Starting phenix.real_space_refine on Sat Mar 16 17:49:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/03_2024/7lpc_23476_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/03_2024/7lpc_23476.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/03_2024/7lpc_23476_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/03_2024/7lpc_23476_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/03_2024/7lpc_23476_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/03_2024/7lpc_23476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/03_2024/7lpc_23476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/03_2024/7lpc_23476_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/03_2024/7lpc_23476_neut_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 28 5.49 5 S 84 5.16 5 C 10144 2.51 5 N 2292 2.21 5 O 2708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 474": "NH1" <-> "NH2" Residue "C ARG 491": "NH1" <-> "NH2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C ARG 557": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 474": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 474": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B ARG 557": "NH1" <-> "NH2" Residue "D ARG 420": "NH1" <-> "NH2" Residue "D ARG 474": "NH1" <-> "NH2" Residue "D ARG 491": "NH1" <-> "NH2" Residue "D GLU 513": "OE1" <-> "OE2" Residue "D ARG 557": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15256 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3526 Classifications: {'peptide': 454} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3526 Classifications: {'peptide': 454} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3526 Classifications: {'peptide': 454} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3526 Classifications: {'peptide': 454} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 52} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 442} Chain breaks: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 232 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 13, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 288 Unusual residues: {'6OU': 6, 'LBN': 2, 'T7X': 1, 'YFP': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-1': 3, '6OU:plan-2': 1, '6OU:plan-3': 2, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 288 Unusual residues: {'6OU': 6, 'LBN': 2, 'T7X': 1, 'YFP': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-1': 3, '6OU:plan-2': 1, '6OU:plan-3': 2, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 288 Unusual residues: {'6OU': 6, 'LBN': 2, 'T7X': 1, 'YFP': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-1': 3, '6OU:plan-2': 1, '6OU:plan-3': 2, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 288 Unusual residues: {'6OU': 6, 'LBN': 2, 'T7X': 1, 'YFP': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'YFP:plan-3': 1, 'LBN:plan-3': 1, '6OU:plan-1': 3, '6OU:plan-2': 1, '6OU:plan-3': 2, 'T7X:plan-2': 1, 'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 8.79, per 1000 atoms: 0.58 Number of scatterers: 15256 At special positions: 0 Unit cell: (119.769, 119.769, 101.426, 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 84 16.00 P 28 15.00 O 2708 8.00 N 2292 7.00 C 10144 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 386 " - pdb=" SG CYS C 390 " distance=2.05 Simple disulfide: pdb=" SG CYS A 386 " - pdb=" SG CYS A 390 " distance=2.05 Simple disulfide: pdb=" SG CYS B 386 " - pdb=" SG CYS B 390 " distance=2.05 Simple disulfide: pdb=" SG CYS D 386 " - pdb=" SG CYS D 390 " distance=2.05 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: 6.32 Conformation dependent library (CDL) restraints added in 2.6 seconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 8 sheets defined 61.2% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 3.630A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 536 through 558 removed outlier: 3.719A pdb=" N ARG C 557 " --> pdb=" O TYR C 554 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 598 removed outlier: 3.999A pdb=" N LEU C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS C 578 " --> pdb=" O LEU C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 