7391 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 0.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.15), residues: 2540 helix: 1.53 (0.11), residues: 1580 sheet: 0.56 (0.31), residues: 290 loop : 1.05 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.008 TRP E 683 HIS 0.010 0.002 HIS A 331 PHE 0.059 0.005 PHE A 335 TYR 0.044 0.008 TYR E 675 ARG 0.006 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 794 time to evaluate : 2.160 Fit side-chains outliers start: 0 outliers final: 6 residues processed: 794 average time/residue: 1.2383 time to fit residues: 1114.0585 Evaluate side-chains 647 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 641 time to evaluate : 2.390 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 3 average time/residue: 0.2232 time to fit residues: 4.4063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 203 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 ASN ** A 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 ASN ** B 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 648 GLN D 291 GLN D 525 ASN D 576 ASN D 648 GLN D 687 HIS D 713 GLN E 533 ASN E 648 GLN E 698 ASN F 525 ASN F 648 GLN G 533 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20974 Z= 0.251 Angle : 0.599 8.957 28424 Z= 0.321 Chirality : 0.043 0.273 3452 Planarity : 0.004 0.042 3469 Dihedral : 6.956 59.544 2781 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.80 % Allowed : 14.56 % Favored : 81.64 % 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: 2.45 (0.16), residues: 2540 helix: 2.31 (0.12), residues: 1600 sheet: 0.51 (0.28), residues: 329 loop : 0.53 (0.27), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 304 HIS 0.007 0.001 HIS A 592 PHE 0.030 0.002 PHE A 335 TYR 0.009 0.002 TYR G 740 ARG 0.004 0.001 ARG F 599 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 679 time to evaluate : 2.213 Fit side-chains revert: symmetry clash outliers start: 82 outliers final: 26 residues processed: 704 average time/residue: 1.1836 time to fit residues: 952.9043 Evaluate side-chains 672 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 646 time to evaluate : 2.196 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 12 residues processed: 16 average time/residue: 0.2271 time to fit residues: 9.5534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 0.0050 chunk 196 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 0.3980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 HIS A 533 ASN A 576 ASN A 686 GLN C 648 GLN D 291 GLN D 686 GLN D 688 ASN E 576 ASN E 648 GLN G 525 ASN G 576 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20974 Z= 0.190 Angle : 0.532 8.564 28424 Z= 0.279 Chirality : 0.041 0.235 3452 Planarity : 0.003 0.029 3469 Dihedral : 6.723 59.668 2781 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.94 % Allowed : 17.39 % Favored : 78.67 % 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: 2.30 (0.17), residues: 2540 helix: 2.27 (0.12), residues: 1606 sheet: 0.28 (0.28), residues: 341 loop : 0.30 (0.28), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 304 HIS 0.004 0.001 HIS A 592 PHE 0.027 0.001 PHE F 301 TYR 0.010 0.001 TYR E 740 ARG 0.005 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 664 time to evaluate : 2.241 Fit side-chains outliers start: 85 outliers final: 37 residues processed: 693 average time/residue: 1.2093 time to fit residues: 954.1387 Evaluate side-chains 681 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 644 time to evaluate : 2.334 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 13 residues processed: 26 average time/residue: 0.4842 time to fit residues: 20.0370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 237 optimal weight: 0.0470 chunk 251 optimal weight: 0.5980 chunk 124 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 686 GLN C 576 ASN C 648 GLN C 698 ASN D 576 ASN D 648 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN D 698 ASN E 531 GLN E 576 ASN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 576 ASN F 688 ASN G 525 ASN G 576 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20974 Z= 0.202 Angle : 0.521 8.262 28424 Z= 0.268 Chirality : 0.041 0.200 3452 Planarity : 0.003 0.037 3469 Dihedral : 6.544 57.163 2781 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.43 % Allowed : 19.24 % Favored : 77.33 % 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: 2.40 (0.17), residues: 2540 helix: 2.34 (0.12), residues: 1606 sheet: 0.53 (0.27), residues: 329 loop : 0.22 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 PHE 0.021 0.001 PHE A 271 TYR 0.010 0.001 TYR E 740 ARG 0.004 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 655 time to evaluate : 2.367 Fit side-chains outliers start: 74 outliers final: 36 residues processed: 682 average time/residue: 1.2406 time to fit residues: 961.2032 Evaluate side-chains 679 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 643 time to evaluate : 2.500 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 15 residues processed: 22 average time/residue: 0.5860 time