Starting phenix.real_space_refine (version: dev) on Wed Apr 6 00:33:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/04_2022/6gyn_0093_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/04_2022/6gyn_0093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/04_2022/6gyn_0093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/04_2022/6gyn_0093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/04_2022/6gyn_0093_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/04_2022/6gyn_0093_updated.pdb" } resolution = 3.4 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= 0.011 sd= 0.132 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 674": "NH1" <-> "NH2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C ARG 375": "NH1" <-> "NH2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "C ARG 587": "NH1" <-> "NH2" Residue "C ARG 668": "NH1" <-> "NH2" Residue "C ARG 674": "NH1" <-> "NH2" Residue "C ARG 700": "NH1" <-> "NH2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D ARG 375": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D ARG 524": "NH1" <-> "NH2" Residue "D ARG 525": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "D ARG 587": "NH1" <-> "NH2" Residue "D ARG 668": "NH1" <-> "NH2" Residue "D ARG 674": "NH1" <-> "NH2" Residue "D ARG 700": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 16932 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 16, 'CIS': 1, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'PC1': 7, '3PE': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'PC1': 7, '3PE': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'PC1': 7, '3PE': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'PC1': 7, '3PE': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 9.65, per 1000 atoms: 0.57 Number of scatterers: 16932 At special positions: 0 Unit cell: (132.66, 132.66, 120.6, 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 132 16.00 P 16 15.00 O 2952 8.00 N 2684 7.00 C 11148 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: 6.84 Conformation dependent library (CDL) restraints added in 2.4 seconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 8 sheets defined 63.6% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 215 through 221 removed outlier: 3.976A pdb=" N GLY A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 260 through 285 removed outlier: 4.032A pdb=" N GLY A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 293 through 314 removed outlier: 3.889A pdb=" N PHE A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 340 removed outlier: 3.892A pdb=" N LYS A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 372 through 409 removed outlier: 3.940A pdb=" N LEU A 385 " --> pdb=" O LYS A 381 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ARG A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU A 391 " --> pdb=" O ARG A 387 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER A 392 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 442 removed outlier: 3.695A pdb=" N PHE A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 450 through 453 No H-bonds generated for 'chain 'A' and resid 450 through 453' Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'A' and resid 489 through 519 removed outlier: 3.699A pdb=" N TRP A 493 " --> pdb=" O MET A 489 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 540 Processing helix chain 'A' and resid 545 through 558 Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 575 through 590 removed outlier: 5.579A pdb=" N LYS A 588 " --> pdb=" O PHE A 584 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 610 removed outlier: 4.203A pdb=" N THR A 609 " --> pdb=" O THR A 605 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 665 Processing helix chain 'A' and resid 686 through 695 removed outlier: 4.019A pdb=" N GLU A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.976A pdb=" N GLY B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 260 through 285 removed outlier: 4.032A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Proline residue: B 281 - end of helix Processing helix chain 'B' and resid 293 through 314 removed outlier: 3.890A pdb=" N PHE B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 340 removed outlier: 3.893A pdb=" N LYS B 339 " --> pdb=" O MET B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 349 Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 372 through 409 removed outlier: 3.940A pdb=" N LEU B 385 " --> pdb=" O LYS B 381 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU B 386 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG B 393 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 442 removed outlier: 3.695A pdb=" N PHE B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) Proline residue: B 440 - end of helix