Starting phenix.real_space_refine on Mon Jul 22 08:24:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/07_2024/6gyn_0093.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/07_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_0093/07_2024/6gyn_0093.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/07_2024/6gyn_0093.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/07_2024/6gyn_0093.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyn_0093/07_2024/6gyn_0093.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.132 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 132 5.16 5 C 11148 2.51 5 N 2684 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 315": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 550": "NH1" <-> "NH2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "B ARG 242": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B ARG 525": "NH1" <-> "NH2" Residue "B ARG 550": "NH1" <-> "NH2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B ARG 674": "NH1" <-> "NH2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "C ARG 242": "NH1" <-> "NH2" Residue "C ARG 315": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C ARG 375": "NH1" <-> "NH2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C ARG 525": "NH1" <-> "NH2" Residue "C ARG 550": "NH1" <-> "NH2" Residue "C ARG 587": "NH1" <-> "NH2" Residue "C ARG 668": "NH1" <-> "NH2" Residue "C ARG 674": "NH1" <-> "NH2" Residue "C ARG 700": "NH1" <-> "NH2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 372": "NH1" <-> "NH2" Residue "D ARG 375": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D ARG 524": "NH1" <-> "NH2" Residue "D ARG 525": "NH1" <-> "NH2" Residue "D ARG 550": "NH1" <-> "NH2" Residue "D ARG 587": "NH1" <-> "NH2" Residue "D ARG 668": "NH1" <-> "NH2" Residue "D ARG 674": "NH1" <-> "NH2" Residue "D ARG 700": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 16932 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "B" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "D" Number of atoms: 4004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 4004 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 477} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {'3PE': 2, 'PC1': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 298 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PC1:plan-2': 3, 'PC1:plan-1': 3} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 9.12, per 1000 atoms: 0.54 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: 6.27 Conformation dependent library (CDL) restraints added in 3.2 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... Secondary structure from input PDB file: 100 helices and 8 sheets defined 70.9% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 236 through 249 Processing helix chain 'A' and resid 259 through 286 removed outlier: 3.759A pdb=" N PHE A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) 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 292 through 313 Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.892A pdb=" N LYS A 339 " --> pdb=" O MET A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP A 345 " --> pdb=" O TRP A 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 350 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 371 through 384 removed outlier: 3.564A pdb=" N ARG A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 390 through 410 removed outlier: 3.792A pdb=" N ILE A 404 " --> pdb=" O GLN A 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 443 removed outlier: 3.695A pdb=" N PHE A 437 " --> pdb=" O GLY A 433 " (cutoff:3.500A) Proline residue: A 440 - end of helix removed outlier: 3.527A pdb=" N GLN A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 488 through 518 removed outlier: 3.699A pdb=" N TRP A 493 " --> pdb=" O MET A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 541 Processing helix chain 'A' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 573 Processing helix chain 'A' and resid 574 through 591 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 600 through 608 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 4.019A pdb=" N GLU A 695 " --> pdb=" O GLU A 691 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 696 " --> pdb=" O VAL A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 708 Processing helix chain 'B' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 236 through 249 Processing helix chain 'B' and resid 259 through 286 removed outlier: 3.758A pdb=" N PHE B 263 " --> pdb=" O SER B 259 " (cutoff:3.500A) 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 292 through 313 Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.893A pdb=" N LYS B 339 " --> pdb=" O MET B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP B 345 " --> pdb=" O TRP B 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 