Starting phenix.real_space_refine on Sun Mar 17 06:24:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/03_2024/6gyn_0093_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/03_2024/6gyn_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_0093/03_2024/6gyn_0093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/03_2024/6gyn_0093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/03_2024/6gyn_0093_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/03_2024/6gyn_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 8.74, per 1000 atoms: 0.52 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: 6.29 Conformation dependent library (CDL) restraints added in 2.7 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: 3.26 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: 4.90 Time building geometry restraints manager: 6.85 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: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 3.250 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 44.650 Find NCS groups from input model: 1.290 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: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.500 ------------------------------------------------------------------------------- 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 : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 MET cc_start: 0.8756 (mmm) cc_final: 0.8070 (mpp) REVERT: A 331 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7481 (mm-40) REVERT: A 335 MET cc_start: 0.7963 (mmm) cc_final: 0.7503 (mmm) REVERT: A 407 MET cc_start: 0.8456 (tpp) cc_final: 0.8184 (tpt) REVERT: A 432 ASP cc_start: 0.8659 (t70) cc_final: 0.8380 (t70) REVERT: B 308 ILE cc_start: 0.8976 (mt) cc_final: 0.8775 (tt) REVERT: B 331 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7456 (mm-40) REVERT: B 335 MET cc_start: 0.8080 (mmm) cc_final: 0.7591 (mmm) REVERT: B 407 MET cc_start: 0.8465 (tpp) cc_final: 0.8168 (tpt) REVERT: B 432 ASP cc_start: 0.8657 (t70) cc_final: 0.8363 (t70) REVERT: B 449 CYS cc_start: 0.8414 (p) cc_final: 0.8126 (p) REVERT: C 308 ILE cc_start: 0.8972 (mt) cc_final: 0.8770 (tt) REVERT: C 331 GLN cc_start: 0.7894 (mm-40) cc_final: 0.7455 (mm-40) REVERT: C 335 MET cc_start: 0.8086 (mmm) cc_final: 0.7599 (mmm) REVERT: C 407 MET cc_start: 0.8464 (tpp) cc_final: 0.8166 (tpt) REVERT: C 432 ASP cc_start: 0.8655 (t70) cc_final: 0.8355 (t70) REVERT: C 449 CYS cc_start: 0.8407 (p) cc_final: 0.8113 (p) REVERT: D 308 ILE cc_start: 0.8974 (mt) cc_final: 0.8771 (tt) REVERT: D 331 GLN cc_start: 0.7892 (mm-40) cc_final: 0.7454 (mm-40) REVERT: D 335 MET cc_start: 0.8087 (mmm) cc_final: 0.7599 (mmm) REVERT: D 407 MET cc_start: 0.8461 (tpp) cc_final: 0.8165 (tpt) REVERT: D 432 ASP cc_start: 0.8652 (t70) cc_final: 0.8355 (t70) REVERT: D 449 CYS cc_start: 0.8400 (p) cc_final: 0.8128 (p) REVERT: D 473 MET cc_start: 0.8524 (ttm) cc_final: 0.8233 (ttm) REVERT: D 593 MET cc_start: 0.8534 (ttt) cc_final: 0.8334 (ttt) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2904 time to fit residues: 130.9968 Evaluate side-chains 162 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.702 ------------------------------------------------------------------------------- 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: 4.9990 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 223 GLN 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1414 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= 0.287 Angle : 0.559 6.952 23152 Z= 0.285 Chirality : 0.042 0.115 2492 Planarity : 0.004 0.035 2820 Dihedral : 10.471 71.638 2960 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.92 % Allowed : 7.15 % Favored : 90.93 % 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: 0.09 (0.18), residues: 1972 helix: 0.45 (0.13), residues: 1292 sheet: 0.69 (0.49), residues: 116 loop : -0.75 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 401 HIS 0.005 0.001 HIS A 475 