Starting phenix.real_space_refine on Mon Mar 11 16:46:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxa_24726/03_2024/7rxa_24726_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxa_24726/03_2024/7rxa_24726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxa_24726/03_2024/7rxa_24726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxa_24726/03_2024/7rxa_24726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxa_24726/03_2024/7rxa_24726_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rxa_24726/03_2024/7rxa_24726_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 30 5.16 5 C 5770 2.51 5 N 1418 2.21 5 O 1468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 425": "NH1" <-> "NH2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 425": "NH1" <-> "NH2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8694 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4221 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 23, 'TRANS': 554} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 548 Unresolved non-hydrogen angles: 675 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 366 Chain: "B" Number of atoms: 4221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4221 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 143} Link IDs: {'PTRANS': 23, 'TRANS': 554} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 548 Unresolved non-hydrogen angles: 675 Unresolved non-hydrogen dihedrals: 441 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 17, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 35, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 366 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {'PGW': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.42, per 1000 atoms: 0.62 Number of scatterers: 8694 At special positions: 0 Unit cell: (71.02, 119.78, 96.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 8 15.00 O 1468 8.00 N 1418 7.00 C 5770 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: 3.57 Conformation dependent library (CDL) restraints added in 1.9 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 2 sheets defined 64.5% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.534A pdb=" N GLU A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 145 through 148 No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 152 through 155 No H-bonds generated for 'chain 'A' and resid 152 through 155' Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.658A pdb=" N ARG A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 200 removed outlier: 3.807A pdb=" N MET A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Proline residue: A 194 - end of helix removed outlier: 4.008A pdb=" N PHE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 237 removed outlier: 3.743A pdb=" N ILE A 224 " --> pdb=" O CYS A 220 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 310 removed outlier: 3.807A pdb=" N TYR A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 3.785A pdb=" N ILE A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 349 removed outlier: 3.683A pdb=" N ILE A 323 " --> pdb=" O LEU A 320 " (cutoff:3.500A) Proline residue: A 324 - end of helix removed outlier: 3.815A pdb=" N ILE A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) Proline residue: A 333 - end of helix removed outlier: 4.300A pdb=" N SER A 336 " --> pdb=" O PRO A 333 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 337 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 339 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 374 removed outlier: 4.283A pdb=" N VAL A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.866A pdb=" N THR A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 Proline residue: A 394 - end of helix Processing helix chain 'A' and resid 423 through 441 removed outlier: 3.551A pdb=" N THR A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 436 " --> pdb=" O TYR A 432 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA A 437 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLN A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 Processing helix chain 'A' and resid 508 through 524 removed outlier: 4.056A pdb=" N ARG A 513 " --> pdb=" O THR A 509 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A 515 " --> pdb=" O ALA A 511 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 519 " --> pdb=" O MET A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 553 removed outlier: 3.513A pdb=" N ASN A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG A 545 " --> pdb=" O TRP A 541 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER A 546 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE A 549 " --> pdb=" O ARG A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 591 removed outlier: 3.534A pdb=" N GLY A 574 " --> pdb=" O LEU A 570 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 582 " --> pdb=" O TRP A 578 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 634 removed outlier: 3.587A pdb=" N LEU A 611 " --> pdb=" O CYS A 607 