350 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 371 through 384 removed outlier: 3.563A pdb=" N ARG B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 Processing helix chain 'B' and resid 390 through 410 removed outlier: 3.791A pdb=" N ILE B 404 " --> pdb=" O GLN B 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP B 410 " --> pdb=" O HIS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 443 removed outlier: 3.695A pdb=" N PHE B 437 " --> pdb=" O GLY B 433 " (cutoff:3.500A) Proline residue: B 440 - end of helix removed outlier: 3.526A pdb=" N GLN B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 488 through 518 removed outlier: 3.700A pdb=" N TRP B 493 " --> pdb=" O MET B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 541 Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 Processing helix chain 'B' and resid 574 through 591 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 600 through 608 Processing helix chain 'B' and resid 609 through 611 No H-bonds generated for 'chain 'B' and resid 609 through 611' Processing helix chain 'B' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU B 664 " --> pdb=" O GLU B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 removed outlier: 4.020A pdb=" N GLU B 695 " --> pdb=" O GLU B 691 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR B 696 " --> pdb=" O VAL B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 708 Processing helix chain 'C' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU C 222 " --> pdb=" O PHE C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 259 through 286 removed outlier: 3.757A pdb=" N PHE C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) 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 292 through 313 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.892A pdb=" N LYS C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP C 345 " --> pdb=" O TRP C 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 350 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 371 through 384 removed outlier: 3.563A pdb=" N ARG C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 390 through 410 removed outlier: 3.791A pdb=" N ILE C 404 " --> pdb=" O GLN C 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 443 removed outlier: 3.695A pdb=" N PHE C 437 " --> pdb=" O GLY C 433 " (cutoff:3.500A) Proline residue: C 440 - end of helix removed outlier: 3.525A pdb=" N GLN C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 460 through 475 Processing helix chain 'C' and resid 488 through 518 removed outlier: 3.700A pdb=" N TRP C 493 " --> pdb=" O MET C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 541 Processing helix chain 'C' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR C 559 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 573 Processing helix chain 'C' and resid 574 through 591 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 600 through 608 Processing helix chain 'C' and resid 609 through 611 No H-bonds generated for 'chain 'C' and resid 609 through 611' Processing helix chain 'C' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU C 664 " --> pdb=" O GLU C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 696 removed outlier: 4.019A pdb=" N GLU C 695 " --> pdb=" O GLU C 691 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 696 " --> pdb=" O VAL C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 708 Processing helix chain 'D' and resid 216 through 222 removed outlier: 3.549A pdb=" N LEU D 222 " --> pdb=" O PHE D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 236 through 249 Processing helix chain 'D' and resid 259 through 286 removed outlier: 3.757A pdb=" N PHE D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) 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 292 through 313 Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.892A pdb=" N LYS D 339 " --> pdb=" O MET D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 350 removed outlier: 3.820A pdb=" N ASP D 345 " --> pdb=" O TRP D 341 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 350 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 Processing helix chain 'D' and resid 371 through 384 removed outlier: 3.563A pdb=" N ARG D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 Processing helix chain 'D' and resid 390 through 410 removed outlier: 3.791A pdb=" N ILE D 404 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP D 410 " --> pdb=" O HIS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 443 removed outlier: 3.694A pdb=" N PHE D 437 " --> pdb=" O GLY D 433 " (cutoff:3.500A) Proline residue: D 440 - end of helix removed outlier: 3.525A pdb=" N GLN D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 460 through 475 Processing helix chain 'D' and resid 488 through 518 removed outlier: 3.700A pdb=" N TRP D 493 " --> pdb=" O MET D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 541 Processing helix chain 'D' and resid 544 through 559 removed outlier: 3.598A pdb=" N TYR D 559 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 573 Processing helix chain 'D' and resid 574 through 591 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 600 through 608 Processing helix chain 'D' and resid 609 through 611 No H-bonds generated for 'chain 'D' and resid 609 through 611' Processing helix chain 'D' and resid 660 through 666 removed outlier: 3.598A pdb=" N LEU D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 removed outlier: 4.019A pdb=" N GLU D 695 " --> pdb=" O GLU D 691 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 696 " --> pdb=" O VAL D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 708 Processing sheet with id=AA1, first strand: chain 'A' and resid 612 through 616 removed outlier: 6.574A pdb=" N ARG A 680 " --> pdb=" O GLN A 636 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR A 621 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA A 675 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A 648 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 612 through 616 removed outlier: 6.572A pdb=" N ARG B 680 " --> pdb=" O GLN B 636 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR B 621 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 675 " --> pdb=" O TYR B 621 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B 648 " --> pdb=" O THR B 644 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 612 through 616 removed outlier: 6.573A pdb=" N ARG C 680 " --> pdb=" O GLN C 636 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR C 621 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 675 " --> pdb=" O TYR C 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 648 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 612 through 616 removed outlier: 6.573A pdb=" N ARG D 680 " --> pdb=" O GLN D 636 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 621 through 623 removed outlier: 6.376A pdb=" N TYR D 621 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA D 675 " --> pdb=" O TYR D 621 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2976 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: 5.09 Time building geometry restraints manager: 6.75 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: 4380 2.80 - 3.32: 15005 3.32 - 3.85: 27134 3.85 - 4.37: 31929 4.37 - 4.90: 55826 Nonbonded interactions: 134274 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 134269 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.180 Process input model: 44.580 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.200 ------------------------------------------------------------------------------- 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= 0.520 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 : 1.787 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: 130.8495 Evaluate side-chains 162 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 ASN A 541 HIS A 602 ASN B 223 GLN B 459 ASN B 541 HIS B 602 ASN C 223 GLN C 459 ASN C 541 HIS C 602 ASN D 223 GLN D 459 ASN D 541 HIS D 602 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17280 Z= 0.338 Angle : 0.598 7.019 23152 Z= 0.308 Chirality : 0.044 0.121 2492 Planarity : 0.004 0.032 2820 Dihedral : 10.656 73.392 2960 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.74 % Allowed : 7.50 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.18), residues: 1972 helix: 0.44 (0.13), residues: 1348 sheet: 0.57 (0.47), residues: 116 loop : -0.80 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 401 HIS 0.005 0.002 HIS B 406 PHE 0.011 0.002 PHE C 689 TYR 0.017 0.002 TYR B 633 ARG 0.003 0.000 ARG C 674 *********************** 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 206 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 1.906 Fit side-chains REVERT: A 331 GLN cc_start: 0.7856 (mm-40) cc_final: 0.7421 (mm-40) REVERT: A 335 MET cc_start: 0.8254 (mmm) cc_final: 0.7588 (mmm) REVERT: B 331 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7420 (mm-40) REVERT: B 335 MET cc_start: 0.8248 (mmm) cc_final: 0.7587 (mmm) REVERT: C 331 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7409 (mm-40) REVERT: C 335 MET cc_start: 0.8254 (mmm) cc_final: 0.7592 (mmm) REVERT: D 331 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7406 (mm-40) REVERT: D 335 MET cc_start: 0.8257 (mmm) cc_final: 0.7593 (mmm) REVERT: D 473 MET cc_start: 0.8525 (ttm) cc_final: 0.8319 (ttm) outliers start: 30 outliers final: 25 residues processed: 197 average time/residue: 0.2384 time to fit residues: 76.6800 Evaluate side-chains 178 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.854 ------------------------------------------------------------------------------- 