Processing helix chain 'B' and resid 450 through 453 No H-bonds generated for 'chain 'B' and resid 450 through 453' Processing helix chain 'B' and resid 461 through 476 Processing helix chain 'B' and resid 489 through 519 removed outlier: 3.700A pdb=" N TRP B 493 " --> pdb=" O MET B 489 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 540 Processing helix chain 'B' and resid 545 through 558 Processing helix chain 'B' and resid 566 through 572 Processing helix chain 'B' and resid 575 through 590 removed outlier: 5.579A pdb=" N LYS B 588 " --> pdb=" O PHE B 584 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU B 589 " --> pdb=" O ASN B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 610 removed outlier: 4.204A pdb=" N THR B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 686 through 695 removed outlier: 4.020A pdb=" N GLU B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 707 Processing helix chain 'C' and resid 215 through 221 removed outlier: 3.976A pdb=" N GLY C 219 " --> pdb=" O GLN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 260 through 285 removed outlier: 4.031A pdb=" N GLY C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Proline residue: C 281 - end of helix Processing helix chain 'C' and resid 293 through 314 removed outlier: 3.889A pdb=" N PHE C 314 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 340 removed outlier: 3.892A pdb=" N LYS C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 349 Processing helix chain 'C' and resid 352 through 363 Processing helix chain 'C' and resid 372 through 409 removed outlier: 3.940A pdb=" N LEU C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU C 386 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG C 387 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG C 390 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 442 removed outlier: 3.695A pdb=" N PHE C 437 " --> pdb=" O GLY C 433 " (cutoff:3.500A) Proline residue: C 440 - end of helix Processing helix chain 'C' and resid 450 through 453 No H-bonds generated for 'chain 'C' and resid 450 through 453' Processing helix chain 'C' and resid 461 through 476 Processing helix chain 'C' and resid 489 through 519 removed outlier: 3.700A pdb=" N TRP C 493 " --> pdb=" O MET C 489 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 519 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 540 Processing helix chain 'C' and resid 545 through 558 Processing helix chain 'C' and resid 566 through 572 Processing helix chain 'C' and resid 575 through 590 removed outlier: 5.580A pdb=" N LYS C 588 " --> pdb=" O PHE C 584 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU C 589 " --> pdb=" O ASN C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 610 removed outlier: 4.204A pdb=" N THR C 609 " --> pdb=" O THR C 605 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS C 610 " --> pdb=" O SER C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 665 Processing helix chain 'C' and resid 686 through 695 removed outlier: 4.019A pdb=" N GLU C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 707 Processing helix chain 'D' and resid 215 through 221 removed outlier: 3.976A pdb=" N GLY D 219 " --> pdb=" O GLN D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 260 through 285 removed outlier: 4.031A pdb=" N GLY D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Proline residue: D 281 - end of helix Processing helix chain 'D' and resid 293 through 314 removed outlier: 3.889A pdb=" N PHE D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 340 removed outlier: 3.892A pdb=" N LYS D 339 " --> pdb=" O MET D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 349 Processing helix chain 'D' and resid 352 through 363 Processing helix chain 'D' and resid 372 through 409 removed outlier: 3.940A pdb=" N LEU D 385 " --> pdb=" O LYS D 381 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU D 386 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG D 387 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU D 388 " --> pdb=" O SER D 384 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU D 389 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG D 390 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 442 removed outlier: 3.694A pdb=" N PHE D 437 " --> pdb=" O GLY D 433 " (cutoff:3.500A) Proline residue: D 440 - end of helix Processing helix chain 'D' and resid 450 through 453 No H-bonds generated for 'chain 'D' and resid 450 through 453' Processing helix chain 'D' and resid 461 through 476 Processing helix chain 'D' and resid 489 through 519 removed outlier: 3.700A pdb=" N TRP D 493 " --> pdb=" O MET D 489 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER D 519 " --> pdb=" O ALA D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 540 Processing