PHE 0.012 0.001 PHE C 689 TYR 0.016 0.002 TYR A 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 224 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 1.955 Fit side-chains REVERT: A 331 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7618 (mm-40) REVERT: A 335 MET cc_start: 0.8113 (mmm) cc_final: 0.7688 (mmm) REVERT: A 424 MET cc_start: 0.8900 (tpp) cc_final: 0.8080 (tpp) REVERT: B 331 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7611 (mm-40) REVERT: B 335 MET cc_start: 0.8281 (mmm) cc_final: 0.7814 (mmm) REVERT: B 449 CYS cc_start: 0.8502 (p) cc_final: 0.8129 (p) REVERT: C 331 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7602 (mm-40) REVERT: C 335 MET cc_start: 0.8293 (mmm) cc_final: 0.7824 (mmm) REVERT: C 449 CYS cc_start: 0.8505 (p) cc_final: 0.8132 (p) REVERT: D 331 GLN cc_start: 0.7831 (mm-40) cc_final: 0.7602 (mm-40) REVERT: D 335 MET cc_start: 0.8291 (mmm) cc_final: 0.7826 (mmm) REVERT: D 449 CYS cc_start: 0.8506 (p) cc_final: 0.8137 (p) REVERT: D 473 MET cc_start: 0.8451 (ttm) cc_final: 0.8239 (ttm) outliers start: 33 outliers final: 25 residues processed: 215 average time/residue: 0.2490 time to fit residues: 85.0915 Evaluate side-chains 188 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 586 CYS Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 586 CYS Chi-restraints excluded: chain D residue 664 LEU 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: 0.8980 chunk 148 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 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: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN B 223 GLN B 399 HIS C 399 HIS D 223 GLN D 399 HIS D 459 ASN D 475 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1993 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= 0.408 Angle : 0.621 6.088 23152 Z= 0.316 Chirality : 0.044 0.122 2492 Planarity : 0.004 0.031 2820 Dihedral : 11.077 71.546 2960 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.62 % Allowed : 7.97 % 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: 0.87 (0.19), residues: 1972 helix: 1.07 (0.14), residues: 1316 sheet: 0.54 (0.49), residues: 116 loop : -0.46 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 401 HIS 0.004 0.001 HIS D 256 PHE 0.012 0.002 PHE B 584 TYR 0.024 0.002 TYR D 633 ARG 0.004 0.001 ARG B 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 226 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 181 time to evaluate : 1.759 Fit side-chains REVERT: A 331 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7565 (mm-40) REVERT: A 335 MET cc_start: 0.8306 (mmm) cc_final: 0.7757 (mmm) REVERT: A 449 CYS cc_start: 0.8625 (p) cc_final: 0.8295 (p) REVERT: B 331 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7562 (mm-40) REVERT: B 335 MET cc_start: 0.8298 (mmm) cc_final: 0.7749 (mmm) REVERT: B 449 CYS cc_start: 0.8614 (p) cc_final: 0.8285 (p) REVERT: C 304 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9110 (p) REVERT: C 331 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7552 (mm-40) REVERT: C 335 MET cc_start: 0.8307 (mmm) cc_final: 0.7759 (mmm) REVERT: C 449 CYS cc_start: 0.8630 (p) cc_final: 0.8298 (p) REVERT: D 304 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9110 (p) REVERT: D 331 GLN cc_start: 0.7897 (mm-40) cc_final: 0.7551 (mm-40) REVERT: D 335 MET cc_start: 0.8306 (mmm) cc_final: 0.7760 (mmm) REVERT: D 449 CYS cc_start: 0.8629 (p) cc_final: 0.8297 (p) outliers start: 45 outliers final: 31 residues processed: 206 average time/residue: 0.2533 time to fit residues: 84.9870 Evaluate side-chains 198 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 664 LEU 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: 5.