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 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 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 500 ILE 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 500 ILE 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 664 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 121 optimal weight: 0.6980 chunk 49 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 158 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS B 406 HIS C 223 GLN C 406 HIS D 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17280 Z= 0.179 Angle : 0.486 5.881 23152 Z= 0.250 Chirality : 0.040 0.119 2492 Planarity : 0.003 0.032 2820 Dihedral : 10.034 68.014 2960 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.87 % Allowed : 10.52 % Favored : 88.60 % 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: 1.23 (0.19), residues: 1972 helix: 1.39 (0.14), residues: 1324 sheet: 0.59 (0.48), residues: 116 loop : -0.44 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 401 HIS 0.004 0.001 HIS D 475 PHE 0.006 0.001 PHE A 261 TYR 0.013 0.001 TYR A 531 ARG 0.002 0.000 ARG A 372 *********************** 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 219 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 204 time to evaluate : 1.819 Fit side-chains REVERT: A 331 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7343 (mm-40) REVERT: A 335 MET cc_start: 0.8265 (mmm) cc_final: 0.7591 (mmm) REVERT: A 449 CYS cc_start: 0.8198 (p) cc_final: 0.7726 (p) REVERT: B 331 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7611 (mm-40) REVERT: B 335 MET cc_start: 0.8264 (mmm) cc_final: 0.7819 (mmm) REVERT: B 424 MET cc_start: 0.8856 (tpp) cc_final: 0.8006 (tpp) REVERT: B 449 CYS cc_start: 0.8173 (p) cc_final: 0.7716 (p) REVERT: C 331 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7390 (mm-40) REVERT: C 335 MET cc_start: 0.8265 (mmm) cc_final: 0.7600 (mmm) REVERT: C 424 MET cc_start: 0.8860 (tpp) cc_final: 0.7997 (tpp) REVERT: C 449 CYS cc_start: 0.8184 (p) cc_final: 0.7723 (p) REVERT: D 331 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7387 (mm-40) REVERT: D 335 MET cc_start: 0.8265 (mmm) cc_final: 0.7598 (mmm) REVERT: D 424 MET cc_start: 0.8864 (tpp) cc_final: 0.8000 (tpp) REVERT: D 449 CYS cc_start: 0.8182 (p) cc_final: 0.7729 (p) outliers start: 15 outliers final: 8 residues processed: 215 average time/residue: 0.2438 time to fit residues: 83.2127 Evaluate side-chains 176 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 398 ILE 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: 4.9990 chunk 134 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 189 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS C 223 GLN C 475 HIS D 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17280 Z= 0.221 Angle : 0.500 5.930 23152 Z= 0.256 Chirality : 0.040 0.121 2492 Planarity : 0.003 0.030 2820 Dihedral : 10.053 63.815 2960 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.44 % Allowed : 9.36 % Favored : 88.20 % 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: 1.74 (0.19), residues: 1972 helix: 1.77 (0.14), residues: 1324 sheet: 0.36 (0.48), residues: 116 loop : -0.15 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 401 HIS 0.003 0.001 HIS A 475 PHE 0.012 0.001 PHE A 252 TYR 0.015 0.001 TYR A 531 ARG 0.002 0.000 ARG C 372 *********************** 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 222 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 1.838 Fit side-chains REVERT: A 331 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7279 (mm-40) REVERT: A 335 MET cc_start: 0.8200 (mmm) cc_final: 0.7569 (mmm) REVERT: A 449 CYS cc_start: 0.8216 (p) cc_final: 0.7750 (p) REVERT: A 538 MET cc_start: 0.8806 (mtm) cc_final: 0.8168 (mtm) REVERT: B 331 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7281 (mm-40) REVERT: B 335 MET cc_start: 0.8197 (mmm) cc_final: 0.7570 (mmm) REVERT: B 449 CYS cc_start: 0.8040 (p) cc_final: 0.7628 (p) REVERT: B 538 MET cc_start: 0.8813 (mtm) cc_final: 0.8128 (mtm) REVERT: C 331 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7272 (mm-40) REVERT: C 335 MET cc_start: 0.8201 (mmm) cc_final: 0.7575 (mmm) REVERT: C 449 CYS cc_start: 0.8058 (p) cc_final: 0.7644 (p) REVERT: C 538 MET cc_start: 0.8816 (mtm) cc_final: 0.8166 (mtm) REVERT: D 331 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7270 (mm-40) REVERT: D 335 MET cc_start: 0.8199 (mmm) cc_final: 0.7571 (mmm) REVERT: D 449 CYS cc_start: 0.8053 (p) cc_final: 0.7643 (p) REVERT: D 538 MET cc_start: 0.8820 (mtm) cc_final: 0.8162 (mtm) outliers start: 42 outliers final: 23 residues processed: 215 average time/residue: 0.2349 time to fit residues: 82.8412 Evaluate side-chains 185 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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 398 ILE 