Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 20:17:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/07_2023/7lpc_23476_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/07_2023/7lpc_23476.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/07_2023/7lpc_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_23476/07_2023/7lpc_23476_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/07_2023/7lpc_23476_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/07_2023/7lpc_23476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/07_2023/7lpc_23476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/07_2023/7lpc_23476_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lpc_23476/07_2023/7lpc_23476_neut_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 189 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: 189 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: 189 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: 189 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: 7.66, per 1000 atoms: 0.50 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: 6.27 Conformation dependent library (CDL) restraints added in 2.1 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: 1.38 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: 4.53 Time building geometry restraints manager: 6.67 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 - 34.08: 8584 34.08 - 68.16: 368 68.16 - 102.24: 40 102.24 - 136.31: 20 136.31 - 170.39: 12 Dihedral angle restraints: 9024 sinusoidal: 3672 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 9021 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.100 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 39.490 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.740 ------------------------------------------------------------------------------- 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 : 20.113 170.393 5572 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 % 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 *********************** 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 : 1.669 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2816 time to fit residues: 75.0638 Evaluate side-chains 159 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3482 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.7781 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 15576 Z= 0.158 Angle : 0.473 5.633 20956 Z= 0.240 Chirality : 0.037 0.198 2308 Planarity : 0.003 0.027 2512 Dihedral : 17.095 128.535 2628 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer Outliers : 0.63 % 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: 2.05 (0.20), residues: 1800 helix: 2.58 (0.15), residues: 1128 sheet: -1.33 (0.45), residues: 84 loop : -0.70 (0.25), residues: 588 *********************** 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 203 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 194 time to evaluate : 1.637 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 200 average time/residue: 0.2833 time to fit residues: 83.1444 Evaluate side-chains 183 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 179 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1498 time to fit residues: 3.3673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 163 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 498 GLN A 354 GLN A 498 GLN B 498 GLN D 354 GLN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.072 15576 Z= 0.448 Angle : 0.685 8.851 20956 Z= 0.339 Chirality : 0.048 0.461 2308 Planarity : 0.004 0.035 2512 Dihedral : 18.898 148.072 2628 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.85 % 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: 0.99 (0.19), residues: 1800 helix: 1.69 (0.15), residues: 1136 sheet: -1.68 (0.48), residues: 84 loop : -1.03 (0.24), residues: 580 *********************** 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 201 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 189 time to evaluate : 1.632 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 195 average time/residue: 0.3099 time to fit residues: 89.6144 Evaluate side-chains 176 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 2.714 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2361 time to fit residues: 4.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 0.5980 chunk 85 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7860 moved from start: 0.3255 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= 0.147 Angle : 0.432 5.690 20956 Z= 0.229 Chirality : 0.036 0.228 2308 Planarity : 0.003 0.036 2512 Dihedral : 15.748 93.887 2628 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer Outliers : 0.42 % 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: 1.89 (0.20), residues: 1800 helix: 2.48 (0.15), residues: 1124 sheet: -1.46 (0.39), residues: 124 loop : -0.70 (0.26), residues: 552 *********************** 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 203 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 1.684 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 202 average time/residue: 0.2943 time to fit residues: 86.4205 Evaluate side-chains 193 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1335 time to fit residues: 2.7360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 2 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 D 354 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 15576 Z= 0.299 Angle : 0.544 7.104 20956 Z= 0.275 Chirality : 0.041 0.332 2308 Planarity : 0.004 0.037 2512 Dihedral : 16.127 91.959 2628 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.85 % 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: 1.44 (0.19), residues: 1800 helix: 2.09 (0.15), residues: 1136 sheet: -1.33 (0.50), residues: 84 loop : -1.03 (0.24), residues: 580 *********************** 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 202 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 190 time to evaluate : 1.656 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 200 average time/residue: 0.2811 time to fit residues: 82.5351 Evaluate side-chains 191 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 