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 658 removed outlier: 3.920A pdb=" N GLU A 643 " --> pdb=" O ASN A 639 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR A 654 " --> pdb=" O MET A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 713 through 723 Processing helix chain 'B' and resid 32 through 45 removed outlier: 3.534A pdb=" N GLU B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 86 Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 145 through 148 No H-bonds generated for 'chain 'B' and resid 145 through 148' Processing helix chain 'B' and resid 152 through 155 No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.658A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 200 removed outlier: 3.806A pdb=" N MET B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Proline residue: B 194 - end of helix removed outlier: 4.008A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 237 removed outlier: 3.743A pdb=" N ILE B 224 " --> pdb=" O CYS B 220 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 310 removed outlier: 3.807A pdb=" N TYR B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN B 283 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Proline residue: B 285 - end of helix removed outlier: 3.785A pdb=" N ILE B 297 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 349 removed outlier: 3.683A pdb=" N ILE B 323 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Proline residue: B 324 - end of helix removed outlier: 3.814A pdb=" N ILE B 332 " --> pdb=" O SER B 329 " (cutoff:3.500A) Proline residue: B 333 - end of helix removed outlier: 4.301A pdb=" N SER B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA B 337 " --> pdb=" O THR B 334 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 339 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 374 removed outlier: 4.283A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.866A pdb=" N THR B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 396 Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 423 through 441 removed outlier: 3.551A pdb=" N THR B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA B 437 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLN B 438 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 Processing helix chain 'B' and resid 508 through 524 removed outlier: 4.057A pdb=" N ARG B 513 " --> pdb=" O THR B 509 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 514 " --> pdb=" O ASP B 510 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 515 " --> pdb=" O ALA B 511 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS B 516 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE B 519 " --> pdb=" O MET B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 553 removed outlier: 3.514A pdb=" N ASN B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER B 546 " --> pdb=" O VAL B 542 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 591 removed outlier: 3.534A pdb=" N GLY B 574 " --> pdb=" O LEU B 570 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER B 585 " --> pdb=" O SER B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 634 removed outlier: 3.587A pdb=" N LEU B 611 " --> pdb=" O CYS B 607 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 615 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 617 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS B 634 " --> pdb=" O SER B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.921A pdb=" N GLU B 643 " --> pdb=" O ASN B 639 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR B 654 " --> pdb=" O MET B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 707 No H-bonds generated for 'chain 'B' and resid 705 through 707' Processing helix chain 'B' and resid 713 through 723 Processing sheet with id= A, first strand: chain 'A' and resid 139 through 141 removed outlier: 5.520A pdb=" N PHE A 61 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLN A 54 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N PHE A 63 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL A 52 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ARG A 65 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N THR A 50 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 139 through 141 removed outlier: 5.520A pdb=" N PHE B 61 " --> pdb=" O GLN B 54 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N GLN B 54 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N PHE B 63 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N VAL B 52 " --> pdb=" O PHE B 63 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ARG B 65 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N THR B 50 " --> pdb=" O ARG B 65 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1308 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: 2.46 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1268 1.31 - 1.43: 2622 1.43 - 1.56: 4958 1.56 - 1.69: 16 1.69 - 1.81: 40 Bond restraints: 8904 Sorted by residual: bond pdb=" C1 PGW A 801 " pdb=" O01 