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 586 CYS 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 586 CYS 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 586 CYS 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: 1.9990 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 170 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 459 ASN C 223 GLN C 459 ASN D 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17280 Z= 0.252 Angle : 0.530 11.078 23152 Z= 0.265 Chirality : 0.042 0.141 2492 Planarity : 0.003 0.028 2820 Dihedral : 9.972 59.153 2960 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.09 % Allowed : 9.07 % 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: 2.13 (0.19), residues: 1972 helix: 2.11 (0.14), residues: 1300 sheet: 0.15 (0.48), residues: 116 loop : 0.11 (0.28), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 401 HIS 0.003 0.001 HIS B 256 PHE 0.010 0.001 PHE A 658 TYR 0.016 0.001 TYR C 531 ARG 0.002 0.000 ARG C 548 *********************** 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 198 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 1.874 Fit side-chains REVERT: A 331 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7238 (mm-40) REVERT: A 335 MET cc_start: 0.8224 (mmm) cc_final: 0.7617 (mmm) REVERT: A 449 CYS cc_start: 0.8097 (p) cc_final: 0.7682 (p) REVERT: A 593 MET cc_start: 0.8497 (ttp) cc_final: 0.7830 (ttp) REVERT: B 331 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7293 (mm-40) REVERT: B 335 MET cc_start: 0.8218 (mmm) cc_final: 0.7615 (mmm) REVERT: B 424 MET cc_start: 0.8736 (tpp) cc_final: 0.8046 (tpp) REVERT: B 449 CYS cc_start: 0.8094 (p) cc_final: 0.7678 (p) REVERT: B 538 MET cc_start: 0.8900 (mtm) cc_final: 0.8580 (mtp) REVERT: C 331 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7285 (mm-40) REVERT: C 335 MET cc_start: 0.8220 (mmm) cc_final: 0.7621 (mmm) REVERT: C 449 CYS cc_start: 0.8106 (p) cc_final: 0.7687 (p) REVERT: C 538 MET cc_start: 0.8905 (mtm) cc_final: 0.8239 (mtm) REVERT: D 331 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7284 (mm-40) REVERT: D 335 MET cc_start: 0.8220 (mmm) cc_final: 0.7618 (mmm) REVERT: D 449 CYS cc_start: 0.8107 (p) cc_final: 0.7693 (p) REVERT: D 538 MET cc_start: 0.8907 (mtm) cc_final: 0.8234 (mtm) outliers start: 36 outliers final: 23 residues processed: 184 average time/residue: 0.2187 time to fit residues: 67.0755 Evaluate side-chains 184 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.827 ------------------------------------------------------------------------------- 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 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 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 586 CYS 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 586 CYS 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: 1.9990 chunk 170 optimal weight: 0.0020 chunk 37 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 99 optimal weight: 0.0570 overall best weight: 0.7308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS C 223 GLN C 475 HIS D 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17280 Z= 0.127 Angle : 0.477 9.657 23152 Z= 0.235 Chirality : 0.039 0.117 2492 Planarity : 0.003 0.030 2820 Dihedral : 9.438 53.996 2960 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.28 % Allowed : 10.17 % Favored : 88.55 % 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: 2.44 (0.20), residues: 1972 helix: 2.37 (0.15), residues: 1300 sheet: 0.23 (0.48), residues: 116 loop : 0.16 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 401 HIS 0.001 0.000 HIS B 406 PHE 0.008 0.001 PHE A 658 TYR 0.013 0.001 TYR C 531 ARG 0.001 0.000 ARG A 548 *********************** 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 207 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 1.903 Fit side-chains REVERT: A 331 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7213 (mm-40) REVERT: A 335 MET cc_start: 0.8141 (mmm) cc_final: 0.7530 (mmm) REVERT: A 424 MET cc_start: 0.8620 (tpp) cc_final: 0.8078 (tpp) REVERT: A 449 CYS cc_start: 0.7885 (p) cc_final: 0.7436 (p) REVERT: A 494 LEU cc_start: 0.8840 (mt) cc_final: 0.8545 (mt) REVERT: A 538 MET cc_start: 0.8736 (mtm) cc_final: 0.8456 (mtp) REVERT: A 593 MET cc_start: 0.8466 (ttp) cc_final: 0.7857 (ttp) REVERT: B 331 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7215 (mm-40) REVERT: B 335 MET cc_start: 0.8167 (mmm) cc_final: 0.7511 (mmm) REVERT: B 424 MET cc_start: 0.8729 (tpp) cc_final: 0.8515 (tpp) REVERT: B 449 CYS cc_start: 0.7957 (p) cc_final: 0.7526 (p) REVERT: B 494 LEU cc_start: 0.8844 (mt) cc_final: 0.8567 (mt) REVERT: B 538 MET cc_start: 0.8865 (mtm) cc_final: 0.8432 (mtm) REVERT: B 593 MET cc_start: 0.8509 (ttp) cc_final: 0.7556 (ttp) REVERT: C 331 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7209 (mm-40) REVERT: C 335 MET