Starting phenix.real_space_refine on Mon Dec 11 06:16:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/12_2023/6gyn_0093_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/12_2023/6gyn_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_0093/12_2023/6gyn_0093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/12_2023/6gyn_0093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/12_2023/6gyn_0093_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/12_2023/6gyn_0093_updated.pdb" } resolution = 3.4 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= 0.011 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 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. 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-1.21rc1-5172/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: {'CIS': 1, 'PTRANS': 16, '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: {'CIS': 1, 'PTRANS': 16, '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: {'CIS': 1, 'PTRANS': 16, '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: {'CIS': 1, 'PTRANS': 16, '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: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 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: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 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: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 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: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 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: 9.31, per 1000 atoms: 0.55 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: 7.09 Conformation dependent library (CDL) restraints added in 3.0 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: 3.14 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: 4.72 Time building geometry restraints manager: 7.56 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 GLY D 480 " pdb=" N TYR D 481 " pdb=" CA TYR D 481 " ideal model delta sigma weight residual 121.70 129.07 -7.37 1.80e+00 3.09e-01 1.68e+01 angle pdb=" C GLY C 480 " pdb=" N TYR C 481 " pdb=" CA TYR C 481 " ideal model delta sigma weight residual 121.70 129.05 -7.35 1.80e+00 3.09e-01 1.67e+01 angle pdb=" C GLY A 480 " pdb=" N TYR A 481 " pdb=" CA TYR A 481 " ideal model delta sigma weight residual 121.70 129.04 -7.34 1.80e+00 3.09e-01 1.66e+01 angle pdb=" C GLY B 480 " pdb=" N TYR B 481 " pdb=" CA TYR B 481 " ideal model delta sigma weight residual 121.70 129.01 -7.31 1.80e+00 3.09e-01 1.65e+01 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 ... (remaining 23147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 9870 14.30 - 28.61: 458 28.61 - 42.91: 116 42.91 - 57.21: 60 57.21 - 71.51: 16 Dihedral angle restraints: 10520 sinusoidal: 4692 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 10517 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 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: 0.010 Normalize map: mean=0, sd=1: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.390 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 45.720 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.849 7.511 23152 Z= 0.454 Chirality : 0.052 0.324 2492 Planarity : 0.006 0.052 2820 Dihedral : 10.497 71.515 6760 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 % Allowed : 0.47 % Favored : 99.53 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 401 HIS 0.010 0.002 HIS D 475 PHE 0.024 0.002 PHE B 379 TYR 0.032 0.003 TYR C 633 ARG 0.009 0.001 ARG B 396 *********************** 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 : 1.958 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: 0.3021 time to fit residues: 135.6724 Evaluate side-chains 151 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5995 ------------------------------------------------------------------------------- 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: 0.8129 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17280 Z= 0.291 Angle : 0.562 6.697 23152 Z= 0.288 Chirality : 0.042 0.120 2492 Planarity : 0.004 0.034 2820 Dihedral : 10.480 71.927 2960 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.63 % Allowed : 8.31 % Favored : 90.06 % 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: 0.01 (0.18), residues: 1972 helix: 0.40 (0.13), residues: 1292 sheet: 0.67 (0.49), residues: 116 loop : -0.81 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 401 HIS 0.005 0.001 HIS C 475 PHE 0.012 0.001 PHE C 689 TYR 0.017 0.002 TYR B 633 ARG 0.002 0.000 ARG A 372 *********************** 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 213 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.985 Fit side-chains outliers start: 28 outliers final: 23 residues processed: 204 average time/residue: 0.2666 time to fit residues: 85.5366 Evaluate side-chains 181 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.892 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1496 time to fit residues: 9.1124 ------------------------------------------------------------------------------- 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: 2.9990 chunk 148 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 0.0670 chunk 192 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 overall best weight: 3.4126 ------------------------------------------------------------------------------- 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 B 223 GLN B 331 GLN B 399 HIS C 223 GLN C 331 GLN D 223 GLN D 331 GLN D 399 HIS D 459 ASN D 475 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17280 