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17280 Z= 0.215 Angle : 0.509 8.922 23152 Z= 0.253 Chirality : 0.040 0.117 2492 Planarity : 0.003 0.031 2820 Dihedral : 10.614 68.593 2960 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.85 % Allowed : 8.31 % Favored : 88.84 % 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: 1.46 (0.19), residues: 1972 helix: 1.56 (0.14), residues: 1316 sheet: 0.50 (0.50), residues: 116 loop : -0.27 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 401 HIS 0.003 0.001 HIS B 430 PHE 0.006 0.001 PHE C 342 TYR 0.015 0.001 TYR B 531 ARG 0.002 0.000 ARG A 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 228 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 179 time to evaluate : 2.013 Fit side-chains REVERT: A 214 MET cc_start: 0.6634 (mtt) cc_final: 0.6347 (mtm) REVERT: A 335 MET cc_start: 0.8230 (mmm) cc_final: 0.7810 (mmm) REVERT: A 424 MET cc_start: 0.8754 (tpp) cc_final: 0.8125 (tpp) REVERT: A 449 CYS cc_start: 0.8507 (p) cc_final: 0.8129 (p) REVERT: A 538 MET cc_start: 0.8873 (mtm) cc_final: 0.8389 (mtm) REVERT: B 214 MET cc_start: 0.6627 (mtt) cc_final: 0.6339 (mtm) REVERT: B 331 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7596 (mm-40) REVERT: B 335 MET cc_start: 0.8259 (mmm) cc_final: 0.7838 (mmm) REVERT: B 424 MET cc_start: 0.8778 (tpp) cc_final: 0.8166 (tpp) REVERT: B 449 CYS cc_start: 0.8485 (p) cc_final: 0.8121 (p) REVERT: B 538 MET cc_start: 0.8873 (mtm) cc_final: 0.8384 (mtm) REVERT: C 214 MET cc_start: 0.6630 (mtt) cc_final: 0.6342 (mtm) REVERT: C 331 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7592 (mm-40) REVERT: C 335 MET cc_start: 0.8231 (mmm) cc_final: 0.7812 (mmm) REVERT: C 424 MET cc_start: 0.8787 (tpp) cc_final: 0.8167 (tpp) REVERT: C 449 CYS cc_start: 0.8497 (p) cc_final: 0.8124 (p) REVERT: C 538 MET cc_start: 0.8868 (mtm) cc_final: 0.8575 (mtm) REVERT: D 331 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7586 (mm-40) REVERT: D 335 MET cc_start: 0.8229 (mmm) cc_final: 0.7812 (mmm) REVERT: D 424 MET cc_start: 0.8794 (tpp) cc_final: 0.8175 (tpp) REVERT: D 449 CYS cc_start: 0.8499 (p) cc_final: 0.8133 (p) REVERT: D 538 MET cc_start: 0.8876 (mtm) cc_final: 0.8591 (mtm) outliers start: 49 outliers final: 26 residues processed: 216 average time/residue: 0.2472 time to fit residues: 84.8601 Evaluate side-chains 190 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 130 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN D 459 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17280 Z= 0.256 Angle : 0.519 9.564 23152 Z= 0.259 Chirality : 0.041 0.124 2492 Planarity : 0.003 0.030 2820 Dihedral : 10.509 65.249 2960 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.67 % Allowed : 7.73 % 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: 1.68 (0.19), residues: 1972 helix: 1.77 (0.14), residues: 1312 sheet: 0.29 (0.48), residues: 116 loop : -0.22 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 401 HIS 0.003 0.001 HIS A 475 PHE 0.007 0.001 PHE D 584 TYR 0.016 0.001 TYR B 531 ARG 0.002 0.000 ARG D 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 220 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 174 time to evaluate : 1.747 Fit side-chains REVERT: A 331 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7464 (mm-40) REVERT: A 335 MET cc_start: 0.8246 (mmm) cc_final: 0.7815 (mmm) REVERT: A 449 CYS cc_start: 0.8521 (p) cc_final: 0.8147 (p) REVERT: B 331 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7565 (mm-40) REVERT: B 335 MET cc_start: 0.8227 (mmm) cc_final: 0.7799 (mmm) REVERT: B 424 MET cc_start: 0.8780 (tpp) cc_final: 0.8218 (tpp) REVERT: B 449 CYS cc_start: 0.8543 (p) cc_final: 0.8187 (p) REVERT: C 331 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7329 (mm-40) REVERT: C 335 MET cc_start: 0.8234 (mmm) cc_final: 0.7545 (mmm) REVERT: C 424 MET cc_start: 0.8785 (tpp) cc_final: 0.8214 (tpp) REVERT: C 449 CYS cc_start: 0.8550 (p) cc_final: 0.8187 (p) REVERT: D 331 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7326 (mm-40) REVERT: D 335 MET cc_start: 0.8233 (mmm) cc_final: 0.7543 (mmm) REVERT: D 424 MET cc_start: 0.8788 (tpp) cc_final: 0.8218 (tpp) REVERT: D 