PGW A 801 " ideal model delta sigma weight residual 1.332 1.422 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C1 PGW B 904 " pdb=" O01 PGW B 904 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C1 PGW A 804 " pdb=" O01 PGW A 804 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 PGW B 903 " pdb=" O01 PGW B 903 " ideal model delta sigma weight residual 1.332 1.420 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 PGW B 901 " pdb=" O01 PGW B 901 " ideal model delta sigma weight residual 1.332 1.419 -0.087 2.00e-02 2.50e+03 1.91e+01 ... (remaining 8899 not shown) Histogram of bond angle deviations from ideal: 100.52 - 107.24: 259 107.24 - 113.96: 5041 113.96 - 120.68: 3881 120.68 - 127.39: 2869 127.39 - 134.11: 106 Bond angle restraints: 12156 Sorted by residual: angle pdb=" N GLU A 154 " pdb=" CA GLU A 154 " pdb=" C GLU A 154 " ideal model delta sigma weight residual 114.64 107.25 7.39 1.52e+00 4.33e-01 2.37e+01 angle pdb=" N GLU B 154 " pdb=" CA GLU B 154 " pdb=" C GLU B 154 " ideal model delta sigma weight residual 114.64 107.26 7.38 1.52e+00 4.33e-01 2.36e+01 angle pdb=" C LYS B 158 " pdb=" N THR B 159 " pdb=" CA THR B 159 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C LYS A 158 " pdb=" N THR A 159 " pdb=" CA THR A 159 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N ILE B 605 " pdb=" CA ILE B 605 " pdb=" C ILE B 605 " ideal model delta sigma weight residual 113.71 109.85 3.86 9.50e-01 1.11e+00 1.65e+01 ... (remaining 12151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 4868 25.61 - 51.23: 220 51.23 - 76.84: 36 76.84 - 102.45: 12 102.45 - 128.07: 6 Dihedral angle restraints: 5142 sinusoidal: 1738 harmonic: 3404 Sorted by residual: dihedral pdb=" C15 PGW B 904 " pdb=" C16 PGW B 904 " pdb=" C17 PGW B 904 " pdb=" C18 PGW B 904 " ideal model delta sinusoidal sigma weight residual 178.71 -53.22 -128.07 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" C15 PGW A 801 " pdb=" C16 PGW A 801 " pdb=" C17 PGW A 801 " pdb=" C18 PGW A 801 " ideal model delta sinusoidal sigma weight residual 178.71 -53.23 -128.06 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" O01 PGW B 903 " pdb=" C01 PGW B 903 " pdb=" C02 PGW B 903 " pdb=" O03 PGW B 903 " ideal model delta sinusoidal sigma weight residual 59.30 -52.04 111.34 1 3.00e+01 1.11e-03 1.45e+01 ... (remaining 5139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 861 0.036 - 0.071: 381 0.071 - 0.106: 134 0.106 - 0.142: 48 0.142 - 0.177: 12 Chirality restraints: 1436 Sorted by residual: chirality pdb=" C02 PGW A 802 " pdb=" C01 PGW A 802 " pdb=" C03 PGW A 802 " pdb=" O01 PGW A 802 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" C02 PGW B 901 " pdb=" C01 PGW B 901 " pdb=" C03 PGW B 901 " pdb=" O01 PGW B 901 " both_signs ideal model delta sigma weight residual False 2.36 2.53 -0.18 2.00e-01 2.50e+01 7.77e-01 chirality pdb=" CA PRO A 128 " pdb=" N PRO A 128 " pdb=" C PRO A 128 " pdb=" CB PRO A 128 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 1433 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 376 " -0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 377 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 377 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 377 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 376 " 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO A 377 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 422 " -0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO B 423 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 423 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 423 " -0.040 5.00e-02 4.00e+02 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 3248 2.89 - 3.39: 7977 3.39 - 3.89: 14263 3.89 - 4.40: 15888 4.40 - 4.90: 27755 Nonbonded interactions: 69131 Sorted by model distance: nonbonded pdb=" O GLY A 580 " pdb=" OG SER A 584 " model vdw 2.381 2.440 nonbonded pdb=" O GLY B 580 " pdb=" OG SER B 584 " model vdw 2.381 2.440 nonbonded pdb=" NE1 TRP B 155 " pdb=" OD1 ASP B 165 " model vdw 2.420 2.520 nonbonded pdb=" NE1 TRP A 155 " pdb=" OD1 ASP A 165 " model vdw 2.420 2.520 nonbonded pdb=" O SER A 374 " pdb=" OH TYR A 521 " model vdw 2.444 2.440 ... (remaining 69126 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 11 through 724 or (resid 801 and (name C01 or name C02 or \ name C03 or name C06 or name C1 or name C10 or name C15 or name C19 or name C2 o \ r name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C \ 26 or name C27 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 \ or name C9 or name O01 or name O02 or name O03 or name O04 or name O11 or name \ O12 or name O13 or name O14 or name P )) or (resid 802 through 803 and (name C01 \ or name C02 or name C03 or name C19 or name C20 or name C21 or name C22 or name \ C23 or name C24 or name C25 or name O01 or name O03 or name O04 or name O11 or \ name O12 or name O13 or name O14 or name P )) or resid 804)) selection = (chain 'B' and (resid 11 through 724 or resid 901 or (resid 902 through 903 and \ (name C01 or name C02 or name C03 or name C19 or name C20 or name C21 or name C2 \ 2 or name C23 or name C24 or name C25 or name O01 or name O03 or name O04 or nam \ e O11 or name O12 or name O13 or name O14 or name P )) or (resid 904 and (name C \ 01 or name C02 or name C03 or name C06 or name C07 or name C1 or name C10 or nam \ e C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or na \ me C9 or name O01 or name O02 or name O03 or name O04 or name O11 or name O12 or \ name O13 or name O14 or name P )))) } 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: 1.110 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: 0.010 Extract box with map and model: 4.130 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.670 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 0.090 8904 Z= 0.410 Angle : 1.113 10.913 12156 Z= 0.544 Chirality : 0.048 0.177 1436 Planarity : 0.007 0.079 1484 Dihedral : 17.168 128.068 2922 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % 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: -4.42 (0.18), residues: 1124 helix: -2.49 (0.13), residues: 780 sheet: -1.78 (0.57), residues: 44 loop : -3.79 (0.26), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 227 HIS 0.006 0.001 HIS A 619 PHE 0.016 0.002 PHE A 61 TYR 0.016 0.001 TYR B 589 ARG 0.004 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.036 Fit side-chains REVERT: A 14 HIS cc_start: 0.8219 (m-70) cc_final: 0.7971 (m90) REVERT: A 355 GLN cc_start: 0.8075 (mm110) cc_final: 0.7838 (mm-40) REVERT: A 428 LYS cc_start: 0.8167 (mttm) cc_final: 0.7966 (mttp) REVERT: A 626 TYR cc_start: 0.8399 (t80) cc_final: 0.8186 (t80) REVERT: B 428 LYS cc_start: 0.8172 (mttm) cc_final: 0.7935 (mttp) REVERT: B 551 ILE cc_start: 0.9078 (tt) cc_final: 0.8717 (tt) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2350 time to fit residues: 36.2660 Evaluate side-chains 82 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 280 GLN A 518 GLN B 185 GLN B 518 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8904 Z= 0.220 Angle : 0.527 6.053 12156 Z= 0.281 Chirality : 0.039 0.150 1436 Planarity : 0.005 0.062 1484 Dihedral : 15.152 126.798 1436 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.22 % Allowed : 10.41 % Favored : 88.38 % 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: -2.15 (0.23), residues: 1124 helix: -0.65 (0.17), residues: 792 sheet: -1.06 (0.58), residues: 44 loop : -3.46 (0.29), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 227 HIS 0.006 0.001 HIS B 619 PHE 0.017 0.001 PHE A 61 TYR 0.016 0.001 TYR A 589 ARG 0.002 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 1.039 Fit side-chains REVERT: A 350 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8255 (mt-10) REVERT: A 355 GLN cc_start: 0.8070 (mm110) cc_final: 0.7857 (mm-40) REVERT: A 551 ILE cc_start: 0.8931 (tt) cc_final: 0.8615 (tt) REVERT: B 84 TRP cc_start: 0.7347 (t60) cc_final: 0.7117 (t60) REVERT: B 350 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8274 (mt-10) REVERT: B 551 ILE cc_start: 0.9080 (tt) cc_final: 0.8682 (tt) REVERT: B 626 TYR cc_start: 0.8481 (t80) cc_final: 0.8241 (t80) outliers start: 9 outliers final: 7 residues processed: 102 average time/residue: 0.1824 time to fit residues: 27.3896 Evaluate side-chains 97 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 658 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 0.0470 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8904 Z= 0.259 Angle : 0.523 6.203 12156 Z= 0.276 Chirality : 0.040 0.151 1436 Planarity : 0.005 0.056 1484 Dihedral : 13.984 127.712 1436 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.89 % Allowed : 12.30 % Favored : 85.81 % 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: -1.11 (0.24), residues: 1124 helix: 0.13 (0.19), residues: 796 sheet: -0.48 (0.62), residues: 44 loop : -3.18 (0.31), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 227 HIS 0.007 0.001 HIS B 619 PHE 0.019 0.001 PHE B 61 TYR 0.017 0.001 TYR A 589 ARG 0.002 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 1.096 Fit side-chains REVERT: A 84 TRP cc_start: 0.7446 (t60) cc_final: 0.7178 (t60) REVERT: A 355 GLN cc_start: 0.8064 (mm110) cc_final: 0.7845 (mm-40) REVERT: A 551 ILE cc_start: 0.9015 (tt) cc_final: 0.8653 (tt) REVERT: A 626 TYR cc_start: 0.8449 (t80) cc_final: 0.8174 (t80) REVERT: B 84 TRP cc_start: 0.7363 (t60) cc_final: 0.7137 (t60) REVERT: B 531 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8676 (mp) outliers start: 14 outliers final: 9 residues processed: 106 average time/residue: 0.1655 time to fit residues: 26.6493 Evaluate side-chains 99 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 110 optimal weight: 0.0570 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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: 0.8137 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8904 Z= 0.186 Angle : 0.483 5.973 12156 Z= 0.254 Chirality : 0.038 0.140 1436 Planarity : 0.004 0.047 1484 Dihedral : 13.109 114.953 1436 