helix chain 'D' and resid 545 through 558 Processing helix chain 'D' and resid 566 through 572 Processing helix chain 'D' and resid 575 through 590 removed outlier: 5.579A pdb=" N LYS D 588 " --> pdb=" O PHE D 584 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU D 589 " --> pdb=" O ASN D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 610 removed outlier: 4.204A pdb=" N THR D 609 " --> pdb=" O THR D 605 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 665 Processing helix chain 'D' and resid 686 through 695 removed outlier: 4.019A pdb=" N GLU D 695 " --> pdb=" O GLU D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 697 through 707 Processing sheet with id= A, first strand: chain 'A' and resid 612 through 616 removed outlier: 6.231A pdb=" N TYR A 682 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE A 635 " --> pdb=" O TYR A 682 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 684 " --> pdb=" O TYR A 633 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR A 633 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 648 through 652 removed outlier: 3.609A pdb=" N LYS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 612 through 616 removed outlier: 6.230A pdb=" N TYR B 682 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE B 635 " --> pdb=" O TYR B 682 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU B 684 " --> pdb=" O TYR B 633 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR B 633 " --> pdb=" O LEU B 684 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 648 through 652 removed outlier: 3.608A pdb=" N LYS B 648 " --> pdb=" O THR B 644 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 612 through 616 removed outlier: 6.231A pdb=" N TYR C 682 " --> pdb=" O ILE C 635 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ILE C 635 " --> pdb=" O TYR C 682 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU C 684 " --> pdb=" O TYR C 633 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR C 633 " --> pdb=" O LEU C 684 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 648 through 652 removed outlier: 3.609A pdb=" N LYS C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 612 through 616 removed outlier: 6.231A pdb=" N TYR D 682 " --> pdb=" O ILE D 635 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ILE D 635 " --> pdb=" O TYR D 682 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU D 684 " --> pdb=" O TYR D 633 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR D 633 " --> pdb=" O LEU D 684 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 648 through 652 removed outlier: 3.608A pdb=" N LYS D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2592 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: 4.71 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2552 1.32 - 1.44: 4691 1.44 - 1.56: 9773 1.56 - 1.68: 32 1.68 - 1.80: 232 Bond restraints: 17280 Sorted by residual: bond pdb=" O13 3PE B 806 " pdb=" P 3PE B 806 " ideal model delta sigma weight residual 1.654 1.592 0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" O13 3PE D 808 " pdb=" P 3PE D 808 " ideal model delta sigma weight residual 1.654 1.593 0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" O13 3PE C 806 " pdb=" P 3PE C 806 " ideal model delta sigma weight residual 1.654 1.593 0.061 2.00e-02 2.50e+03 9.33e+00 bond pdb=" O13 3PE A 804 " pdb=" P 3PE A 804 " ideal model delta sigma weight residual 1.654 1.594 0.060 2.00e-02 2.50e+03 9.11e+00 bond pdb=" O13 PC1 B 803 " pdb=" P PC1 B 803 " ideal model delta sigma weight residual 1.652 1.593 0.059 2.00e-02 2.50e+03 8.66e+00 ... (remaining 17275 not shown) Histogram of bond angle deviations from ideal: 97.53 - 104.82: 296 104.82 - 112.11: 8044 112.11 - 119.41: 6354 119.41 - 126.70: 8226 126.70 - 133.99: 232 Bond angle restraints: 23152 Sorted by residual: angle pdb=" C ARG C 390 " pdb=" N LEU C 391 " pdb=" CA LEU C 391 " ideal model delta sigma weight residual 120.28 123.91 -3.63 1.44e+00 4.82e-01 6.34e+00 angle pdb=" C ARG D 390 " pdb=" N LEU D 391 " pdb=" CA LEU D 391 " ideal model delta sigma weight residual 120.28 123.91 -3.63 1.44e+00 4.82e-01 6.34e+00 angle pdb=" C ARG B 390 " pdb=" N LEU B 391 " pdb=" CA LEU B 391 " ideal model delta sigma weight residual 120.28 123.89 -3.61 1.44e+00 4.82e-01 6.27e+00 angle pdb=" C ARG A 390 " pdb=" N LEU A 391 " pdb=" CA LEU A 391 " ideal model delta sigma weight residual 120.28 123.87 -3.59 1.44e+00 4.82e-01 6.21e+00 angle pdb=" CA TRP A 401 " pdb=" CB TRP A 401 " pdb=" CG TRP A 401 " ideal model delta sigma weight residual 113.60 108.93 4.67 1.90e+00 2.77e-01 6.03e+00 ... (remaining 23147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.05: 9366 11.05 - 22.10: 770 22.10 - 33.16: 128 33.16 - 44.21: 52 44.21 - 55.26: 28 Dihedral angle restraints: 10344 