449 CYS cc_start: 0.8550 (p) cc_final: 0.8195 (p) outliers start: 46 outliers final: 34 residues processed: 204 average time/residue: 0.2127 time to fit residues: 72.1104 Evaluate side-chains 194 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 160 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 500 ILE Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 586 CYS Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 500 ILE Chi-restraints excluded: chain D residue 580 GLU Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 664 LEU 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: 5.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 189 optimal weight: 0.6980 chunk 157 optimal weight: 0.0980 chunk 87 optimal weight: 0.0770 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN D 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 17280 Z= 0.161 Angle : 0.486 9.574 23152 Z= 0.238 Chirality : 0.039 0.122 2492 Planarity : 0.003 0.031 2820 Dihedral : 10.115 59.938 2960 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.34 % Allowed : 9.42 % Favored : 89.24 % 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: 1.92 (0.19), residues: 1972 helix: 1.95 (0.14), residues: 1316 sheet: 0.32 (0.48), residues: 116 loop : -0.14 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 401 HIS 0.002 0.001 HIS B 430 PHE 0.005 0.001 PHE A 540 TYR 0.014 0.001 TYR D 531 ARG 0.002 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 197 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 1.514 Fit side-chains REVERT: A 331 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7129 (mm-40) REVERT: A 335 MET cc_start: 0.8210 (mmm) cc_final: 0.7594 (mmm) REVERT: A 424 MET cc_start: 0.8694 (tpp) cc_final: 0.8271 (tpp) REVERT: A 449 CYS cc_start: 0.8439 (p) cc_final: 0.8054 (p) REVERT: A 538 MET cc_start: 0.8789 (mtm) cc_final: 0.8581 (mtm) REVERT: A 593 MET cc_start: 0.8518 (ttp) cc_final: 0.7695 (ttp) REVERT: B 331 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7261 (mm-40) REVERT: B 335 MET cc_start: 0.8198 (mmm) cc_final: 0.7589 (mmm) REVERT: B 424 MET cc_start: 0.8733 (tpp) cc_final: 0.8155 (tpp) REVERT: B 449 CYS cc_start: 0.8433 (p) cc_final: 0.7966 (p) REVERT: B 538 MET cc_start: 0.8793 (mtm) cc_final: 0.8546 (mtm) REVERT: B 593 MET cc_start: 0.8375 (ttp) cc_final: 0.6620 (ttp) REVERT: C 331 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7254 (mm-40) REVERT: C 335 MET cc_start: 0.8193 (mmm) cc_final: 0.7587 (mmm) REVERT: C 424 MET cc_start: 0.8741 (tpp) cc_final: 0.8158 (tpp) REVERT: C 449 CYS cc_start: 0.8439 (p) cc_final: 0.7969 (p) REVERT: C 494 LEU cc_start: 0.8888 (mt) cc_final: 0.8583 (mt) REVERT: C 593 MET cc_start: 0.8369 (ttp) cc_final: 0.6623 (ttp) REVERT: D 331 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7253 (mm-40) REVERT: D 335 MET cc_start: 0.8194 (mmm) cc_final: 0.7589 (mmm) REVERT: D 424 MET cc_start: 0.8745 (tpp) cc_final: 0.8156 (tpp) REVERT: D 449 CYS cc_start: 0.8440 (p) cc_final: 0.7982 (p) REVERT: D 593 MET cc_start: 0.8481 (ttp) cc_final: 0.7600 (ttp) outliers start: 23 outliers final: 20 residues processed: 190 average time/residue: 0.2250 time to fit residues: 70.8938 Evaluate side-chains 182 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 276 ASN Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 580 GLU Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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: 0.8121 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 17280 Z= 0.135 Angle : 0.457 7.793 23152 Z= 0.227 Chirality : 0.039 0.116 2492 Planarity : 0.003 0.032 2820 Dihedral : 9.645 58.662 2960 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.51 % Allowed : 8.95 % Favored : 89.53 % 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: 2.15 (0.19), residues: 1972 helix: 2.10 (0.14), residues: 1312 sheet: 0.36 (0.48), residues: 116 loop : 0.08 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 