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.22 % Allowed : 13.78 % Favored : 85.00 % 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: -0.45 (0.25), residues: 1124 helix: 0.66 (0.19), residues: 792 sheet: -0.01 (0.67), residues: 44 loop : -3.05 (0.31), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 227 HIS 0.005 0.001 HIS A 619 PHE 0.016 0.001 PHE A 61 TYR 0.013 0.001 TYR B 589 ARG 0.001 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 1.290 Fit side-chains REVERT: A 84 TRP cc_start: 0.7356 (t60) cc_final: 0.7104 (t60) REVERT: A 531 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8708 (mp) REVERT: A 551 ILE cc_start: 0.9026 (tt) cc_final: 0.8687 (tt) REVERT: B 84 TRP cc_start: 0.7338 (t60) cc_final: 0.7079 (t60) REVERT: B 551 ILE cc_start: 0.8973 (tt) cc_final: 0.8630 (tt) outliers start: 9 outliers final: 8 residues processed: 100 average time/residue: 0.1843 time to fit residues: 27.4952 Evaluate side-chains 100 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8904 Z= 0.204 Angle : 0.488 6.036 12156 Z= 0.257 Chirality : 0.039 0.143 1436 Planarity : 0.004 0.043 1484 Dihedral : 12.645 104.600 1436 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.16 % Allowed : 14.86 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1124 helix: 0.95 (0.19), residues: 782 sheet: 0.27 (0.69), residues: 44 loop : -2.79 (0.32), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 227 HIS 0.006 0.001 HIS B 619 PHE 0.016 0.001 PHE A 61 TYR 0.013 0.001 TYR A 589 ARG 0.001 0.000 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 95 time to evaluate : 0.981 Fit side-chains REVERT: A 84 TRP cc_start: 0.7357 (t60) cc_final: 0.7108 (t60) REVERT: A 531 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8716 (mp) REVERT: A 551 ILE cc_start: 0.9029 (tt) cc_final: 0.8684 (tt) REVERT: B 84 TRP cc_start: 0.7342 (t60) cc_final: 0.7099 (t60) REVERT: B 531 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8691 (mp) REVERT: B 551 ILE cc_start: 0.9010 (tt) cc_final: 0.8694 (tt) outliers start: 16 outliers final: 12 residues processed: 105 average time/residue: 0.1653 time to fit residues: 26.2645 Evaluate side-chains 107 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 57 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8118 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8904 Z= 0.147 Angle : 0.465 5.846 12156 Z= 0.244 Chirality : 0.038 0.137 1436 Planarity : 0.004 0.040 1484 Dihedral : 11.826 82.570 1436 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.03 % Allowed : 15.00 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1124 helix: 1.21 (0.20), residues: 780 sheet: 0.35 (0.69), residues: 44 loop : -2.77 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.004 0.001 HIS B 619 PHE 0.020 0.001 PHE A 307 TYR 0.012 0.001 TYR B 589 ARG 0.001 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.040 Fit side-chains REVERT: A 84 TRP cc_start: 0.7403 (t60) cc_final: 0.7056 (t60) REVERT: A 531 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 551 ILE cc_start: 0.9039 (tt) cc_final: 0.8681 (tt) REVERT: B 84 TRP cc_start: 0.7337 (t60) cc_final: 0.7048 (t60) REVERT: B 531 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8672 (mp) REVERT: B 551 ILE cc_start: 0.8998 (tt) cc_final: 0.8699 (tt) outliers start: 15 outliers final: 10 residues processed: 109 average time/residue: 0.1831 time to fit residues: 30.5489 Evaluate side-chains 108 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 585 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.8980 chunk 12 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 0.0050 overall best weight: 0.8196 ------------------------------------------------------------------------------- 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: 0.8126 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8904 Z= 0.171 Angle : 0.479 5.914 12156 Z= 0.251 Chirality : 0.038 0.145 1436 Planarity : 0.004 0.039 1484 Dihedral : 11.159 78.077 1436 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.89 % Allowed : 15.00 % Favored : 83.11 % 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: 0.41 (0.26), residues: 1124 helix: 1.30 (0.20), residues: 788 sheet: 0.40 (0.70), residues: 44 loop : -2.68 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 227 HIS 0.006 0.001 HIS B 619 PHE 0.014 0.001 PHE B 61 TYR 0.012 0.001 TYR A 589 ARG 0.001 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.017 Fit side-chains REVERT: A 84 TRP cc_start: 0.7391 (t60) cc_final: 0.7003 (t60) REVERT: A 531 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 551 ILE cc_start: 0.9035 (tt) cc_final: 0.8671 (tt) REVERT: B 84 TRP cc_start: 0.7387 (t60) cc_final: 0.6995 (t60) REVERT: B 531 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8695 (mp) REVERT: B 551 ILE cc_start: 0.9019 (tt) cc_final: 0.8708 (tt) outliers start: 14 outliers final: 9 residues processed: 103 average time/residue: 0.1661 time to fit residues: 25.9180 Evaluate side-chains 105 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.2980 