removed outlier: 3.881A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 670 Processing helix chain 'C' and resid 674 through 688 Processing helix chain 'C' and resid 690 through 713 removed outlier: 3.906A pdb=" N LYS C 694 " --> pdb=" O ALA C 690 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 713 " --> pdb=" O GLU C 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.631A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 536 through 558 removed outlier: 3.719A pdb=" N ARG A 557 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 598 removed outlier: 3.998A pdb=" N LEU A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 removed outlier: 3.880A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 670 Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 690 through 713 removed outlier: 3.906A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.630A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 536 through 558 removed outlier: 3.718A pdb=" N ARG B 557 " --> pdb=" O TYR B 554 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 3.998A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 3.882A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 670 Processing helix chain 'B' and resid 674 through 688 Processing helix chain 'B' and resid 690 through 713 removed outlier: 3.906A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 713 " --> pdb=" O GLU B 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.630A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 536 through 558 removed outlier: 3.718A pdb=" N ARG D 557 " --> pdb=" O TYR D 554 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 598 removed outlier: 3.998A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS D 578 " --> pdb=" O LEU D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 642 removed outlier: 3.881A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 642 " --> pdb=" O PHE D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 670 Processing helix chain 'D' and resid 674 through 688 Processing helix chain 'D' and resid 690 through 713 removed outlier: 3.905A pdb=" N LYS D 694 " --> pdb=" O ALA D 690 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D 713 " --> pdb=" O GLU D 709 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 742 through 747 removed outlier: 3.606A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 724 through 730 removed outlier: 6.891A pdb=" N ASP C 737 " --> pdb=" O VAL C 728 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 742 through 747 removed outlier: 3.606A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 724 through 730 removed outlier: 6.891A pdb=" N ASP A 737 " --> pdb=" O VAL A 728 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 742 through 747 removed outlier: 3.606A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 724 through 730 removed outlier: 6.890A pdb=" N ASP B 737 " --> pdb=" O VAL B 728 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 742 through 747 removed outlier: 3.606A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 724 through 730 removed outlier: 6.891A pdb=" N ASP D 737 " --> pdb=" O VAL D 728 " (cutoff:3.500A) 856 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.48 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2196 1.31 - 1.44: 4487 1.44 - 1.57: 8643 1.57 - 1.70: 70 1.70 - 1.83: 180 Bond restraints: 15576 Sorted by residual: bond pdb=" O22 6OU D 910 " pdb=" P23 6OU D 910 " ideal model delta sigma weight residual 1.643 1.779 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" O22 6OU A 910 " pdb=" P23 6OU A 910 " ideal model delta sigma weight residual 1.643 1.779 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" O22 6OU C 910 " pdb=" P23 6OU C 910 " ideal model delta sigma weight residual 1.643 1.779 -0.136 2.00e-02 2.50e+03 4.61e+01 bond pdb=" O22 6OU B 910 " pdb=" P23 6OU B 910 " ideal model delta sigma weight residual 1.643 1.779 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" O2 LBN B 905 " pdb=" P1 LBN B 905 " ideal model delta sigma weight residual 1.650 1.784 -0.134 2.00e-02 2.50e+03 4.46e+01 ... (remaining 15571 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.12: 