Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 20:16:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxg_29532/04_2023/8fxg_29532_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxg_29532/04_2023/8fxg_29532.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxg_29532/04_2023/8fxg_29532_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxg_29532/04_2023/8fxg_29532_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxg_29532/04_2023/8fxg_29532_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxg_29532/04_2023/8fxg_29532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxg_29532/04_2023/8fxg_29532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxg_29532/04_2023/8fxg_29532_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fxg_29532/04_2023/8fxg_29532_neut_updated.pdb" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 Na 1 4.78 5 C 12236 2.51 5 N 3060 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "C PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 318": "OE1" <-> "OE2" Residue "D PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18481 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4533 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 18, 'TRANS': 577} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 225 Chain: "B" Number of atoms: 4533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4533 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 18, 'TRANS': 577} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 225 Chain: "C" Number of atoms: 4533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4533 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 18, 'TRANS': 577} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 225 Chain: "D" Number of atoms: 4533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4533 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 18, 'TRANS': 577} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 423 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 13, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 225 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {' NA': 1, 'P0T': 2, 'XJ7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'P0T': 2, 'XJ7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'P0T': 2, 'XJ7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 86 Unusual residues: {'P0T': 2, 'XJ7': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.67, per 1000 atoms: 0.52 Number of scatterers: 18481 At special positions: 0 Unit cell: (160.82, 160.82, 117.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 4 15.00 Na 1 11.00 O 3092 8.00 N 3060 7.00 C 12236 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: 6.92 Conformation dependent library (CDL) restraints added in 2.7 seconds 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 4 sheets defined 56.5% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 185 Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 213 through 219 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 370 through 373 No H-bonds generated for 'chain 'A' and resid 370 through 373' Processing helix chain 'A' and resid 376 through 412 removed outlier: 3.820A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 458 Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.501A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 518 removed outlier: 3.924A pdb=" N LEU A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 513 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR A 514 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR A 515 " --> pdb=" O ASN A 511 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N THR A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLY A 518 " --> pdb=" O TYR A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 559 Processing helix chain 'A' and resid 593 through 605 removed outlier: 3.931A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 605 " --> pdb=" O PHE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 649 removed outlier: 3.519A pdb=" N TYR A 634 " --> pdb=" O VAL A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 673 removed outlier: 3.540A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 185 Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 213 through 219 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 261 through 281 Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 370 through 373 No H-bonds generated for 'chain 'B' and resid 370 through 373' Processing helix chain 'B' and resid 376 through 412 removed outlier: 3.820A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 458 Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 471 through 491 removed outlier: 3.500A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 518 removed outlier: 3.924A pdb=" N LEU B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR B 515 " --> pdb=" O ASN B 511 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG B 517 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLY B 518 " --> pdb=" O TYR B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 559 Processing helix chain 'B' and resid 593 through 605 removed outlier: 3.931A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ILE B 605 " --> pdb=" O PHE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 649 removed outlier: 3.519A pdb=" N TYR B 634 " --> pdb=" O VAL B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 673 removed outlier: 3.540A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 197 through 199 No H-bonds generated for 'chain 'C' and resid 197 through 199' Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 370 through 373 No H-bonds generated for 'chain 'C' and resid 370 through 373' Processing helix chain 'C' and resid 376 through 412 removed outlier: 3.820A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 458 Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 471 through 491 removed outlier: 3.501A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 518 removed outlier: 3.924A pdb=" N LEU C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU C 513 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYR C 515 " --> pdb=" O ASN C 511 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR C 516 " --> pdb=" O LEU C 512 