Z= 0.392 Angle : 0.616 6.119 23152 Z= 0.314 Chirality : 0.044 0.124 2492 Planarity : 0.004 0.031 2820 Dihedral : 11.029 70.925 2960 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.86 % Allowed : 8.02 % Favored : 90.12 % 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: 0.85 (0.19), residues: 1972 helix: 1.05 (0.14), residues: 1316 sheet: 0.56 (0.49), residues: 116 loop : -0.47 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 401 HIS 0.004 0.001 HIS B 256 PHE 0.012 0.002 PHE B 584 TYR 0.025 0.002 TYR D 633 ARG 0.004 0.001 ARG C 548 *********************** 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 209 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 1.884 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 195 average time/residue: 0.2547 time to fit residues: 80.8428 Evaluate side-chains 180 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 164 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1547 time to fit residues: 7.2224 ------------------------------------------------------------------------------- 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: 0.8980 chunk 134 optimal weight: 6.9990 chunk 92 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 189 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17280 Z= 0.131 Angle : 0.480 8.873 23152 Z= 0.238 Chirality : 0.039 0.117 2492 Planarity : 0.003 0.032 2820 Dihedral : 10.256 66.103 2960 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.81 % Allowed : 9.07 % Favored : 90.12 % 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: 1.50 (0.19), residues: 1972 helix: 1.62 (0.15), residues: 1312 sheet: 0.66 (0.50), residues: 116 loop : -0.39 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 401 HIS 0.002 0.000 HIS D 475 PHE 0.006 0.001 PHE A 703 TYR 0.014 0.001 TYR B 531 ARG 0.001 0.000 ARG C 548 *********************** 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 : 2.079 Fit side-chains outliers start: 14 outliers final: 5 residues processed: 197 average time/residue: 0.2556 time to fit residues: 80.3238 Evaluate side-chains 167 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 2.028 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1772 time to fit residues: 4.1741 ------------------------------------------------------------------------------- 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: 6.9990 chunk 107 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN C 223 GLN D 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17280 Z= 0.288 Angle : 0.551 10.713 23152 Z= 0.272 Chirality : 0.042 0.132 2492 Planarity : 0.003 0.030 2820 Dihedral : 10.531 63.473 2960 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.10 % Allowed : 9.77 % Favored : 89.13 % 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: 1316 sheet: 0.43 (0.49), residues: 116 loop : -0.40 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 401 HIS 0.003 0.001 HIS C 475 PHE 0.015 0.001 PHE C 634 TYR 0.016 0.001 TYR C 531 ARG 0.003 0.000 ARG B 680 *********************** 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 183 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 164 time to evaluate : 2.038 Fit side-chains outliers start: 19 outliers final: 14 residues processed: 175 average time/residue: 0.2534 time to fit residues: 72.7786 Evaluate side-chains 171 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 157 time to evaluate : 1.913 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1691 time to fit residues: 6.8332 ------------------------------------------------------------------------------- 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: 0.9990 chunk 46 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.8151 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 17280 Z= 0.236 Angle : 0.511 9.759 23152 Z= 0.255 Chirality : 0.041 0.120 2492 Planarity : 0.003 0.031 2820 Dihedral : 10.187 57.861 2960 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.76 % Allowed : 9.19 % Favored : 90.06 % 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: 1.78 (0.19), residues: 1972 helix: 1.88 (0.14), residues: 1312 sheet: 0.29 (0.48), residues: 116 loop : -0.27 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.002 0.001 HIS C 430 PHE 0.006 0.001 PHE D 634 TYR 0.015 0.001 TYR D 531 ARG 0.003 0.000 ARG D 680 *********************** 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 171 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 2.097 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 163 average time/residue: 0.2465 time to fit residues: 67.0215 Evaluate side-chains 156 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 2.012 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1618 time to fit residues: 3.5518 ------------------------------------------------------------------------------- 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: 3.9990 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 105 optimal weight: 0.0040 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 17280 Z= 0.162 Angle : 0.483 9.771 23152 Z= 0.238 Chirality : 0.039 0.120 2492 Planarity : 0.003 0.031 2820 Dihedral : 9.766 57.345 2960 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.47 % Allowed : 9.19 % Favored : 90.35 % 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: 1.96 (0.19), residues: 1972 helix: 2.00 (0.14), residues: 1316 sheet: 0.31 (0.48), residues: 116 loop : -0.16 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.002 0.001 HIS A 406 PHE 0.005 0.001 PHE A 379 TYR 0.014 0.001 TYR C 531 ARG 