152 104.12 - 111.60: 6971 111.60 - 119.08: 5369 119.08 - 126.56: 8269 126.56 - 134.04: 195 Bond angle restraints: 20956 Sorted by residual: angle pdb=" O1 T7X D 904 " pdb=" P1 T7X D 904 " pdb=" O13 T7X D 904 " ideal model delta sigma weight residual 94.60 109.51 -14.91 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1 T7X A 904 " pdb=" P1 T7X A 904 " pdb=" O13 T7X A 904 " ideal model delta sigma weight residual 94.60 109.51 -14.91 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1 T7X B 904 " pdb=" P1 T7X B 904 " pdb=" O13 T7X B 904 " ideal model delta sigma weight residual 94.60 109.51 -14.91 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1 T7X C 904 " pdb=" P1 T7X C 904 " pdb=" O13 T7X C 904 " ideal model delta sigma weight residual 94.60 109.50 -14.90 3.00e+00 1.11e-01 2.47e+01 angle pdb=" O1 LBN C 905 " pdb=" P1 LBN C 905 " pdb=" O2 LBN C 905 " ideal model delta sigma weight residual 93.45 107.71 -14.26 3.00e+00 1.11e-01 2.26e+01 ... (remaining 20951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 8812 35.46 - 70.93: 432 70.93 - 106.39: 68 106.39 - 141.85: 36 141.85 - 177.32: 32 Dihedral angle restraints: 9380 sinusoidal: 4028 harmonic: 5352 Sorted by residual: dihedral pdb=" CB CYS D 386 " pdb=" SG CYS D 386 " pdb=" SG CYS D 390 " pdb=" CB CYS D 390 " ideal model delta sinusoidal sigma weight residual 93.00 40.92 52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS C 386 " pdb=" SG CYS C 386 " pdb=" SG CYS C 390 " pdb=" CB CYS C 390 " ideal model delta sinusoidal sigma weight residual 93.00 40.94 52.06 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CB CYS A 386 " pdb=" SG CYS A 386 " pdb=" SG CYS A 390 " pdb=" CB CYS A 390 " ideal model delta sinusoidal sigma weight residual 93.00 40.95 52.05 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 2304 0.965 - 1.930: 0 1.930 - 2.895: 0 2.895 - 3.860: 0 3.860 - 4.825: 4 Chirality restraints: 2308 Sorted by residual: chirality pdb=" C1 T7X A 904 " pdb=" C2 T7X A 904 " pdb=" C6 T7X A 904 " pdb=" O1 T7X A 904 " both_signs ideal model delta sigma weight residual False -2.42 2.41 -4.83 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 T7X C 904 " pdb=" C2 T7X C 904 " pdb=" C6 T7X C 904 " pdb=" O1 T7X C 904 " both_signs ideal model delta sigma weight residual False -2.42 2.40 -4.82 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C1 T7X B 904 " pdb=" C2 T7X B 904 " pdb=" C6 T7X B 904 " pdb=" O1 T7X B 904 " both_signs ideal model delta sigma weight residual False -2.42 2.40 -4.82 2.00e-01 2.50e+01 5.81e+02 ... (remaining 2305 not shown) Planarity restraints: 2512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 369 " -0.026 2.00e-02 2.50e+03 3.52e-02 2.17e+01 pdb=" CG PHE B 369 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE B 369 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE B 369 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 369 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 369 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 369 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 369 " -0.025 2.00e-02 2.50e+03 3.52e-02 2.17e+01 pdb=" CG PHE D 369 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE D 369 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 PHE D 369 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE D 369 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE D 369 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 369 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 369 " -0.026 2.00e-02 2.50e+03 3.52e-02 2.16e+01 pdb=" CG PHE C 369 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 PHE C 369 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE C 369 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE C 369 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 369 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 369 " -0.005 2.00e-02 2.50e+03 ... (remaining 2509 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1080 2.73 - 3.27: 15040 3.27 - 3.82: 23852 3.82 - 4.36: 29267 4.36 - 4.90: 51945 Nonbonded interactions: 121184 Sorted by model distance: nonbonded pdb=" N GLU D 536 " pdb=" OE1 GLU