to fit residues: 19.9330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 chunk 103 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 225 optimal weight: 4.9990 chunk 63 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN A 533 ASN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 ASN A 686 GLN C 648 GLN C 698 ASN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 ASN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 525 ASN G 576 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20974 Z= 0.188 Angle : 0.513 8.607 28424 Z= 0.264 Chirality : 0.041 0.236 3452 Planarity : 0.003 0.027 3469 Dihedral : 6.347 59.686 2781 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.52 % Allowed : 19.80 % Favored : 76.68 % 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: 2.46 (0.17), residues: 2540 helix: 2.44 (0.12), residues: 1606 sheet: 0.43 (0.27), residues: 319 loop : 0.16 (0.28), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 304 HIS 0.004 0.001 HIS E 708 PHE 0.027 0.001 PHE G 301 TYR 0.010 0.001 TYR D 740 ARG 0.008 0.000 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 637 time to evaluate : 2.590 Fit side-chains outliers start: 76 outliers final: 41 residues processed: 666 average time/residue: 1.2192 time to fit residues: 924.0992 Evaluate side-chains 678 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 637 time to evaluate : 2.238 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 19 residues processed: 23 average time/residue: 0.4128 time to fit residues: 16.3478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN ** A 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN C 648 GLN D 648 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 525 ASN G 576 ASN G 681 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20974 Z= 0.208 Angle : 0.518 10.378 28424 Z= 0.267 Chirality : 0.041 0.204 3452 Planarity : 0.003 0.028 3469 Dihedral : 6.250 59.406 2781 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.57 % Allowed : 20.40 % Favored : 76.03 % 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: 2.48 (0.17), residues: 2540 helix: 2.48 (0.13), residues: 1606 sheet: 0.40 (0.27), residues: 319 loop : 0.11 (0.28), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 304 HIS 0.005 0.001 HIS E 708 PHE 0.021 0.001 PHE A 271 TYR 0.008 0.001 TYR E 740 ARG 0.002 0.000 ARG C 644 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 645 time to evaluate : 2.340 Fit side-chains outliers start: 77 outliers final: 44 residues processed: 674 average time/residue: 1.2783 time to fit residues: 978.2897 Evaluate side-chains 678 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 634 time to evaluate : 2.267 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 21 residues processed: 24 average time/residue: 0.4157 time to fit residues: 17.1813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 chunk 183 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 140 optimal weight: 0.8980 chunk 250 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN A 686 GLN C 576 ASN C 648 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 688 ASN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 688 ASN G 525 ASN G 576 ASN G 681 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20974 Z= 0.191 Angle : 0.528 9.899 28424 Z= 0.272 Chirality : 0.041 0.191 3452 Planarity : 0.003 0.028 3469 Dihedral : 6.158 59.254 2781 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.34 % Allowed : 20.91 % Favored : 75.75 % 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: 2.50 (0.17), residues: 2540 helix: 2.49 (0.13), residues: 1606 sheet: 0.45 (0.27), residues: 329 loop : 0.11 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 273 HIS 0.004 0.001 HIS E 708 PHE 0.024 0.001 PHE F 301 TYR 0.008 0.001 TYR E 740 ARG 0.002 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 642 time to evaluate : 2.289 Fit side-chains outliers start: 72 outliers final: 39 residues processed: 674 average time/residue: 1.2389 time to fit residues: 947.5421 Evaluate side-chains 688 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 649 time to evaluate : 2.507 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 17 residues processed: 24 average time/residue: 0.3947 time to fit residues: 16.5811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 159 optimal weight: 0.0170 chunk 170 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 overall best weight: 1.