cc_start: 0.8125 (mmm) cc_final: 0.7471 (mmm) REVERT: C 424 MET cc_start: 0.8593 (tpp) cc_final: 0.8133 (tpp) REVERT: C 449 CYS cc_start: 0.7958 (p) cc_final: 0.7530 (p) REVERT: C 494 LEU cc_start: 0.8851 (mt) cc_final: 0.8578 (mt) REVERT: C 538 MET cc_start: 0.8866 (mtm) cc_final: 0.8429 (mtm) REVERT: C 593 MET cc_start: 0.8507 (ttp) cc_final: 0.7562 (ttp) REVERT: D 331 GLN cc_start: 0.7712 (mm-40) cc_final: 0.7210 (mm-40) REVERT: D 335 MET cc_start: 0.8130 (mmm) cc_final: 0.7471 (mmm) REVERT: D 424 MET cc_start: 0.8602 (tpp) cc_final: 0.8135 (tpp) REVERT: D 449 CYS cc_start: 0.7957 (p) cc_final: 0.7535 (p) REVERT: D 494 LEU cc_start: 0.8847 (mt) cc_final: 0.8566 (mt) REVERT: D 538 MET cc_start: 0.8867 (mtm) cc_final: 0.8425 (mtm) outliers start: 22 outliers final: 14 residues processed: 199 average time/residue: 0.2510 time to fit residues: 81.8067 Evaluate side-chains 186 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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 473 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 379 PHE 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 473 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 664 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS C 223 GLN C 475 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17280 Z= 0.177 Angle : 0.492 8.836 23152 Z= 0.244 Chirality : 0.040 0.119 2492 Planarity : 0.003 0.029 2820 Dihedral : 9.228 53.626 2960 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.40 % Allowed : 10.00 % Favored : 88.60 % 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: 2.60 (0.20), residues: 1972 helix: 2.48 (0.15), residues: 1300 sheet: 0.32 (0.47), residues: 116 loop : 0.25 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 401 HIS 0.002 0.001 HIS D 256 PHE 0.007 0.001 PHE A 658 TYR 0.013 0.001 TYR A 531 ARG 0.001 0.000 ARG C 372 *********************** 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 190 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.689 Fit side-chains REVERT: A 214 MET cc_start: 0.6590 (mtt) cc_final: 0.6285 (mtm) REVERT: A 269 MET cc_start: 0.9086 (tpp) cc_final: 0.8360 (tpp) REVERT: A 331 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7223 (mm-40) REVERT: A 335 MET cc_start: 0.8176 (mmm) cc_final: 0.7550 (mmm) REVERT: A 449 CYS cc_start: 0.7963 (p) cc_final: 0.7518 (p) REVERT: A 538 MET cc_start: 0.8749 (mtm) cc_final: 0.8474 (mtp) REVERT: A 593 MET cc_start: 0.8536 (ttp) cc_final: 0.8036 (ttp) REVERT: A 654 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8331 (m-30) REVERT: B 331 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7226 (mm-40) REVERT: B 335 MET cc_start: 0.8187 (mmm) cc_final: 0.7538 (mmm) REVERT: B 424 MET cc_start: 0.8748 (tpp) cc_final: 0.8501 (tpp) REVERT: B 449 CYS cc_start: 0.7960 (p) cc_final: 0.7518 (p) REVERT: B 538 MET cc_start: 0.8929 (mtm) cc_final: 0.8681 (mtm) REVERT: B 593 MET cc_start: 0.8558 (ttp) cc_final: 0.7763 (ttp) REVERT: B 654 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8339 (m-30) REVERT: C 331 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7218 (mm-40) REVERT: C 335 MET cc_start: 0.8179 (mmm) cc_final: 0.7534 (mmm) REVERT: C 449 CYS cc_start: 0.7976 (p) cc_final: 0.7532 (p) REVERT: C 538 MET cc_start: 0.8886 (mtm) cc_final: 0.8492 (mtm) REVERT: C 593 MET cc_start: 0.8536 (ttp) cc_final: 0.7754 (ttp) REVERT: C 654 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8338 (m-30) REVERT: D 331 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7223 (mm-40) REVERT: D 335 MET cc_start: 0.8202 (mmm) cc_final: 0.7563 (mmm) REVERT: D 449 CYS cc_start: 0.7975 (p) cc_final: 0.7532 (p) REVERT: D 538 MET cc_start: 0.8889 (mtm) cc_final: 0.8488 (mtm) REVERT: D 593 MET cc_start: 0.8471 (ttp) cc_final: 0.7377 (ttp) REVERT: D 654 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8334 (m-30) outliers start: 24 outliers final: 11 residues processed: 179 average time/residue: 0.2323 time to fit residues: 69.2701 Evaluate side-chains 181 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 166 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 473 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 473 MET Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 654 ASP 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: 0.8980 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.2980 chunk 128 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2692 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= 0.116 Angle : 0.490 10.489 23152 Z= 0.239 Chirality : 0.039 0.118 2492 Planarity : 0.003 0.030 2820 Dihedral : 8.738 53.083 2960 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.28 % Allowed : 10.23 % Favored : 88.49 % 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: 2.76 (0.20), residues: 1972 helix: 2.58 (0.15), residues: 1304 sheet: 0.48 (0.47), residues: 