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG C 517 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLY C 518 " --> pdb=" O TYR C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 559 Processing helix chain 'C' and resid 593 through 605 removed outlier: 3.931A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 605 " --> pdb=" O PHE C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 649 removed outlier: 3.520A pdb=" N TYR C 634 " --> pdb=" O VAL C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 658 through 673 removed outlier: 3.540A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 197 through 199 No H-bonds generated for 'chain 'D' and resid 197 through 199' Processing helix chain 'D' and resid 213 through 219 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 281 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 298 through 305 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 370 through 373 No H-bonds generated for 'chain 'D' and resid 370 through 373' Processing helix chain 'D' and resid 376 through 412 removed outlier: 3.820A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 458 Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.501A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 518 removed outlier: 3.924A pdb=" N LEU D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL D 506 " --> pdb=" O VAL D 502 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLY D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 513 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N TYR D 515 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR D 516 " --> pdb=" O LEU D 512 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG D 517 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLY D 518 " --> pdb=" O TYR D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 559 Processing helix chain 'D' and resid 593 through 605 removed outlier: 3.931A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE D 605 " --> pdb=" O PHE D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 649 removed outlier: 3.520A pdb=" N TYR D 634 " --> pdb=" O VAL D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 658 through 673 removed outlier: 3.540A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 329 through 331 Processing sheet with id= B, first strand: chain 'B' and resid 329 through 331 Processing sheet with id= C, first strand: chain 'C' and resid 329 through 331 Processing sheet with id= D, first strand: chain 'D' and resid 329 through 331 904 hydrogen bonds defined for protein. 2700 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: 4.98 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2740 1.30 - 1.43: 5297 1.43 - 1.56: 10735 1.56 - 1.68: 32 1.68 - 1.81: 128 Bond restraints: 18932 Sorted by residual: bond pdb=" C05 P0T C 802 " pdb=" C06 P0T C 802 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C05 P0T B 802 " pdb=" C06 P0T B 802 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C05 P0T A 802 " pdb=" C06 P0T A 802 " ideal model delta sigma weight residual 1.521 1.657 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C05 P0T D 802 " pdb=" C06 P0T D 802 " ideal model delta sigma weight residual 1.521 1.656 -0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C05 P0T B 801 " pdb=" C06 P0T B 801 " ideal model delta sigma weight residual 1.521 1.653 -0.132 2.00e-02 2.50e+03 4.36e+01 ... (remaining 18927 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.30: 440 106.30 - 113.53: 10491 113.53 - 120.77: 9076 120.77 - 128.01: 5587 128.01 - 135.24: 214 Bond angle restraints: 25808 Sorted by residual: angle pdb=" C ASN B 232 " pdb=" N PRO B 233 " pdb=" CA PRO B 233 " ideal model delta sigma weight residual 118.85 113.36 5.49 1.09e+00 8.42e-01 2.53e+01 angle pdb=" C ASN C 232 " pdb=" N PRO C 233 " pdb=" CA PRO C 233 " ideal model delta sigma weight residual 118.85 113.38 5.47 1.09e+00 8.42e-01 2.51e+01 angle pdb=" C ASN A 232 " pdb=" N PRO A 233 " pdb=" CA PRO A 233 " ideal model delta sigma weight residual 118.85 113.39 5.46 1.09e+00 8.42e-01 2.51e+01 angle pdb=" C ASN D 232 " pdb=" N PRO D 233 " pdb=" CA PRO D 233 " ideal model delta sigma weight residual 118.85 113.43 5.42 1.09e+00 8.42e-01 2.47e+01 angle pdb=" N LEU B 537 " pdb=" CA LEU B 537 " pdb=" C LEU B 537 " ideal model delta sigma weight residual 112.90 107.05 5.85 1.31e+00 5.83e-01 1.99e+01 ... (remaining 25803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 10597 33.68 - 67.36: 211 67.36 - 101.04: 28 101.04 - 134.71: 0 134.71 - 168.39: 12 Dihedral angle restraints: 10848 sinusoidal: 3876 harmonic: 6972 Sorted by residual: dihedral pdb=" C17 XJ7 D 803 " pdb=" C18 XJ7 D 803 " pdb=" C19 XJ7 D 803 " pdb=" C20 XJ7 D 803 " ideal model delta sinusoidal sigma weight residual 177.64 -13.97 -168.39 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C17 XJ7 A 803 " pdb=" C18 XJ7 A 803 " pdb=" C19 XJ7 A 803 " pdb=" C20 XJ7 A 803 " ideal model delta sinusoidal sigma weight residual 177.64 -13.99 -168.37 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C17 XJ7 C 803 " pdb=" C18 XJ7 C 803 " pdb=" C19 XJ7 C 803 " pdb=" C20 XJ7 C 803 " ideal model delta sinusoidal sigma weight residual 177.64 -14.01 -168.35 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 10845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.014: 3024 1.014 - 2.028: 0 2.028 - 3.042: 0 3.042 - 4.056: 0 4.056 - 5.069: 4 Chirality restraints: 3028 Sorted by residual: chirality pdb=" C3 XJ7 B 803 " pdb=" C2 XJ7 B 803 " pdb=" C24 XJ7 B 803 " pdb=" O3 XJ7 B 803 " both_signs ideal model delta sigma weight residual False -2.50 2.57 -5.07 2.00e-01 2.50e+01 6.42e+02 chirality pdb=" C3 XJ7 A 803 " pdb=" C2 XJ7 A 803 " pdb=" C24 XJ7 A 803 " pdb=" O3 XJ7 A 803 " both_signs ideal model delta sigma weight residual False -2.50 2.57 -5.07 2.00e-01 2.50e+01 6.42e+02 chirality pdb=" C3 XJ7 D 803 " pdb=" C2 XJ7 D 803 " pdb=" C24 XJ7 D 803 " pdb=" O3 XJ7 D 803 " both_signs ideal model delta sigma weight residual False -2.50 2.57 -5.07 2.00e-01 2.50e+01 6.42e+02 ... (remaining 3025 not shown) Planarity restraints: 3132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 162 " 0.015 2.00e-02 2.50e+03 1.19e-02 2.85e+00 pdb=" CG TYR D 162 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR D 162 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 162 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 162 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 162 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 162 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR D 162 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 162 " -0.015 2.00e-02 2.50e+03 1.19e-02 2.82e+00 pdb=" CG TYR B 162 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 162 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 162 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 162 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 162 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 162 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 162 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 162 " -0.015 2.00e-02 2.50e+03 1.18e-02 2.79e+00 pdb=" CG TYR A 162 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 162 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 162 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 162 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 162 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 162 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 162 " 0.003 2.00e-02 2.50e+03 ... (remaining 3129 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3243 2.77 - 3.30: 17380 3.30 - 3.84: 29176 3.84 - 4.37: 31000 4.37 - 4.90: 57185 Nonbonded interactions: 137984 Sorted by model distance: nonbonded pdb=" O GLN C 520 " pdb=" OH TYR C 525 " model vdw 2.239 2.440 nonbonded pdb=" O GLN A 520 " pdb=" OH TYR A 525 " model vdw 2.240 2.440 nonbonded pdb=" O GLN D 520 " pdb=" OH TYR D 525 " model vdw 2.240 2.440 nonbonded pdb=" O GLN B 520 " pdb=" OH TYR B 525 " model vdw 2.240 2.440 nonbonded pdb=" O ALA D 257 " pdb=" NZ LYS D 307 " model vdw 2.341 2.520 ... (remaining 137979 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 75 through 728 or resid 801 through 803)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.070 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: 7.630 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 44.630 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.110 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.006 0.136 18932 Z= 0.405 Angle : 0.720 10.244 25808 Z= 0.384 Chirality : 0.191 5.069 3028 Planarity : 0.003 0.034 3132 Dihedral : 15.430 168.393 6336 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.00 % 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: 2.02 (0.17), residues: 2344 helix: 2.70 (0.14), residues: 1392 sheet: 1.32 (0.45), residues: 88 loop : -1.05 (0.19), residues: 864 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.168 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2448 time to fit residues: 97.3103 Evaluate side-chains 132 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.7980 chunk 178 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 95 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 112 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 214 optimal weight: 9.9990 overall best weight: 3.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 18932 Z= 0.279 Angle : 0.575 7.994 25808 Z= 0.275 Chirality : 0.039 0.227 3028 Planarity : 0.003 0.039 3132 Dihedral : 9.099 113.145 2664 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer Outliers : 1.94 % 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: 2.11 (0.17), residues: 2344 helix: 2.72 (0.14), residues: 1392 sheet: 1.83 (0.51), residues: 88 loop : -0.97 (0.19), residues: 864 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 2.259 Fit side-chains outliers start: 34 outliers final: 31 residues processed: 152 average time/residue: 0.2334 time to fit residues: 62.0325 Evaluate side-chains 150 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 119 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1600 time to fit residues: 12.4794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 30.0000 chunk 66 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 214 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 191 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 18932 Z= 0.340 Angle : 0.571 11.009 25808 Z= 0.284 Chirality : 0.039 0.165 3028 Planarity : 0.003 0.042 3132 Dihedral : 8.015 102.791 2664 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 0.63 % 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: 1.72 (0.17), residues: 2344 helix: 2.39 (0.13), residues: 1388 sheet: 1.45 (0.50), residues: 88 loop : -1.04 (0.19), residues: 868 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 2.350 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 137 average time/residue: 0.2372 time to fit residues: 56.0340 Evaluate side-chains 123 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 2.240 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1694 time to fit residues: 5.7288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.2980 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 18932 Z= 0.195 Angle : 0.475 9.770 25808 Z= 0.235 Chirality : 0.036 0.151 3028 Planarity : 0.003 0.042 3132 Dihedral : 6.852 87.248 2664 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.74 % 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: 1.94 (0.17), residues: 2344 helix: 2.66 (0.14), residues: 1380 sheet: 1.52 (0.49), residues: 88 loop : -1.09 (0.19), residues: 876 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 2.119 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 140 average time/residue: 0.2470 time to fit residues: 58.9541 Evaluate side-chains 129 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 2.055 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1654 time to fit residues: 5.2619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 165 HIS B 316 GLN C 165 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 18932 Z= 0.280 Angle : 0.525 11.202 25808 Z= 0.260 Chirality : 0.038 0.157 3028 Planarity : 0.003 0.043 3132 Dihedral : 7.014 93.700 2664 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.80 % 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: 1.86 (0.17), residues: 2344 helix: 2.49 (0.14), residues: 1388 sheet: 1.00 (0.44), residues: 120 loop : -0.99 (0.20), residues: 