185 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1556 time to fit residues: 3.7659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 0.0470 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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: 0.7883 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 15576 Z= 0.174 Angle : 0.444 5.401 20956 Z= 0.232 Chirality : 0.037 0.246 2308 Planarity : 0.003 0.038 2512 Dihedral : 14.510 79.063 2628 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 0.42 % 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: 1.83 (0.20), residues: 1800 helix: 2.42 (0.15), residues: 1128 sheet: -1.22 (0.51), residues: 84 loop : -0.87 (0.24), residues: 588 *********************** 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 200 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 194 time to evaluate : 1.527 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 199 average time/residue: 0.2829 time to fit residues: 82.6774 Evaluate side-chains 190 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1631 time to fit residues: 2.7832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.0980 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 173 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 15576 Z= 0.278 Angle : 0.526 6.873 20956 Z= 0.267 Chirality : 0.040 0.324 2308 Planarity : 0.004 0.038 2512 Dihedral : 15.356 84.763 2628 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer Outliers : 0.49 % 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: 1.53 (0.19), residues: 1800 helix: 2.17 (0.15), residues: 1132 sheet: -1.16 (0.51), residues: 84 loop : -1.01 (0.24), residues: 584 *********************** 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 194 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 1.611 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 190 average time/residue: 0.2930 time to fit residues: 81.3457 Evaluate side-chains 190 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 187 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1561 time to fit residues: 3.1094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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: 0.7861 moved from start: 0.3772 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= 0.138 Angle : 0.417 4.864 20956 Z= 0.221 Chirality : 0.036 0.224 2308 Planarity : 0.003 0.039 2512 Dihedral : 13.328 73.249 2628 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer Outliers : 0.21 % 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: 1.98 (0.20), residues: 1800 helix: 2.57 (0.15), residues: 1128 sheet: -1.00 (0.52), residues: 84 loop : -0.91 (0.24), residues: 588 *********************** 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 193 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 190 time to evaluate : 1.679 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 193 average time/residue: 0.2901 time to fit residues: 81.7588 Evaluate side-chains 185 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 1.746 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1700 time to fit residues: 2.5681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 146 optimal weight: 0.9980 chunk 152 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.7855 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 15576 Z= 0.141 Angle : 0.412 4.757 20956 Z= 0.219 Chirality : 0.036 0.224 2308 Planarity : 0.003 0.039 2512 Dihedral : 12.651 77.093 2628 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 0.21 % 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: 2.66 (0.15), residues: 1128 sheet: -0.74 (0.54), residues: 84 loop : -0.87 (0.24), residues: 588 *********************** 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 189 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.752 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 186 average time/residue: 0.2928 time to fit residues: 79.9294 Evaluate side-chains 186 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1645 time to fit residues: 3.1384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3894 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 : 0.410 4.806 20956 Z= 0.218 Chirality : 0.036 0.221 2308 Planarity : 0.003 0.039 2512 Dihedral : 12.365 79.233 2628 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer Outliers : 0.07 % 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: 2.11 (0.20), residues: 1800 helix: 2.68 (0.15), residues: 1128 sheet: -1.36 (0.44), residues: 124 loop : -0.72 (0.26), residues: 548 ********************** 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: 1 poor density : 188 time to evaluate : 1.636 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 188 average time/residue: 0.2925 time to fit residues: 80.0564 Evaluate side-chains 187 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 1.559 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1285 time to fit residues: 2.3954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 131 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 0.0040 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 0.0040 chunk 18 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 676 ASN A 676 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 676 ASN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.194081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.146954 restraints weight = 14839.189| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.60 r_work: 0.3142 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.4036 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= 0.109 Angle : 0.376 4.829 20956 Z= 0.203 Chirality : 0.034 0.184 2308 Planarity : 0.003 0.040 2512 Dihedral : 11.221 86.072 2628 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.07 % 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: 2.34 (0.20), residues: 1800 helix: 2.82 (0.15), residues: 1128 sheet: -1.25 (0.45), residues: 124 loop : -0.55 (0.27), residues: 548 =============================================================================== Job complete usr+sys time: 2658.24 seconds wall clock time: 49 minutes 20.74 seconds (2960.74 seconds total)