sinusoidal: 4516 harmonic: 5828 Sorted by residual: dihedral pdb=" CA GLY A 480 " pdb=" C GLY A 480 " pdb=" N TYR A 481 " pdb=" CA TYR A 481 " ideal model delta harmonic sigma weight residual 0.00 -21.88 21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA GLY B 480 " pdb=" C GLY B 480 " pdb=" N TYR B 481 " pdb=" CA TYR B 481 " ideal model delta harmonic sigma weight residual 0.00 -21.82 21.82 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA GLY D 480 " pdb=" C GLY D 480 " pdb=" N TYR D 481 " pdb=" CA TYR D 481 " ideal model delta harmonic sigma weight residual 0.00 -21.80 21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 10341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2010 0.065 - 0.130: 458 0.130 - 0.195: 20 0.195 - 0.259: 0 0.259 - 0.324: 4 Chirality restraints: 2492 Sorted by residual: chirality pdb=" C2 PC1 C 801 " pdb=" C1 PC1 C 801 " pdb=" C3 PC1 C 801 " pdb=" O21 PC1 C 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C2 PC1 B 801 " pdb=" C1 PC1 B 801 " pdb=" C3 PC1 B 801 " pdb=" O21 PC1 B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" C2 PC1 A 808 " pdb=" C1 PC1 A 808 " pdb=" C3 PC1 A 808 " pdb=" O21 PC1 A 808 " both_signs ideal model delta sigma weight residual False -2.49 -2.17 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 2489 not shown) Planarity restraints: 2820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 439 " -0.035 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO B 440 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 440 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 440 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 439 " 0.035 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO C 440 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 440 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 440 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 439 " 0.035 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO D 440 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO D 440 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 440 " 0.029 5.00e-02 4.00e+02 ... (remaining 2817 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4396 2.80 - 3.32: 15093 3.32 - 3.85: 27238 3.85 - 4.37: 32209 4.37 - 4.90: 55882 Nonbonded interactions: 134818 Sorted by model distance: nonbonded pdb=" OG SER C 641 " pdb=" OD2 ASP C 676 " model vdw 2.273 2.440 nonbonded pdb=" OG SER D 641 " pdb=" OD2 ASP D 676 " model vdw 2.273 2.440 nonbonded pdb=" OG SER B 641 " pdb=" OD2 ASP B 676 " model vdw 2.273 2.440 nonbonded pdb=" OG SER A 641 " pdb=" OD2 ASP A 676 " model vdw 2.274 2.440 nonbonded pdb=" NH1 ARG C 378 " pdb=" O LEU C 442 " model vdw 2.344 2.520 ... (remaining 134813 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 214 through 708 or (resid 801 and (name C23 or name C24 or \ name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ O31 or name O32)) or (resid 803 and (name C22 or name C23 or name C24 or name C \ 25 or name C26)))) selection = (chain 'B' and (resid 214 through 708 or (resid 801 and (name C23 or name C24 or \ name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ O31 or name O32)) or (resid 803 and (name C22 or name C23 or name C24 or name C \ 25 or name C26)))) selection = (chain 'C' and (resid 214 through 708 or (resid 801 and (name C23 or name C24 or \ name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ O31 or name O32)) or (resid 803 and (name C22 or name C23 or name C24 or name C \ 25 or name C26)))) selection = (chain 'D' and (resid 214 through 708 or (resid 801 and (name C23 or name C24 or \ name C25 or name C26 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ O31 or name O32)) or (resid 803 and (name C22 or name C23 or name C24 or name C \ 25 or name C26)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 132 5.16 5 C 11148 2.51 5 N 2684 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.530 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: 3.900 Check model and map are aligned: 0.240 Convert atoms to be neutral: 0.140 Process input model: 42.980 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.008 0.062 17280 Z= 0.517 Angle : 0.848 7.511 23152 Z= 0.452 Chirality : 0.052 0.324 2492 Planarity : 0.006 0.052 2820 Dihedral : 9.321 55.262 6584 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -2.56 (0.15), residues: 1972 helix: -1.78 (0.11), residues: 1312 sheet: 0.54 (0.48), residues: 116 loop : -1.46 (0.24), residues: 544 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2908 time to fit residues: 131.6300 Evaluate side-chains 151 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.241 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 459 ASN A 602 ASN A 637 HIS B 406 HIS B 602 ASN B 637 HIS C 406 HIS C 602 ASN C 637 HIS D 406 HIS D 602 ASN D 637 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 17280 Z= 0.291 Angle : 0.574 9.873 23152 Z= 0.289 Chirality : 0.042 0.133 2492 Planarity : 0.004 0.035 2820 Dihedral : 8.338 56.409 2784 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 1.