116 loop : 0.33 (0.30), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 401 HIS 0.002 0.000 HIS D 406 PHE 0.007 0.001 PHE A 658 TYR 0.014 0.001 TYR A 531 ARG 0.001 0.000 ARG D 701 *********************** 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 207 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 2.058 Fit side-chains REVERT: A 214 MET cc_start: 0.6480 (mtt) cc_final: 0.6132 (mtm) REVERT: A 269 MET cc_start: 0.9024 (tpp) cc_final: 0.8370 (tpp) REVERT: A 335 MET cc_start: 0.8121 (mmm) cc_final: 0.7495 (mmm) REVERT: A 424 MET cc_start: 0.8751 (tpp) cc_final: 0.8496 (tpp) REVERT: A 449 CYS cc_start: 0.7884 (p) cc_final: 0.7444 (p) REVERT: A 494 LEU cc_start: 0.8804 (mt) cc_final: 0.8499 (mt) REVERT: A 593 MET cc_start: 0.8481 (ttp) cc_final: 0.8088 (ttp) REVERT: A 654 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: B 335 MET cc_start: 0.8119 (mmm) cc_final: 0.7498 (mmm) REVERT: B 424 MET cc_start: 0.8745 (tpp) cc_final: 0.8470 (tpp) REVERT: B 449 CYS cc_start: 0.7905 (p) cc_final: 0.7528 (p) REVERT: B 494 LEU cc_start: 0.8823 (mt) cc_final: 0.8543 (mt) REVERT: B 538 MET cc_start: 0.8900 (mtm) cc_final: 0.8689 (mtm) REVERT: B 593 MET cc_start: 0.8559 (ttp) cc_final: 0.7744 (ttp) REVERT: B 654 ASP cc_start: 0.8709 (OUTLIER) cc_final: 0.8390 (m-30) REVERT: C 335 MET cc_start: 0.8115 (mmm) cc_final: 0.7494 (mmm) REVERT: C 424 MET cc_start: 0.8743 (tpp) cc_final: 0.8488 (tpp) REVERT: C 449 CYS cc_start: 0.7900 (p) cc_final: 0.7526 (p) REVERT: C 494 LEU cc_start: 0.8821 (mt) cc_final: 0.8532 (mt) REVERT: C 593 MET cc_start: 0.8432 (ttp) cc_final: 0.8108 (ttp) REVERT: C 654 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: D 335 MET cc_start: 0.8111 (mmm) cc_final: 0.7490 (mmm) REVERT: D 424 MET cc_start: 0.8753 (tpp) cc_final: 0.8494 (tpp) REVERT: D 449 CYS cc_start: 0.7910 (p) cc_final: 0.7535 (p) REVERT: D 494 LEU cc_start: 0.8819 (mt) cc_final: 0.8536 (mt) REVERT: D 593 MET cc_start: 0.8476 (ttp) cc_final: 0.7759 (ttp) REVERT: D 654 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8380 (m-30) outliers start: 22 outliers final: 13 residues processed: 197 average time/residue: 0.2334 time to fit residues: 75.7132 Evaluate side-chains 203 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 PHE Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 379 PHE Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 379 PHE Chi-restraints excluded: chain D residue 580 GLU Chi-restraints excluded: chain D residue 654 ASP 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: 4.9990 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 159 optimal weight: 0.0020 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS B 475 HIS C 223 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17280 Z= 0.166 Angle : 0.511 10.097 23152 Z= 0.247 Chirality : 0.040 0.116 2492 Planarity : 0.003 0.029 2820 Dihedral : 8.712 53.008 2960 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.10 % Allowed : 10.93 % Favored : 87.97 % 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: 2.79 (0.20), residues: 1972 helix: 2.60 (0.14), residues: 1308 sheet: 0.51 (0.47), residues: 116 loop : 0.32 (0.30), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 401 HIS 0.002 0.001 HIS A 406 PHE 0.010 0.001 PHE C 658 TYR 0.014 0.001 TYR A 531 ARG 0.001 0.000 ARG C 387 *********************** 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 205 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.885 Fit side-chains REVERT: A 214 MET cc_start: 0.6489 (mtt) cc_final: 0.6137 (mtm) REVERT: A 335 MET cc_start: 0.8055 (mmm) cc_final: 0.7488 (mmm) REVERT: A 449 CYS cc_start: 0.7995 (p) cc_final: 0.7629 (p) REVERT: A 494 LEU cc_start: 0.8884 (mt) cc_final: 0.8596 (mt) REVERT: A 538 MET cc_start: 0.8875 (mtm) cc_final: 0.8665 (mtp) REVERT: A 593 MET cc_start: 0.8495 (ttp) cc_final: 0.8115 (ttp) REVERT: A 654 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8332 (m-30) REVERT: B 335 MET cc_start: 0.8051 (mmm) cc_final: 0.7496 (mmm) REVERT: B 424 MET cc_start: 0.8745 (tpp) cc_final: 0.8483 (tpp) REVERT: B 449 CYS cc_start: 0.8015 (p) cc_final: 0.7636 (p) REVERT: B 494 LEU cc_start: 0.8862 (mt) cc_final: 0.8579 (mt) REVERT: B 593 MET cc_start: 0.8570 (ttp) cc_final: 0.7806 (ttp) REVERT: B 654 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: C 335 MET cc_start: 0.8046 (mmm) cc_final: 0.7489 (mmm) REVERT: C 449 CYS cc_start: 0.8024 (p) cc_final: 0.7643 (p) REVERT: C 494 LEU cc_start: 0.8888 (mt) cc_final: 0.8597 (mt) REVERT: C 538 MET cc_start: 0.8740 (mtm) cc_final: 0.8515 (mtp) REVERT: C 593 MET cc_start: 0.8508 (ttp) cc_final: 0.8072 (ttp) REVERT: C 654 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: D 335 MET cc_start: 0.8044 (mmm) cc_final: 0.7487 (mmm) REVERT: D 449 CYS cc_start: 0.8026 (p) cc_final: 0.7651 (p) REVERT: D 494 LEU cc_start: 0.8884 (mt) cc_final: 