401 HIS 0.002 0.000 HIS A 430 PHE 0.005 0.001 PHE A 356 TYR 0.014 0.001 TYR B 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 198 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 1.858 Fit side-chains REVERT: A 269 MET cc_start: 0.9041 (tpp) cc_final: 0.8318 (tpp) REVERT: A 331 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7359 (mm-40) REVERT: A 335 MET cc_start: 0.8168 (mmm) cc_final: 0.7767 (mmm) REVERT: A 424 MET cc_start: 0.8703 (tpp) cc_final: 0.8201 (tpp) REVERT: A 449 CYS cc_start: 0.8368 (p) cc_final: 0.7927 (p) REVERT: A 494 LEU cc_start: 0.8860 (mt) cc_final: 0.8546 (mt) REVERT: A 593 MET cc_start: 0.8546 (ttp) cc_final: 0.7751 (ttp) REVERT: B 271 LEU cc_start: 0.9320 (mm) cc_final: 0.9040 (mt) REVERT: B 331 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7262 (mm-40) REVERT: B 335 MET cc_start: 0.8149 (mmm) cc_final: 0.7501 (mmm) REVERT: B 424 MET cc_start: 0.8739 (tpp) cc_final: 0.8152 (tpp) REVERT: B 449 CYS cc_start: 0.8365 (p) cc_final: 0.7922 (p) REVERT: B 494 LEU cc_start: 0.8859 (mt) cc_final: 0.8556 (mt) REVERT: C 271 LEU cc_start: 0.9316 (mm) cc_final: 0.9034 (mt) REVERT: C 331 GLN cc_start: 0.7734 (mm-40) cc_final: 0.7254 (mm-40) REVERT: C 335 MET cc_start: 0.8148 (mmm) cc_final: 0.7502 (mmm) REVERT: C 424 MET cc_start: 0.8709 (tpp) cc_final: 0.8102 (tpp) REVERT: C 449 CYS cc_start: 0.8374 (p) cc_final: 0.7925 (p) REVERT: C 494 LEU cc_start: 0.8865 (mt) cc_final: 0.8547 (mt) REVERT: D 271 LEU cc_start: 0.9318 (mm) cc_final: 0.9040 (mt) REVERT: D 331 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7253 (mm-40) REVERT: D 335 MET cc_start: 0.8146 (mmm) cc_final: 0.7501 (mmm) REVERT: D 424 MET cc_start: 0.8716 (tpp) cc_final: 0.8101 (tpp) REVERT: D 449 CYS cc_start: 0.8369 (p) cc_final: 0.7842 (p) REVERT: D 494 LEU cc_start: 0.8861 (mt) cc_final: 0.8553 (mt) REVERT: D 593 MET cc_start: 0.8513 (ttp) cc_final: 0.7698 (ttp) outliers start: 26 outliers final: 18 residues processed: 184 average time/residue: 0.2231 time to fit residues: 68.2685 Evaluate side-chains 180 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 162 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 580 GLU Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 664 LEU 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: 0.9980 chunk 112 optimal weight: 10.0000 chunk 56 optimal weight: 0.1980 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.8118 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 : 0.002 0.021 17280 Z= 0.143 Angle : 0.486 11.235 23152 Z= 0.235 Chirality : 0.039 0.115 2492 Planarity : 0.003 0.032 2820 Dihedral : 9.326 58.091 2960 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.40 % Allowed : 9.30 % Favored : 89.30 % 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: 2.20 (0.19), residues: 1972 helix: 2.14 (0.14), residues: 1316 sheet: 0.29 (0.47), residues: 116 loop : 0.09 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 401 HIS 0.002 0.001 HIS C 406 PHE 0.004 0.001 PHE D 356 TYR 0.015 0.001 TYR A 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 188 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 2.406 Fit side-chains REVERT: A 331 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7349 (mm-40) REVERT: A 335 MET cc_start: 0.8193 (mmm) cc_final: 0.7756 (mmm) REVERT: A 449 CYS cc_start: 0.8412 (p) cc_final: 0.8051 (p) REVERT: A 494 LEU cc_start: 0.8864 (mt) cc_final: 0.8549 (mt) REVERT: A 593 MET cc_start: 0.8549 (ttp) cc_final: 0.7794 (ttp) REVERT: B 331 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7355 (mm-40) REVERT: B 335 MET cc_start: 0.8156 (mmm) cc_final: 0.7739 (mmm) REVERT: B 449 CYS cc_start: 0.8406 (p) cc_final: 0.8042 (p) REVERT: B 494 LEU cc_start: 0.8865 (mt) cc_final: 0.8561 (mt) REVERT: B 593 MET cc_start: 0.8546 (ttp) cc_final: 0.7587 (ttp) REVERT: C 331 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7084 (mm-40) REVERT: C 335 MET cc_start: 0.8154 (mmm) cc_final: 0.7519 (mmm) REVERT: C 449 CYS cc_start: 0.8412 (p) cc_final: 0.8045 (p) REVERT: C 494 LEU cc_start: 0.8872 (mt) cc_final: 0.8567 (mt) REVERT: C 593 MET cc_start: 0.8532 (ttp) cc_final: 0.7577 (ttp) REVERT: D 331 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7087 (mm-40) REVERT: D 335 MET cc_start: 0.8153 (mmm) cc_final: 0.7516 (mmm) REVERT: D 449 CYS cc_start: 0.8415 (p) cc_final: 0.7978 (p) REVERT: D 494 LEU cc_start: 0.8864 (mt) cc_final: 0.8570 (mt) REVERT: D 593 MET cc_start: 0.8528 (ttp) cc_final: 0.7771 (ttp) outliers start: 24 outliers final: 16 residues processed: 177 average time/residue: 0.2298 time to fit residues: 67.4572 Evaluate side-chains 178 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 162 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 398 ILE Chi-restraints excluded: chain D residue 580 GLU Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8110 moved from start: 0.2667 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= 0.128 Angle : 0.476 11.703 23152 Z= 0.231 Chirality : 0.039 0.115 2492 Planarity : 0.003 0.032 2820 Dihedral : 9.075 59.655 2960 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.64 % Allowed : 10.00 % Favored : 89.36 % 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: 2.32 (0.19), residues: 1972 helix: 2.23 (0.14), residues: 1316 sheet: 0.30 (0.47), residues: 116 loop : 0.16 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 401 HIS 0.003 0.001 HIS B 406 PHE 0.004 0.001 PHE B 356 TYR 0.014 0.001 TYR B 531 ARG 0.002 0.000 ARG B 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 183 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 172 time to evaluate : 1.893 Fit side-chains REVERT: A 331 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7343 (mm-40) REVERT: A 335 MET cc_start: 0.8111 (mmm) cc_final: 0.7696 (mmm) REVERT: A 449 CYS cc_start: 0.8351 (p) cc_final: 0.7910 (p) REVERT: A 494 LEU cc_start: 0.8858 (mt) cc_final: 0.8552 (mt) REVERT: A 593 MET cc_start: 0.8542 (ttp) cc_final: 0.7846 (ttp) REVERT: B 331 GLN cc_start: 0.7501 (mm-40) cc_final: 0.7276 (mm-40) REVERT: B 335 MET cc_start: 0.8100 (mmm) cc_final: 0.7679 (mmm) REVERT: B 424 MET cc_start: 0.8695 (tpp) cc_final: 0.7908 (tpp) REVERT: B 449 CYS cc_start: 0.8345 (p) cc_final: 0.7906 (p) REVERT: B 494 LEU cc_start: 0.8838 (mt) cc_final: 0.8536 (mt) REVERT: B 593 MET cc_start: 0.8512 (ttp) cc_final: 0.7554 (ttp) REVERT: C 331 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7265 (mm-40) REVERT: C 335 MET cc_start: 0.8096 (mmm) cc_final: 0.7677 (mmm) REVERT: C 424 MET cc_start: 0.8706 (tpp) cc_final: 0.7921 (tpp) REVERT: C 449 CYS cc_start: 0.8352 (p) cc_final: 0.7914 (p) REVERT: C 494 LEU cc_start: 0.8822 (mt) cc_final: 0.8498 (mt) REVERT: C 593 MET cc_start: 0.8514 (ttp) cc_final: 0.7561 (ttp) REVERT: D 214 MET cc_start: 0.6580 (mtm) cc_final: 0.6371 (tpp) REVERT: D 331 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7264 (mm-40) REVERT: D 335 MET cc_start: 0.8091 (mmm) cc_final: 0.7673 (mmm) REVERT: D 424 MET cc_start: 0.8709 (tpp) cc_final: 0.7919 (tpp) REVERT: D 449 CYS cc_start: 0.8360 (p) cc_final: 0.7922 (p) REVERT: D 494 LEU cc_start: 0.8802 (mt) cc_final: 0.8484 (mt) REVERT: D 593 MET cc_start: 0.8516 (ttp) cc_final: 0.7810 (ttp) outliers start: 11 outliers final: 8 residues processed: 178 average time/residue: 0.2234 time to fit residues: 65.6455 Evaluate side-chains 176 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 580 GLU Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain D residue 580 GLU Chi-restraints excluded: chain D residue 632 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.8133 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17280 Z= 0.179 Angle : 0.490 10.253 23152 Z= 0.240 Chirality : 0.040 0.115 2492 Planarity : 0.003 0.031 2820 Dihedral : 9.136 59.855 2960 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.99 % Allowed : 9.83 % Favored : 89.19 % 