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.03 (0.18), residues: 1972 helix: 0.41 (0.13), residues: 1292 sheet: 0.69 (0.49), residues: 116 loop : -0.81 (0.25), residues: 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 2.051 Fit side-chains outliers start: 29 outliers final: 21 residues processed: 208 average time/residue: 0.2566 time to fit residues: 85.1972 Evaluate side-chains 180 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1489 time to fit residues: 8.8082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 0.1980 chunk 192 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 331 GLN A 475 HIS B 223 GLN B 331 GLN B 475 HIS C 223 GLN C 331 GLN C 475 HIS D 223 GLN D 331 GLN D 475 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 17280 Z= 0.353 Angle : 0.594 9.580 23152 Z= 0.298 Chirality : 0.043 0.137 2492 Planarity : 0.003 0.031 2820 Dihedral : 9.102 59.667 2784 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 1.00 (0.19), residues: 1972 helix: 1.19 (0.14), residues: 1296 sheet: 0.63 (0.49), residues: 116 loop : -0.41 (0.27), residues: 560 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.983 Fit side-chains outliers start: 27 outliers final: 16 residues processed: 196 average time/residue: 0.2411 time to fit residues: 76.7133 Evaluate side-chains 178 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 2.100 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1620 time to fit residues: 7.5691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 92 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN D 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.018 17280 Z= 0.129 Angle : 0.484 9.465 23152 Z= 0.234 Chirality : 0.039 0.128 2492 Planarity : 0.003 0.033 2820 Dihedral : 8.376 58.878 2784 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.19), residues: 1972 helix: 1.68 (0.15), residues: 1296 sheet: 0.70 (0.50), residues: 116 loop : -0.32 (0.27), residues: 560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 2.072 Fit side-chains outliers start: 14 outliers final: 2 residues processed: 203 average time/residue: 0.2589 time to fit residues: 83.0768 Evaluate side-chains 174 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 172 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1855 time to fit residues: 3.3867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 130 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 170 optimal weight: 0.0370 chunk 47 optimal weight: 7.9990 overall best weight: 2.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN B 475 HIS C 223 GLN D 223 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 17280 Z= 0.245 Angle : 0.530 9.853 23152 Z= 0.259 Chirality : 0.041 0.131 2492 Planarity : 0.003 0.031 2820 Dihedral : 8.504 58.114 2784 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 1.65 (0.19), residues: 1972 helix: 1.78 (0.14), residues: 1316 sheet: 0.51 (0.49), residues: 116 loop : -0.40 (0.27), residues: 540 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 2.039 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 178 average time/residue: 0.2405 time to fit residues: 70.2097 Evaluate side-chains 172 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 157 time to evaluate : 2.065 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1650 time to fit residues: 7.3000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 399 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 17280 Z= 0.382 Angle : 0.607 9.446 23152 Z= 0.300 Chirality : 0.044 0.134 2492 Planarity : 0.003 0.028 2820 Dihedral : 9.219 58.562 2784 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 1972 helix: 1.73 (0.14), residues: 1312 sheet: 0.28 (0.48), residues: 116 loop : -0.35 (0.27), residues: 544 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 2.060 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 160 average time/residue: 0.2390 time to fit residues: 63.4560 Evaluate side-chains 155 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 2.016 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1630 time to fit residues: 4.8438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 105 optimal weight: 0.0670 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN C 475 HIS D 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 17280 Z= 0.121 Angle : 0.494 9.949 23152 Z= 0.235 Chirality : 0.038 0.126 2492 Planarity : 0.003 0.032 2820 Dihedral : 8.382 58.931 2784 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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 (0.19), residues: 1972 helix: 2.04 (0.14), residues: 1312 sheet: 0.32 (0.48), residues: 116 loop : -0.15 (0.28), residues: 544 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 2.100 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 174 average time/residue: 0.2359 time to fit residues: 67.8889 Evaluate side-chains 165 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1445 time to fit residues: 2.9959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 475 HIS C 223 GLN C 475 HIS D 475 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 17280 Z= 0.174 Angle : 0.509 10.818 23152 Z= 0.247 Chirality : 0.040 0.128 2492 Planarity : 0.003 0.031 2820 Dihedral : 8.431 59.951 2784 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 2.05 (0.19), residues: 1972 helix: 2.06 (0.14), residues: 1316 sheet: 0.34 (0.48), residues: 116 loop : -0.10 (0.28), residues: 540 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 2.190 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 167 average time/residue: 0.2505 time to fit residues: 68.8167 Evaluate side-chains 152 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 146 time to evaluate : 2.133 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1691 time to fit residues: 4.6893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 3.9990 chunk 180 optimal weight: 0.4980 chunk 165 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 159 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 475 HIS B 475 HIS C 223 GLN D 223 GLN D 475 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 17280 Z= 0.130 Angle : 0.527 12.665 23152 Z= 0.250 Chirality : 0.039 0.139 2492 Planarity : 0.003 0.032 2820 Dihedral : 8.216 56.610 2784 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 2.12 (0.19), residues: 1972 helix: 2.11 (0.14), residues: 1308 sheet: 0.42 (0.47), residues: 116 loop : -0.02 (0.28), residues: 548 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 2.235 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 161 average time/residue: 0.2521 time to fit residues: 67.4082 Evaluate side-chains 154 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1813 time to fit residues: 3.0245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 120 optimal weight: 0.0980 chunk 95 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 223 GLN B 475 HIS D 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 17280 Z= 0.138 Angle : 0.513 12.276 23152 Z= 0.246 Chirality : 0.039 0.127 2492 Planarity : 0.003 0.032 2820 Dihedral : 8.054 59.531 2784 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 2.25 (0.19), residues: 1972 helix: 2.20 (0.14), residues: 1304 sheet: 0.47 (0.47), residues: 116 loop : 0.07 (0.28), residues: 552 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 160 time to evaluate : 2.089 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 160 average time/residue: 0.2485 time to fit residues: 65.9943 Evaluate side-chains 156 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1898 time to fit residues: 3.1940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 65 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS D 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.084768 restraints weight = 30783.829| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.48 r_work: 0.3098 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.28 restraints_weight: 0.2500 r_work: 0.3077 rms_B_bonded: 2.30 restraints_weight: 0.1250 r_work: 0.3066 rms_B_bonded: 2.35 restraints_weight: 0.0625 r_work: 0.3054 rms_B_bonded: 2.42 restraints_weight: 0.0312 r_work: 0.3042 rms_B_bonded: 2.52 restraints_weight: 0.0156 r_work: 0.3030 rms_B_bonded: 2.64 restraints_weight: 0.0078 r_work: 0.3017 rms_B_bonded: 2.78 restraints_weight: 0.0039 r_work: 0.3004 rms_B_bonded: 2.93 restraints_weight: 0.0020 r_work: 0.2991 rms_B_bonded: 3.11 restraints_weight: 0.0010 r_work: 0.2976 rms_B_bonded: 3.32 restraints_weight: 0.0005 r_work: 0.2962 rms_B_bonded: 3.54 restraints_weight: 0.0002 r_work: 0.2946 rms_B_bonded: 3.79 restraints_weight: 0.0001 r_work: 0.2930 rms_B_bonded: 4.06 restraints_weight: 0.0001 r_work: 0.2912 rms_B_bonded: 4.37 restraints_weight: 0.0000 r_work: 0.2894 rms_B_bonded: 4.70 restraints_weight: 0.0000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 17280 Z= 0.140 Angle : 0.500 9.694 23152 Z= 0.242 Chirality : 0.039 0.129 2492 Planarity : 0.003 0.032 2820 Dihedral : 8.065 59.567 2784 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 2.33 (0.19), residues: 1972 helix: 2.24 (0.14), residues: 1312 sheet: 0.51 (0.48), residues: 116 loop : 0.10 (0.29), residues: 544 =============================================================================== Job complete usr+sys time: 2747.41 seconds wall clock time: 51 minutes 33.00 seconds (3093.00 seconds total)