D 536 " model vdw 2.188 2.520 nonbonded pdb=" N GLU A 536 " pdb=" OE1 GLU A 536 " model vdw 2.189 2.520 nonbonded pdb=" N GLU C 536 " pdb=" OE1 GLU C 536 " model vdw 2.189 2.520 nonbonded pdb=" N GLU B 536 " pdb=" OE1 GLU B 536 " model vdw 2.189 2.520 nonbonded pdb=" O PHE B 517 " pdb=" OG SER B 520 " model vdw 2.364 2.440 ... (remaining 121179 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.330 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: 4.590 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 42.830 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 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 : 0.013 0.136 15576 Z= 0.851 Angle : 1.228 14.915 20956 Z= 0.516 Chirality : 0.214 4.825 2308 Planarity : 0.004 0.036 2512 Dihedral : 25.017 177.316 5928 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.19), residues: 1800 helix: 1.60 (0.15), residues: 1140 sheet: -1.57 (0.50), residues: 84 loop : -1.26 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 697 HIS 0.006 0.002 HIS C 410 PHE 0.078 0.003 PHE B 369 TYR 0.043 0.002 TYR B 401 ARG 0.005 0.001 ARG A 420 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.832 Fit side-chains REVERT: C 677 MET cc_start: 0.8268 (ttt) cc_final: 0.8029 (ttp) REVERT: C 743 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7335 (ttm110) REVERT: A 478 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6624 (mt-10) REVERT: A 504 LYS cc_start: 0.7028 (mmtt) cc_final: 0.6309 (mmtt) REVERT: D 536 GLU cc_start: 0.8217 (mp0) cc_final: 0.7941 (mp0) REVERT: D 677 MET cc_start: 0.8354 (ttt) cc_final: 0.8035 (ttp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2992 time to fit residues: 80.2544 Evaluate side-chains 158 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 92 optimal weight: 30.0000 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 700 GLN A 354 GLN A 700 GLN B 354 GLN B 498 GLN B 700 GLN D 354 GLN D 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15576 Z= 0.164 Angle : 0.476 6.732 20956 Z= 0.241 Chirality : 0.038 0.248 2308 Planarity : 0.003 0.027 2512 Dihedral : 24.664 171.851 2984 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.49 % Allowed : 3.52 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.20), residues: 1800 helix: 2.55 (0.15), residues: 1128 sheet: -1.35 (0.45), residues: 84 loop : -0.74 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 740 HIS 0.002 0.001 HIS B 289 PHE 0.018 0.001 PHE B 369 TYR 0.007 0.001 TYR B 511 ARG 0.003 0.000 ARG A 721 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 1.701 Fit side-chains REVERT: C 504 LYS cc_start: 0.6328 (mmtt) cc_final: 0.5621 (mmtt) REVERT: A 504 LYS cc_start: 0.6826 (mmtt) cc_final: 0.5873 (mmtt) REVERT: B 504 LYS cc_start: 0.7222 (mmtt) cc_final: 0.5993 (mmtt) REVERT: B 568 MET cc_start: 0.8152 (mtt) cc_final: 0.7926 (mtt) REVERT: D 504 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6108 (mmtt) REVERT: D 568 MET cc_start: 0.8107 (mtt) cc_final: 0.7905 (mtp) outliers start: 7 outliers final: 2 residues processed: 190 average time/residue: 0.3069 time to fit residues: 85.8872 Evaluate side-chains 171 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain D residue 660 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 30.0000 chunk 50 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 163 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 162 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 0.2980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 GLN A 498 GLN B 498 GLN D 354 GLN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15576 Z= 0.364 Angle : 0.614 8.998 20956 Z= 0.306 Chirality : 0.044 0.367 2308 Planarity : 0.004 0.034 2512 Dihedral : 24.117 173.397 2984 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.70 % Allowed : 6.34 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 1800 helix: 1.94 (0.15), residues: 1140 sheet: -1.50 (0.48), residues: 84 loop : -0.93 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 697 HIS 0.002 0.001 HIS A 358 PHE 0.023 0.002 PHE A 649 TYR 0.012 0.002 TYR B 584 ARG 0.003 0.001 ARG B 743 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 183 