0.002 0.000 ARG C 680 *********************** 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 170 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 2.007 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 164 average time/residue: 0.2254 time to fit residues: 61.6279 Evaluate side-chains 157 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 154 time to evaluate : 1.825 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1454 time to fit residues: 3.2697 ------------------------------------------------------------------------------- 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: 0.9980 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 120 optimal weight: 0.0980 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17280 Z= 0.127 Angle : 0.478 10.507 23152 Z= 0.234 Chirality : 0.039 0.121 2492 Planarity : 0.003 0.032 2820 Dihedral : 9.572 56.432 2960 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.35 % Allowed : 9.53 % Favored : 90.12 % 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: 2.07 (0.19), residues: 1972 helix: 2.06 (0.14), residues: 1316 sheet: 0.34 (0.47), residues: 116 loop : -0.04 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.001 0.000 HIS A 406 PHE 0.004 0.001 PHE B 356 TYR 0.014 0.001 TYR C 531 ARG 0.002 0.000 ARG C 680 *********************** 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 181 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 2.016 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 176 average time/residue: 0.2538 time to fit residues: 73.7521 Evaluate side-chains 168 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1905 time to fit residues: 3.9514 ------------------------------------------------------------------------------- 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: 0.9980 chunk 180 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 105 optimal weight: 0.0470 chunk 76 optimal weight: 0.0870 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN D 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2696 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= 0.121 Angle : 0.511 12.195 23152 Z= 0.245 Chirality : 0.039 0.153 2492 Planarity : 0.003 0.032 2820 Dihedral : 9.390 54.417 2960 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.35 % Allowed : 9.83 % Favored : 89.83 % 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: 2.34 (0.19), residues: 1972 helix: 2.26 (0.14), residues: 1292 sheet: 0.37 (0.47), residues: 116 loop : 0.18 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 401 HIS 0.002 0.000 HIS A 406 PHE 0.005 0.001 PHE B 356 TYR 0.014 0.001 TYR A 531 ARG 0.002 0.000 ARG D 680 *********************** 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 170 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 2.075 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 165 average time/residue: 0.2489 time to fit residues: 67.8631 Evaluate side-chains 161 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 1.987 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2141 time to fit residues: 4.0676 ------------------------------------------------------------------------------- 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: 1.9990 chunk 186 optimal weight: 5.9990 chunk 113 optimal weight: 0.0030 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 120 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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: 0.8094 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17280 Z= 0.133 Angle : 0.506 12.230 23152 Z= 0.243 Chirality : 0.039 0.126 2492 Planarity : 0.003 0.032 2820 Dihedral : 9.424 58.654 2960 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.35 % Allowed : 10.06 % Favored : 89.59 % 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: 2.21 (0.19), residues: 1972 helix: 2.13 (0.14), residues: 1316 sheet: 0.39 (0.47), residues: 116 loop : 0.11 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.002 0.001 HIS D 406 PHE 0.004 0.001 PHE B 356 TYR 0.014 0.001 TYR C 531 ARG 0.002 0.000 ARG D 680 ********************** 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 172 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.882 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 168 average time/residue: 0.2604 time to fit residues: 70.1537 Evaluate side-chains 166 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 163 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1674 time to fit residues: 3.3139 ------------------------------------------------------------------------------- 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: 0.7980 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.108341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083550 restraints weight = 31073.447| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.47 r_work: 0.2956 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 17280 Z= 0.161 Angle : 0.506 12.711 23152 Z= 0.245 Chirality : 0.039 0.125 2492 Planarity : 0.003 0.032 2820 Dihedral : 9.388 59.783 2960 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.17 % Allowed : 10.41 % Favored : 89.42 % 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: 2.16 (0.14), residues: 1316 sheet: 0.36 (0.47), residues: 116 loop : 0.13 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 401 HIS 0.003 0.001 HIS D 399 PHE 0.005 0.001 PHE B 229 TYR 0.014 0.001 TYR B 531 ARG 0.003 0.000 ARG A 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3044.51 seconds wall clock time: 56 minutes 52.87 seconds (3412.87 seconds total)