chunk 65 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.0370 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.5660 ------------------------------------------------------------------------------- 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: 0.8106 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8904 Z= 0.135 Angle : 0.463 5.824 12156 Z= 0.243 Chirality : 0.038 0.139 1436 Planarity : 0.004 0.037 1484 Dihedral : 10.729 76.032 1436 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.62 % Allowed : 15.14 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1124 helix: 1.40 (0.20), residues: 788 sheet: 0.63 (0.73), residues: 44 loop : -2.97 (0.31), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.004 0.001 HIS A 619 PHE 0.012 0.001 PHE A 61 TYR 0.012 0.001 TYR B 589 ARG 0.001 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.021 Fit side-chains REVERT: A 84 TRP cc_start: 0.7403 (t60) cc_final: 0.7018 (t60) REVERT: A 531 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 551 ILE cc_start: 0.9031 (tt) cc_final: 0.8668 (tt) REVERT: B 84 TRP cc_start: 0.7350 (t60) cc_final: 0.6983 (t60) REVERT: B 531 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8682 (mp) REVERT: B 551 ILE cc_start: 0.9011 (tt) cc_final: 0.8695 (tt) outliers start: 12 outliers final: 10 residues processed: 106 average time/residue: 0.1658 time to fit residues: 26.3439 Evaluate side-chains 109 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 31 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.8112 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8904 Z= 0.156 Angle : 0.471 5.865 12156 Z= 0.246 Chirality : 0.038 0.142 1436 Planarity : 0.004 0.037 1484 Dihedral : 10.563 75.010 1436 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.62 % Allowed : 15.14 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1124 helix: 1.47 (0.20), residues: 788 sheet: 0.77 (0.76), residues: 44 loop : -2.96 (0.31), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 227 HIS 0.005 0.001 HIS A 619 PHE 0.013 0.001 PHE A 61 TYR 0.012 0.001 TYR B 589 ARG 0.001 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.006 Fit side-chains REVERT: A 84 TRP cc_start: 0.7434 (t60) cc_final: 0.7060 (t60) REVERT: A 531 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8721 (mp) REVERT: A 551 ILE cc_start: 0.9034 (tt) cc_final: 0.8670 (tt) REVERT: B 84 TRP cc_start: 0.7362 (t60) cc_final: 0.6992 (t60) REVERT: B 531 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8711 (mp) REVERT: B 551 ILE cc_start: 0.9014 (tt) cc_final: 0.8696 (tt) outliers start: 12 outliers final: 10 residues processed: 104 average time/residue: 0.1698 time to fit residues: 26.4264 Evaluate side-chains 106 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8143 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8904 Z= 0.248 Angle : 0.512 6.070 12156 Z= 0.268 Chirality : 0.040 0.147 1436 Planarity : 0.004 0.037 1484 Dihedral : 10.838 75.140 1436 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.62 % Allowed : 15.27 % Favored : 83.11 % 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: 0.54 (0.26), residues: 1124 helix: 1.39 (0.19), residues: 786 sheet: 0.70 (0.76), residues: 44 loop : -2.63 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 227 HIS 0.007 0.001 HIS A 619 PHE 0.017 0.001 PHE A 61 TYR 0.013 0.001 TYR A 589 ARG 0.001 0.000 ARG A 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.924 Fit side-chains REVERT: A 84 TRP cc_start: 0.7487 (t60) cc_final: 0.7091 (t60) REVERT: A 531 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 551 ILE cc_start: 0.9047 (tt) cc_final: 0.8682 (tt) REVERT: B 84 TRP cc_start: 0.7453 (t60) cc_final: 0.7051 (t60) REVERT: B 531 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8769 (mp) REVERT: B 551 ILE cc_start: 0.9038 (tt) cc_final: 0.8681 (tt) outliers start: 12 outliers final: 10 residues processed: 96 average time/residue: 0.1687 time to fit residues: 24.1954 Evaluate side-chains 98 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 585 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.125696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.097347 restraints weight = 10988.018| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.77 r_work: 0.2914 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8904 Z= 0.156 Angle : 0.473 5.875 12156 Z= 0.249 Chirality : 0.038 0.141 1436 Planarity : 0.004 0.037 1484 Dihedral : 10.568 73.657 1436 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.62 % Allowed : 15.27 % Favored : 83.11 % 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: 0.70 (0.26), residues: 1124 helix: 1.54 (0.20), residues: 784 sheet: 0.80 (0.76), residues: 44 loop : -2.63 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 227 HIS 0.004 0.001 HIS B 619 PHE 0.013 0.001 PHE B 61 TYR 0.012 0.001 TYR A 589 ARG 0.001 0.000 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1821.77 seconds wall clock time: 33 minutes 48.26 seconds (2028.26 seconds total)