time to evaluate : 1.747 Fit side-chains REVERT: C 308 MET cc_start: 0.6007 (mtp) cc_final: 0.5765 (mmm) REVERT: C 504 LYS cc_start: 0.7205 (mmtt) cc_final: 0.6130 (mmtt) REVERT: A 308 MET cc_start: 0.6364 (mtp) cc_final: 0.6086 (mmm) REVERT: A 445 MET cc_start: 0.9121 (mmm) cc_final: 0.8757 (mmp) REVERT: A 509 ASP cc_start: 0.7595 (m-30) cc_final: 0.7373 (m-30) REVERT: A 654 ASP cc_start: 0.8399 (m-30) cc_final: 0.8187 (m-30) REVERT: B 308 MET cc_start: 0.6276 (mtp) cc_final: 0.6040 (mmm) REVERT: B 504 LYS cc_start: 0.7558 (mmtt) cc_final: 0.6331 (mmtt) REVERT: B 568 MET cc_start: 0.8084 (mtt) cc_final: 0.7766 (mtt) REVERT: D 369 PHE cc_start: 0.7707 (m-80) cc_final: 0.7355 (m-80) REVERT: D 504 LYS cc_start: 0.7470 (mmtt) cc_final: 0.6209 (mmtt) REVERT: D 743 ARG cc_start: 0.7815 (ttm110) cc_final: 0.7575 (tpp-160) outliers start: 10 outliers final: 5 residues processed: 189 average time/residue: 0.2915 time to fit residues: 81.0967 Evaluate side-chains 187 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 182 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN C 498 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15576 Z= 0.140 Angle : 0.425 6.172 20956 Z= 0.224 Chirality : 0.036 0.179 2308 Planarity : 0.003 0.036 2512 Dihedral : 21.745 177.293 2984 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.85 % Allowed : 7.54 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.20), residues: 1800 helix: 2.54 (0.15), residues: 1128 sheet: -1.25 (0.40), residues: 124 loop : -0.52 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 740 HIS 0.001 0.000 HIS B 378 PHE 0.013 0.001 PHE A 659 TYR 0.006 0.001 TYR D 555 ARG 0.003 0.000 ARG D 721 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 199 time to evaluate : 1.581 Fit side-chains REVERT: C 308 MET cc_start: 0.6058 (mtp) cc_final: 0.5833 (mmm) REVERT: C 387 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8718 (mm) REVERT: C 496 PHE cc_start: 0.7084 (t80) cc_final: 0.6382 (m-10) REVERT: C 504 LYS cc_start: 0.7283 (mmtt) cc_final: 0.6122 (mmtt) REVERT: C 654 ASP cc_start: 0.8497 (m-30) cc_final: 0.8228 (m-30) REVERT: A 308 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.6148 (mmm) REVERT: A 496 PHE cc_start: 0.7228 (t80) cc_final: 0.6598 (m-10) REVERT: A 654 ASP cc_start: 0.8464 (m-30) cc_final: 0.8251 (m-30) REVERT: A 709 GLU cc_start: 0.7071 (tt0) cc_final: 0.6870 (tt0) REVERT: B 308 MET cc_start: 0.6405 (mtp) cc_final: 0.6155 (mmm) REVERT: B 496 PHE cc_start: 0.7184 (t80) cc_final: 0.6513 (m-10) REVERT: B 504 LYS cc_start: 0.7531 (mmtt) cc_final: 0.6357 (mmtt) REVERT: B 568 MET cc_start: 0.8055 (mtt) cc_final: 0.7760 (mtt) REVERT: B 654 ASP cc_start: 0.8490 (m-30) cc_final: 0.8226 (m-30) REVERT: D 369 PHE cc_start: 0.7699 (m-80) cc_final: 0.7416 (m-80) REVERT: D 496 PHE cc_start: 0.7197 (t80) cc_final: 0.6548 (m-10) REVERT: D 504 LYS cc_start: 0.7321 (mmtt) cc_final: 0.6141 (mmtt) outliers start: 12 outliers final: 6 residues processed: 207 average time/residue: 0.2927 time to fit residues: 88.2817 Evaluate side-chains 198 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 387 ILE Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 0 optimal weight: 40.0000 chunk 88 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 43 optimal weight: 0.0270 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 354 GLN A 354 GLN B 354 GLN D 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15576 Z= 0.216 Angle : 0.488 8.137 20956 Z= 0.249 Chirality : 0.038 0.258 2308 Planarity : 0.004 0.036 2512 Dihedral : 21.580 177.374 2984 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.41 % Allowed : 8.24 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.19), residues: 1800 helix: 2.37 (0.15), residues: 1132 sheet: -1.16 (0.50), residues: 84 loop : -0.75 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 740 HIS 0.001 0.000 HIS B 358 PHE 0.016 0.002 PHE D 649 TYR 0.009 0.001 TYR B 530 ARG 0.002 0.000 ARG A 701 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 201 time to evaluate : 1.628 Fit side-chains REVERT: C 308 MET cc_start: 0.6198 (mtp) cc_final: 0.5988 (mmm) REVERT: C 496 PHE cc_start: 0.7162 (t80) cc_final: 0.6429 (m-10) REVERT: C 504 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6290 (mmtt) REVERT: A 308 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.6080 (mmm) REVERT: A 496 PHE cc_start: 0.7240 (t80) cc_final: 0.6588 (m-10) REVERT: A 654 ASP cc_start: 0.8484 (m-30) cc_final: 0.8249 (m-30) REVERT: B 308 MET cc_start: 0.6433 (mtp) cc_final: 0.6166 (mmm) REVERT: B 496 PHE cc_start: 0.7205 (t80) cc_final: 0.6514 (m-10) REVERT: B 504 LYS cc_start: 0.7499 (mmtt) cc_final: 0.6233 (mmtt) REVERT: B 568 MET cc_start: 0.8064 (mtt) cc_final: 0.7738 (mtt) REVERT: B 654 ASP cc_start: 0.8509 (m-30) cc_final: 0.8229 (m-30) REVERT: D 369 PHE cc_start: 0.7751 (m-80) cc_final: 0.7430 (m-80) REVERT: D 496 PHE cc_start: 0.7237 (t80) cc_final: 0.6530 (m-10) REVERT: D 504 LYS cc_start: 0.7425 (mmtt) cc_final: 0.6172 (mmtt) REVERT: D 654 ASP cc_start: 0.8490 (m-30) cc_final: 0.8231 (m-30) outliers start: 20 outliers final: 9 residues processed: 215 average time/residue: 0.2831 time to fit residues: 89.2164 Evaluate side-chains 202 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 192 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 712 PHE Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 102 optimal weight: 10.0000 chunk 42 optimal weight: 0.0970 chunk 174 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15576 Z= 0.197 Angle : 0.458 7.166 20956 Z= 0.237 Chirality : 0.037 0.208 2308 Planarity : 0.003 0.037 2512 Dihedral : 20.733 169.783 2984 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.13 % Allowed : 8.80 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.20), residues: 1800 helix: 2.41 (0.15), residues: 1132 sheet: -0.98 (0.52), residues: 84 loop : -0.75 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 740 HIS 0.001 0.000 HIS B 378 PHE 0.013 0.001 PHE C 649 TYR 0.008 0.001 TYR D 530 ARG 0.002 0.000 ARG D 409 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 193 time to evaluate : 1.511 Fit side-chains REVERT: C 308 MET cc_start: 0.6230 (mtp) cc_final: 0.6014 (mmm) REVERT: C 496 PHE cc_start: 0.7171 (t80) cc_final: 0.6470 (m-10) REVERT: C 504 LYS cc_start: 0.7397 (mmtt) cc_final: 0.6244 (mptt) REVERT: A 308 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.6102 (mmm) REVERT: A 496 PHE cc_start: 0.7262 (t80) cc_final: 0.6631 (m-10) REVERT: A 654 ASP cc_start: 0.8493 (m-30) cc_final: 0.8254 (m-30) REVERT: B 308 MET cc_start: 0.6418 (mtp) cc_final: 0.6171 (mmm) REVERT: B 496 PHE cc_start: 0.7237 (t80) cc_final: 0.6572 (m-10) REVERT: B 504 LYS cc_start: 0.7527 (mmtt) cc_final: 0.6281 (mmtt) REVERT: B 568 MET cc_start: 0.8085 (mtt) cc_final: 0.7753 (mtt) REVERT: D 369 PHE cc_start: 0.7754 (m-80) cc_final: 0.7452 (m-80) REVERT: D 445 MET cc_start: 0.9081 (mmm) cc_final: 0.8694 (mmp) REVERT: D 496 PHE cc_start: 0.7230 (t80) cc_final: 0.6559 (m-10) REVERT: D 504 LYS cc_start: 0.7359 (mmtt) cc_final: 0.6164 (mmtt) REVERT: D 654 ASP cc_start: 0.8491 (m-30) cc_final: 0.8247 (m-30) outliers start: 16 outliers final: 10 residues processed: 205 average time/residue: 0.2868 time to fit residues: 85.4199 Evaluate side-chains 200 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 127 optimal weight: 0.0980 chunk 98 optimal weight: 5.9990 chunk 146 optimal weight: 0.0170 chunk 97 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 0.0970 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 676 ASN D 354 GLN D 676 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15576 Z= 0.108 Angle : 0.384 6.025 20956 Z= 0.205 Chirality : 0.034 0.154 2308 Planarity : 0.003 0.038 2512 Dihedral : 19.014 164.566 2984 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.06 % Allowed : 9.30 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.20), residues: 1800 helix: 2.74 (0.15), residues: 1132 sheet: -0.77 (0.54), residues: 84 loop : -0.49 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 740 HIS 0.002 0.000 HIS C 378 PHE 0.012 0.001 PHE A 659 TYR 0.007 0.001 TYR A 555 ARG 0.001 0.000 ARG C 409 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 1.646 Fit side-chains REVERT: C 308 MET cc_start: 0.6349 (mtp) cc_final: 0.6094 (mmm) REVERT: C 445 MET cc_start: 