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: 2.35 (0.19), residues: 1972 helix: 2.23 (0.14), residues: 1316 sheet: 0.25 (0.47), residues: 116 loop : 0.24 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 401 HIS 0.003 0.001 HIS B 406 PHE 0.005 0.001 PHE D 584 TYR 0.015 0.001 TYR C 531 ARG 0.002 0.000 ARG B 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 193 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 1.967 Fit side-chains REVERT: A 331 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7344 (mm-40) REVERT: A 335 MET cc_start: 0.8125 (mmm) cc_final: 0.7664 (mmm) REVERT: A 424 MET cc_start: 0.8730 (tpp) cc_final: 0.8012 (tpp) REVERT: A 432 ASP cc_start: 0.8372 (t0) cc_final: 0.8161 (t0) REVERT: A 449 CYS cc_start: 0.8405 (p) cc_final: 0.7967 (p) REVERT: A 494 LEU cc_start: 0.8901 (mt) cc_final: 0.8575 (mt) REVERT: A 593 MET cc_start: 0.8571 (ttp) cc_final: 0.7878 (ttp) REVERT: B 331 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7095 (mm-40) REVERT: B 335 MET cc_start: 0.8121 (mmm) cc_final: 0.7441 (mmm) REVERT: B 424 MET cc_start: 0.8722 (tpp) cc_final: 0.7923 (tpp) REVERT: B 432 ASP cc_start: 0.8355 (t0) cc_final: 0.8146 (t0) REVERT: B 449 CYS cc_start: 0.8410 (p) cc_final: 0.7981 (p) REVERT: B 494 LEU cc_start: 0.8900 (mt) cc_final: 0.8584 (mt) REVERT: B 538 MET cc_start: 0.8902 (mtm) cc_final: 0.8690 (mtm) REVERT: B 593 MET cc_start: 0.8497 (ttp) cc_final: 0.7424 (ttp) REVERT: B 654 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: C 331 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7085 (mm-40) REVERT: C 335 MET cc_start: 0.8115 (mmm) cc_final: 0.7435 (mmm) REVERT: C 424 MET cc_start: 0.8756 (tpp) cc_final: 0.7966 (tpp) REVERT: C 432 ASP cc_start: 0.8362 (t0) cc_final: 0.8158 (t0) REVERT: C 449 CYS cc_start: 0.8417 (p) cc_final: 0.7979 (p) REVERT: C 494 LEU cc_start: 0.8901 (mt) cc_final: 0.8569 (mt) REVERT: C 538 MET cc_start: 0.8870 (mtm) cc_final: 0.8654 (mtm) REVERT: C 593 MET cc_start: 0.8484 (ttp) cc_final: 0.7424 (ttp) REVERT: C 654 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8367 (m-30) REVERT: D 331 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7085 (mm-40) REVERT: D 335 MET cc_start: 0.8111 (mmm) cc_final: 0.7433 (mmm) REVERT: D 424 MET cc_start: 0.8755 (tpp) cc_final: 0.7960 (tpp) REVERT: D 432 ASP cc_start: 0.8370 (t0) cc_final: 0.8166 (t0) REVERT: D 449 CYS cc_start: 0.8421 (p) cc_final: 0.8001 (p) REVERT: D 494 LEU cc_start: 0.8892 (mt) cc_final: 0.8573 (mt) REVERT: D 593 MET cc_start: 0.8539 (ttp) cc_final: 0.7837 (ttp) outliers start: 17 outliers final: 10 residues processed: 182 average time/residue: 0.2477 time to fit residues: 72.1432 Evaluate side-chains 188 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 632 MET Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 632 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 632 MET Chi-restraints excluded: chain D residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 143 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.107933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082844 restraints weight = 30961.263| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.48 r_work: 0.2939 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17280 Z= 0.150 Angle : 0.498 12.043 23152 Z= 0.238 Chirality : 0.039 0.114 2492 Planarity : 0.003 0.032 2820 Dihedral : 9.011 58.489 2960 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.87 % Allowed : 10.17 % Favored : 88.95 % 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: 2.46 (0.19), residues: 1972 helix: 2.32 (0.14), residues: 1316 sheet: 0.28 (0.47), residues: 116 loop : 0.30 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 401 HIS 0.002 0.001 HIS B 406 PHE 0.004 0.001 PHE C 342 TYR 0.014 0.001 TYR B 531 ARG 0.002 0.000 ARG A 680 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2975.00 seconds wall clock time: 55 minutes 0.95 seconds (3300.95 seconds total)