836 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 2.181 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 134 average time/residue: 0.2460 time to fit residues: 56.3290 Evaluate side-chains 125 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 2.120 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1669 time to fit residues: 5.0698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 4.9990 chunk 205 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 189 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 119 optimal weight: 0.0670 overall best weight: 1.5522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 655 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 18932 Z= 0.152 Angle : 0.443 8.642 25808 Z= 0.219 Chirality : 0.035 0.158 3028 Planarity : 0.003 0.041 3132 Dihedral : 6.149 75.906 2664 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.18), residues: 2344 helix: 2.79 (0.14), residues: 1384 sheet: 1.61 (0.48), residues: 88 loop : -1.10 (0.19), residues: 872 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 2.131 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 144 average time/residue: 0.2437 time to fit residues: 60.8930 Evaluate side-chains 133 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1761 time to fit residues: 4.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 129 optimal weight: 0.7980 chunk 192 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 18932 Z= 0.218 Angle : 0.481 9.398 25808 Z= 0.237 Chirality : 0.036 0.178 3028 Planarity : 0.003 0.042 3132 Dihedral : 6.298 75.369 2664 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 1.03 % 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: 1.95 (0.17), residues: 2344 helix: 2.69 (0.14), residues: 1384 sheet: 1.52 (0.47), residues: 88 loop : -1.15 (0.19), residues: 872 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 2.274 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 134 average time/residue: 0.2387 time to fit residues: 55.6229 Evaluate side-chains 135 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1656 time to fit residues: 7.4244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.0570 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 154 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 178 optimal weight: 20.0000 chunk 206 optimal weight: 2.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 18932 Z= 0.190 Angle : 0.463 9.188 25808 Z= 0.228 Chirality : 0.036 0.165 3028 Planarity : 0.003 0.042 3132 Dihedral : 6.128 69.274 2664 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.57 % 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: 2.00 (0.17), residues: 2344 helix: 2.73 (0.14), residues: 1384 sheet: 1.58 (0.47), residues: 88 loop : -1.15 (0.19), residues: 872 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 131 time to evaluate : 2.358 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 138 average time/residue: 0.2490 time to fit residues: 59.9692 Evaluate side-chains 132 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 2.123 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1542 time to fit residues: 4.4456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.3980 chunk 198 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 127 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 191 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 139 optimal weight: 0.0170 chunk 224 optimal weight: 3.9990 overall best weight: 0.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 18932 Z= 0.104 Angle : 0.406 8.333 25808 Z= 0.198 Chirality : 0.034 0.152 3028 Planarity : 0.002 0.041 3132 Dihedral : 5.044 57.724 2664 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.11 % 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: 2.38 (0.18), residues: 2344 helix: 3.05 (0.14), residues: 1380 sheet: 1.91 (0.49), residues: 88 loop : -1.02 (0.19), residues: 876 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 2.193 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 155 average time/residue: 0.2452 time to fit residues: 65.6229 Evaluate side-chains 133 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 2.249 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1671 time to fit residues: 3.7250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 216 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 148 optimal weight: 0.5980 chunk 199 optimal weight: 0.0980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 18932 Z= 0.159 Angle : 0.442 8.034 25808 Z= 0.215 Chirality : 0.035 0.179 3028 Planarity : 0.003 0.040 3132 Dihedral : 5.315 56.840 2664 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 0.29 % 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 (0.18), residues: 2344 helix: 2.99 (0.14), residues: 1384 sheet: 1.91 (0.50), residues: 88 loop : -1.08 (0.19), residues: 872 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4688 Ramachandran restraints generated. 2344 Oldfield, 0 Emsley, 2344 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 2.163 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 137 average time/residue: 0.2381 time to fit residues: 57.0707 Evaluate side-chains 133 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 130 time to evaluate : 2.149 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1673 time to fit residues: 3.9996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 192 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.093567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.076130 restraints weight = 43043.075| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.25 r_work: 0.2898 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 18932 Z= 0.112 Angle : 0.408 7.739 25808 Z= 0.199 Chirality : 0.034 0.164 3028 Planarity : 0.002 0.041 3132 Dihedral : 4.876 49.660 2664 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.17 % 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 (0.18), residues: 2344 helix: 3.07 (0.14), residues: 1384 sheet: 2.05 (0.51), residues: 88 loop : -1.06 (0.19), residues: 872 =============================================================================== Job complete usr+sys time: 3066.57 seconds wall clock time: 56 minutes 58.96 seconds (3418.96 seconds total)