0.9046 (mmm) cc_final: 0.8643 (mmp) REVERT: C 496 PHE cc_start: 0.7127 (t80) cc_final: 0.6494 (m-10) REVERT: C 504 LYS cc_start: 0.7380 (mmtt) cc_final: 0.6229 (mmtt) REVERT: A 308 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.6089 (mmm) REVERT: A 445 MET cc_start: 0.9029 (mmm) cc_final: 0.8741 (mmp) REVERT: A 496 PHE cc_start: 0.7100 (t80) cc_final: 0.6447 (m-10) REVERT: A 654 ASP cc_start: 0.8378 (m-30) cc_final: 0.8168 (m-30) REVERT: A 709 GLU cc_start: 0.7095 (tt0) cc_final: 0.6872 (tt0) REVERT: B 445 MET cc_start: 0.9026 (mmm) cc_final: 0.8658 (mmp) REVERT: B 496 PHE cc_start: 0.7148 (t80) cc_final: 0.6557 (m-10) REVERT: B 504 LYS cc_start: 0.7515 (mmtt) cc_final: 0.6259 (mmtt) REVERT: B 568 MET cc_start: 0.8145 (mtt) cc_final: 0.7867 (mtt) REVERT: D 369 PHE cc_start: 0.7608 (m-80) cc_final: 0.7353 (m-80) REVERT: D 496 PHE cc_start: 0.7174 (t80) cc_final: 0.6589 (m-10) REVERT: D 504 LYS cc_start: 0.7294 (mmtt) cc_final: 0.6132 (mmtt) REVERT: D 654 ASP cc_start: 0.8396 (m-30) cc_final: 0.8166 (m-30) outliers start: 15 outliers final: 8 residues processed: 204 average time/residue: 0.3189 time to fit residues: 95.3468 Evaluate side-chains 187 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.0870 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15576 Z= 0.317 Angle : 0.554 9.070 20956 Z= 0.279 Chirality : 0.041 0.277 2308 Planarity : 0.004 0.037 2512 Dihedral : 20.908 159.279 2984 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.13 % Allowed : 9.86 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.19), residues: 1800 helix: 2.25 (0.15), residues: 1132 sheet: -0.68 (0.54), residues: 84 loop : -0.89 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 740 HIS 0.003 0.001 HIS B 358 PHE 0.022 0.002 PHE A 649 TYR 0.010 0.002 TYR B 584 ARG 0.002 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.582 Fit side-chains REVERT: C 308 MET cc_start: 0.6378 (mtp) cc_final: 0.6147 (mmm) REVERT: C 496 PHE cc_start: 0.7248 (t80) cc_final: 0.6574 (m-10) REVERT: C 504 LYS cc_start: 0.7375 (mmtt) cc_final: 0.6318 (mptt) REVERT: C 741 CYS cc_start: 0.7927 (m) cc_final: 0.7580 (m) REVERT: A 308 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.6172 (mmm) REVERT: A 496 PHE cc_start: 0.7239 (t80) cc_final: 0.6607 (m-10) REVERT: B 496 PHE cc_start: 0.7210 (t80) cc_final: 0.6585 (m-10) REVERT: B 504 LYS cc_start: 0.7570 (mmtt) cc_final: 0.6360 (mmtt) REVERT: B 568 MET cc_start: 0.8095 (mtt) cc_final: 0.7767 (mtt) REVERT: B 741 CYS cc_start: 0.7914 (m) cc_final: 0.7529 (m) REVERT: D 369 PHE cc_start: 0.7718 (m-80) cc_final: 0.7369 (m-80) REVERT: D 496 PHE cc_start: 0.7248 (t80) cc_final: 0.6593 (m-10) REVERT: D 504 LYS cc_start: 0.7412 (mmtt) cc_final: 0.6180 (mmtt) outliers start: 16 outliers final: 11 residues processed: 187 average time/residue: 0.2919 time to fit residues: 80.0499 Evaluate side-chains 187 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 712 PHE Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 688 LYS Chi-restraints excluded: chain D residue 712 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.0970 chunk 166 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 152 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15576 Z= 0.133 Angle : 0.410 6.703 20956 Z= 0.218 Chirality : 0.035 0.123 2308 Planarity : 0.003 0.038 2512 Dihedral : 19.314 156.996 2984 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.85 % Allowed : 10.35 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.20), residues: 1800 helix: 2.65 (0.15), residues: 1124 sheet: -1.25 (0.44), residues: 124 loop : -0.65 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 740 HIS 0.001 0.000 HIS B 378 PHE 0.012 0.001 PHE B 659 TYR 0.007 0.001 TYR B 530 ARG 0.001 0.000 ARG B 409 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 1.641 Fit side-chains REVERT: C 308 MET cc_start: 0.6377 (mtp) cc_final: 0.6150 (mmm) REVERT: C 445 MET cc_start: 0.9084 (mmm) cc_final: 0.8694 (mmp) REVERT: C 496 PHE cc_start: 0.7196 (t80) cc_final: 0.6556 (m-10) REVERT: C 504 LYS cc_start: 0.7396 (mmtt) cc_final: 0.6180 (mptt) REVERT: C 741 CYS cc_start: 0.7935 (m) cc_final: 0.7612 (m) REVERT: A 308 