0.8598 (mt) REVERT: D 538 MET cc_start: 0.8740 (mtm) cc_final: 0.8512 (mtp) REVERT: D 593 MET cc_start: 0.8549 (ttp) cc_final: 0.7711 (ttp) REVERT: D 654 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8390 (m-30) outliers start: 19 outliers final: 11 residues processed: 200 average time/residue: 0.2424 time to fit residues: 80.0442 Evaluate side-chains 191 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 176 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 586 CYS Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 580 GLU Chi-restraints excluded: chain D residue 586 CYS Chi-restraints excluded: chain D residue 654 ASP 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 115 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 113 optimal weight: 0.0040 chunk 88 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 chunk 155 optimal weight: 0.0470 chunk 16 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 overall best weight: 0.4890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 HIS C 223 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2853 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= 0.111 Angle : 0.480 7.972 23152 Z= 0.232 Chirality : 0.039 0.116 2492 Planarity : 0.003 0.030 2820 Dihedral : 8.465 53.366 2960 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.81 % Allowed : 10.99 % Favored : 88.20 % 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: 2.90 (0.20), residues: 1972 helix: 2.68 (0.14), residues: 1308 sheet: 0.67 (0.48), residues: 116 loop : 0.34 (0.30), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 401 HIS 0.002 0.000 HIS B 256 PHE 0.008 0.001 PHE C 658 TYR 0.011 0.001 TYR C 531 ARG 0.003 0.000 ARG A 378 ********************** 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 206 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 1.846 Fit side-chains REVERT: A 214 MET cc_start: 0.6479 (mtt) cc_final: 0.6114 (mtm) REVERT: A 269 MET cc_start: 0.9050 (tpp) cc_final: 0.8373 (tpp) REVERT: A 335 MET cc_start: 0.7904 (mmm) cc_final: 0.7307 (mmm) REVERT: A 449 CYS cc_start: 0.7818 (p) cc_final: 0.7392 (p) REVERT: A 593 MET cc_start: 0.8450 (ttp) cc_final: 0.8065 (ttp) REVERT: A 654 ASP cc_start: 0.8705 (OUTLIER) cc_final: 0.8392 (m-30) REVERT: B 335 MET cc_start: 0.7903 (mmm) cc_final: 0.7313 (mmm) REVERT: B 424 MET cc_start: 0.8747 (tpp) cc_final: 0.8447 (tpp) REVERT: B 449 CYS cc_start: 0.7830 (p) cc_final: 0.7411 (p) REVERT: B 538 MET cc_start: 0.8734 (mtm) cc_final: 0.8503 (mtp) REVERT: B 593 MET cc_start: 0.8538 (ttp) cc_final: 0.7797 (ttp) REVERT: B 654 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8400 (m-30) REVERT: C 335 MET cc_start: 0.7898 (mmm) cc_final: 0.7306 (mmm) REVERT: C 449 CYS cc_start: 0.7834 (p) cc_final: 0.7419 (p) REVERT: C 538 MET cc_start: 0.8704 (mtm) cc_final: 0.8444 (mtp) REVERT: C 593 MET cc_start: 0.8521 (ttp) cc_final: 0.8005 (ttp) REVERT: C 654 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8427 (m-30) REVERT: D 335 MET cc_start: 0.7899 (mmm) cc_final: 0.7305 (mmm) REVERT: D 449 CYS cc_start: 0.7838 (p) cc_final: 0.7429 (p) REVERT: D 538 MET cc_start: 0.8705 (mtm) cc_final: 0.8443 (mtp) REVERT: D 593 MET cc_start: 0.8505 (ttp) cc_final: 0.7663 (ttp) REVERT: D 654 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8387 (m-30) outliers start: 14 outliers final: 8 residues processed: 203 average time/residue: 0.2439 time to fit residues: 79.3892 Evaluate side-chains 186 residues out of total 1792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 174 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain D residue 580 GLU Chi-restraints excluded: chain D residue 654 ASP 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: 0.7980 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 155 optimal weight: 0.1980 chunk 65 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 475 HIS B 475 HIS C 475 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.110162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.085257 restraints weight = 30618.517| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.46 r_work: 0.2980 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17280 Z= 0.153 Angle : 0.515 8.489 23152 Z= 0.247 Chirality : 0.040 0.120 2492 Planarity : 0.003 0.029 2820 Dihedral : 8.545 52.499 2960 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.93 % Allowed : 11.10 % Favored : 87.97 % 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: 2.94 (0.20), residues: 1972 helix: 2.70 (0.14), residues: 1308 sheet: 0.67 (0.47), residues: 116 loop : 0.41 (0.30), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 401 HIS 0.004 0.001 HIS A 475 PHE 0.007 0.001 PHE C 658 TYR 0.012 0.001 TYR B 531 ARG 0.002 0.000 ARG B 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.17 seconds wall clock time: 55 minutes 28.14 seconds (3328.14 seconds total)