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 513 ASN A 686 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN C 648 GLN C 678 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 648 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 681 ASN G 698 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20974 Z= 0.299 Angle : 0.581 11.441 28424 Z= 0.300 Chirality : 0.042 0.200 3452 Planarity : 0.003 0.030 3469 Dihedral : 6.262 59.576 2781 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.83 % Allowed : 22.07 % Favored : 75.10 % 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: 2540 helix: 2.37 (0.13), residues: 1606 sheet: 0.43 (0.27), residues: 329 loop : 0.08 (0.28), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 281 HIS 0.008 0.001 HIS E 708 PHE 0.027 0.002 PHE G 301 TYR 0.012 0.002 TYR D 740 ARG 0.002 0.000 ARG E 644 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 631 time to evaluate : 2.282 Fit side-chains outliers start: 61 outliers final: 41 residues processed: 656 average time/residue: 1.2487 time to fit residues: 933.5034 Evaluate side-chains 667 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 626 time to evaluate : 2.175 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 20 residues processed: 23 average time/residue: 0.4283 time to fit residues: 17.0935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.0020 chunk 240 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 chunk 101 optimal weight: 0.0170 chunk 183 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 211 optimal weight: 1.9990 chunk 220 optimal weight: 0.5980 chunk 232 optimal weight: 0.9990 overall best weight: 0.2824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN C 678 GLN C 686 GLN D 686 GLN D 688 ASN E 648 GLN E 678 GLN F 525 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN G 681 ASN G 698 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20974 Z= 0.153 Angle : 0.561 12.631 28424 Z= 0.283 Chirality : 0.041 0.222 3452 Planarity : 0.003 0.027 3469 Dihedral : 6.084 59.223 2781 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.36 % Allowed : 22.76 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.17), residues: 2540 helix: 2.52 (0.13), residues: 1606 sheet: 0.38 (0.27), residues: 329 loop : 0.10 (0.29), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 273 HIS 0.004 0.000 HIS A 592 PHE 0.027 0.001 PHE F 574 TYR 0.007 0.001 TYR A 259 ARG 0.003 0.000 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 624 time to evaluate : 2.285 Fit side-chains outliers start: 51 outliers final: 31 residues processed: 648 average time/residue: 1.2227 time to fit residues: 899.3619 Evaluate side-chains 649 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 618 time to evaluate : 2.347 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 19 residues processed: 14 average time/residue: 0.5117 time to fit residues: 12.6557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 259 optimal weight: 0.3980 chunk 238 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 159 optimal weight: 0.1980 chunk 126 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 686 GLN ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN G 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20974 Z= 0.196 Angle : 0.562 11.776 28424 Z= 0.287 Chirality : 0.041 0.225 3452 Planarity : 0.003 0.029 3469 Dihedral : 6.061 58.280 2781 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.67 % Allowed : 23.92 % Favored : 74.41 % 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: 2.45 (0.17), residues: 2540 helix: 2.47 (0.13), residues: 1606 sheet: 0.33 (0.27), residues: 329 loop : 0.10 (0.29), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 273 HIS 0.006 0.001 HIS A 592 PHE 0.029 0.001 PHE G 301 TYR 0.010 0.001 TYR D 740 ARG 0.002 0.000 ARG A 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5080 Ramachandran restraints generated. 2540 Oldfield, 0 Emsley, 2540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 615 time to evaluate : 2.308 Fit side-chains outliers start: 36 outliers final: 28 residues processed: 637 average time/residue: 1.2699 time to fit residues: 917.6944 Evaluate side-chains 643 residues out of total 2418 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 615 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 20 residues processed: 10 average time/residue: 0.4966 time to fit residues: 9.9142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.0170 chunk 219 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 190 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 212 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 515 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 525 ASN G 681 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.139879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112266 restraints weight = 32724.297| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.03 r_work: 0.3327 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20974 Z= 0.169 Angle : 0.574 13.475 28424 Z= 0.289 Chirality : 0.041 0.216 3452 Planarity : 0.003 0.026 3469 Dihedral : 5.970 57.082 2781 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.72 % Allowed : 24.29 % 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: 2.44 (0.17), residues: 2540 helix: 2.51 (0.13), residues: 1606 sheet: 0.07 (0.27), residues: 341 loop : 0.14 (0.29), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 273 HIS 0.004 0.000 HIS E 708 PHE 0.027 0.001 PHE A 271 TYR 0.009 0.001 TYR A 259 ARG 0.002 0.000 ARG A 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12612.96 seconds wall clock time: 221 minutes 42.06 seconds (13302.06 seconds total)