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.6027 (mmm) REVERT: A 496 PHE cc_start: 0.7209 (t80) cc_final: 0.6597 (m-10) REVERT: B 445 MET cc_start: 0.9073 (mmm) cc_final: 0.8712 (mmp) REVERT: B 496 PHE cc_start: 0.7209 (t80) cc_final: 0.6593 (m-10) REVERT: B 504 LYS cc_start: 0.7508 (mmtt) cc_final: 0.6266 (mmtt) REVERT: B 568 MET cc_start: 0.8067 (mtt) cc_final: 0.7751 (mtt) REVERT: B 741 CYS cc_start: 0.7869 (m) cc_final: 0.7471 (m) REVERT: D 369 PHE cc_start: 0.7539 (m-80) cc_final: 0.7259 (m-80) REVERT: D 445 MET cc_start: 0.9078 (mmm) cc_final: 0.8678 (mmp) REVERT: D 496 PHE cc_start: 0.7229 (t80) cc_final: 0.6602 (m-10) REVERT: D 504 LYS cc_start: 0.7422 (mmtt) cc_final: 0.6185 (mptt) outliers start: 12 outliers final: 10 residues processed: 182 average time/residue: 0.3286 time to fit residues: 86.9340 Evaluate side-chains 186 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 175 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.1980 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 165 optimal weight: 0.3980 chunk 142 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15576 Z= 0.151 Angle : 0.414 4.725 20956 Z= 0.220 Chirality : 0.035 0.114 2308 Planarity : 0.003 0.038 2512 Dihedral : 18.848 150.402 2984 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.77 % Allowed : 10.56 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.20), residues: 1800 helix: 2.68 (0.15), residues: 1124 sheet: -1.15 (0.45), residues: 124 loop : -0.68 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 740 HIS 0.002 0.000 HIS B 378 PHE 0.011 0.001 PHE A 659 TYR 0.008 0.001 TYR C 530 ARG 0.001 0.000 ARG B 409 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 1.722 Fit side-chains REVERT: C 445 MET cc_start: 0.9058 (mmm) cc_final: 0.8665 (mmp) REVERT: C 496 PHE cc_start: 0.7178 (t80) cc_final: 0.6535 (m-10) REVERT: C 504 LYS cc_start: 0.7404 (mmtt) cc_final: 0.6169 (mptt) REVERT: C 536 GLU cc_start: 0.8255 (mp0) cc_final: 0.8055 (mp0) REVERT: C 741 CYS cc_start: 0.7940 (m) cc_final: 0.7596 (m) REVERT: A 308 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.6045 (mmm) REVERT: A 496 PHE cc_start: 0.7141 (t80) cc_final: 0.6528 (m-10) REVERT: B 445 MET cc_start: 0.9082 (mmm) cc_final: 0.8707 (mmp) REVERT: B 496 PHE cc_start: 0.7157 (t80) cc_final: 0.6537 (m-10) REVERT: B 504 LYS cc_start: 0.7499 (mmtt) cc_final: 0.6264 (mmtt) REVERT: B 568 MET cc_start: 0.8114 (mtt) cc_final: 0.7802 (mtt) REVERT: B 741 CYS cc_start: 0.7873 (m) cc_final: 0.7487 (m) REVERT: D 369 PHE cc_start: 0.7529 (m-80) cc_final: 0.7262 (m-80) REVERT: D 445 MET cc_start: 0.9067 (mmm) cc_final: 0.8659 (mmp) REVERT: D 496 PHE cc_start: 0.7193 (t80) cc_final: 0.6560 (m-10) REVERT: D 504 LYS cc_start: 0.7418 (mmtt) cc_final: 0.6179 (mptt) outliers start: 11 outliers final: 10 residues processed: 185 average time/residue: 0.3343 time to fit residues: 90.6519 Evaluate side-chains 194 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 494 GLN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 712 PHE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 494 GLN Chi-restraints excluded: chain D residue 688 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 18 optimal weight: 0.0470 chunk 26 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.187039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.137880 restraints weight = 14955.859| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.47 r_work: 0.2922 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15576 Z= 0.169 Angle : 0.423 4.957 20956 Z= 0.225 Chirality : 0.035 0.116 2308 Planarity : 0.003 0.038 2512 Dihedral : 18.575 152.525 2984 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.92 % Allowed : 10.56 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 1800 helix: 2.62 (0.15), residues: 1124 sheet: -1.12 (0.45), residues: 124 loop : -0.72 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 740 HIS 0.002 0.001 HIS C 378 PHE 0.012 0.001 PHE B 649 TYR 0.008 0.001 TYR D 555 ARG 0.002 0.000 ARG D 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3059.11 seconds wall clock time: 55 minutes 53.50 seconds (3353.50 seconds total)