Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 18:06:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhb_13969/07_2023/7qhb_13969_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhb_13969/07_2023/7qhb_13969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhb_13969/07_2023/7qhb_13969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhb_13969/07_2023/7qhb_13969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhb_13969/07_2023/7qhb_13969_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qhb_13969/07_2023/7qhb_13969_updated.pdb" } resolution = 3.5 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= 0.003 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 S 94 5.16 5 Cl 4 4.86 5 C 9886 2.51 5 N 2374 2.21 5 O 2694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 751": "OE1" <-> "OE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B GLU 688": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B GLU 813": "OE1" <-> "OE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 751": "OE1" <-> "OE2" Residue "D GLU 419": "OE1" <-> "OE2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D GLU 688": "OE1" <-> "OE2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "D GLU 813": "OE1" <-> "OE2" Residue "I ARG 48": "NH1" <-> "NH2" Residue "I ARG 231": "NH1" <-> "NH2" Residue "I GLU 232": "OE1" <-> "OE2" Residue "J ARG 48": "NH1" <-> "NH2" Residue "J ARG 231": "NH1" <-> "NH2" Residue "J GLU 232": "OE1" <-> "OE2" Residue "A GLU 1202": "OE1" <-> "OE2" Residue "B GLU 901": "OE1" <-> "OE2" Residue "C GLU 1202": "OE1" <-> "OE2" Residue "D GLU 901": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 15052 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2934 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2999 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2934 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 229 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 13, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2999 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 78 Chain: "I" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1328 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "J" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1328 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 118 Unusual residues: {'79N': 1, 'CYZ': 1, 'OLC': 1, 'PAM': 2} Inner-chain residues flagged as termini: ['pdbres="GLU A1202 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 98 Unusual residues: {'79N': 2, 'CYZ': 1, 'PAM': 1} Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 95 Unusual residues: {'CYZ': 1, 'OLC': 1, 'PAM': 2} Inner-chain residues flagged as termini: ['pdbres="GLU C1202 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {'79N': 1, 'CYZ': 1, 'PAM': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'PAM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'PAM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 7.76, per 1000 atoms: 0.52 Number of scatterers: 15052 At special positions: 0 Unit cell: (126.14, 107.06, 134.62, 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) Cl 4 17.00 S 94 16.00 O 2694 8.00 N 2374 7.00 C 9886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 714 " - pdb=" SG CYS A 769 " distance=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 714 " - pdb=" SG CYS C 769 " distance=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS I 52 " - pdb=" SG CYS I 91 " distance=2.03 Simple disulfide: pdb=" SG CYS I 90 " - pdb=" SG CYS I 100 " distance=2.04 Simple disulfide: pdb=" SG CYS J 52 " - pdb=" SG CYS J 91 " distance=2.03 Simple disulfide: pdb=" SG CYS J 90 " - pdb=" SG CYS J 100 " distance=2.04 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: 5.99 Conformation dependent library (CDL) restraints added in 2.3 seconds 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 18 sheets defined 50.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 413 through 416 Processing helix chain 'A' and resid 420 through 432 Processing helix chain 'A' and resid 458 through 464 Processing helix chain 'A' and resid 479 through 484 removed outlier: 4.040A pdb=" N VAL A 484 " --> pdb=" O VAL A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 541 Processing helix chain 'A' and resid 569 through 581 removed outlier: 3.639A pdb=" N TRP A 574 " --> pdb=" O PHE A 570 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 620 removed outlier: 3.828A pdb=" N PHE A 603 " --> pdb=" O GLY A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 661 through 670 Processing helix chain 'A' and resid 682 through 690 Processing helix chain 'A' and resid 703 through 710 Processing helix chain 'A' and resid 739 through 751 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 785 through 788 Processing helix chain 'A' and resid 790 through 814 Processing helix chain 'B' and resid 424 through 436 Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 523 through 546 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 625 removed outlier: 4.881A pdb=" N ALA B 621 " --> pdb=" O THR B 617 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA B 622 " --> pdb=" O ALA B 618 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 624 " --> pdb=" O LEU B 620 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 743 through 756 Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 789 through 818 removed outlier: 5.269A pdb=" N GLY B 794 " --> pdb=" O SER B 790 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 795 " --> pdb=" O ASN B 791 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 413 through 416 Processing helix chain 'C' and resid 420 through 432 Processing helix chain 'C' and resid 458 through 464 Processing helix chain 'C' and resid 479 through 484 removed outlier: 4.040A pdb=" N VAL C 484 " --> pdb=" O VAL C 480 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 541 Processing helix chain 'C' and resid 569 through 581 removed outlier: 3.640A pdb=" N TRP C 574 " --> pdb=" O PHE C 570 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 620 removed outlier: 3.828A pdb=" N PHE C 603 " --> pdb=" O GLY C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 650 through 657 Processing helix chain 'C' and resid 661 through 670 Processing helix chain 'C' and resid 682 through 690 Processing helix chain 'C' and resid 703 through 710 Processing helix chain 'C' and resid 739 through 751 Processing helix chain 'C' and resid 754 through 763 Processing helix chain 'C' and resid 785 through 788 Processing helix chain 'C' and resid 790 through 814 Processing helix chain 'D' and resid 424 through 436 Processing helix chain 'D' and resid 462 through 468 Processing helix chain 'D' and resid 483 through 486 No H-bonds generated for 'chain 'D' and resid 483 through 486' Processing helix chain 'D' and resid 516 through 518 No H-bonds generated for 'chain 'D' and resid 516 through 518' Processing helix chain 'D' and resid 523 through 546 Processing helix chain 'D' and resid 573 through 584 Processing helix chain 'D' and resid 596 through 625 removed outlier: 4.881A pdb=" N ALA D 621 " --> pdb=" O THR D 617 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA D 622 " --> pdb=" O ALA D 618 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE D 623 " --> pdb=" O ASN D 619 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 624 " --> pdb=" O LEU D 620 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 654 through 661 Processing helix chain 'D' and resid 665 through 675 Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 743 through 756 Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 789 through 818 removed outlier: 5.269A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 39 Processing helix chain 'I' and resid 118 through 127 Processing helix chain 'I' and resid 129 through 150 Processing helix chain 'I' and resid 156 through 183 Processing helix chain 'I' and resid 203 through 233 Processing helix chain 'J' and resid 19 through 39 Processing helix chain 'J' and resid 118 through 127 Processing helix chain 'J' and resid 129 through 150 Processing helix chain 'J' and resid 156 through 183 Processing helix chain 'J' and resid 203 through 233 Processing sheet with id= A, first strand: chain 'A' and resid 391 through 395 Processing sheet with id= B, first strand: chain 'A' and resid 485 through 487 Processing sheet with id= C, first strand: chain 'A' and resid 698 through 700 removed outlier: 3.794A pdb=" N ILE A 498 " --> pdb=" O VAL A 719 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 394 through 399 removed outlier: 6.552A pdb=" N LYS B 439 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 397 " --> pdb=" O LYS B 439 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LYS B 441 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 399 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR B 443 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 451 through 453 removed outlier: 3.905A pdb=" N ALA B 452 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'B' and resid 496 through 499 removed outlier: 3.985A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 702 through 705 removed outlier: 3.798A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 391 through 395 Processing sheet with id= J, first strand: chain 'C' and resid 485 through 487 Processing sheet with id= K, first strand: chain 'C' and resid 698 through 700 removed outlier: 3.794A pdb=" N ILE C 498 " --> pdb=" O VAL C 719 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 394 through 399 removed outlier: 6.552A pdb=" N LYS D 439 " --> pdb=" O VAL D 395 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 397 " --> pdb=" O LYS D 439 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LYS D 441 " --> pdb=" O VAL D 397 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR D 399 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR D 443 " --> pdb=" O THR D 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 451 through 453 removed outlier: 3.905A pdb=" N ALA D 452 " --> pdb=" O ASN D 461 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= O, first strand: chain 'D' and resid 496 through 499 removed outlier: 3.985A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 702 through 705 removed outlier: 3.798A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 45 through 49 Processing sheet with id= R, first strand: chain 'J' and resid 45 through 49 738 hydrogen bonds defined for protein. 2172 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: 4.35 Time building geometry restraints manager: 6.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2348 1.31 - 1.44: 4367 1.44 - 1.57: 8485 1.57 - 1.71: 8 1.71 - 1.84: 146 Bond restraints: 15354 Sorted by residual: bond pdb=" CB THR C 605 " pdb=" CG2 THR C 605 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.70e+01 bond pdb=" CG LEU B 789 " pdb=" CD1 LEU B 789 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.69e+01 bond pdb=" CG LEU D 789 " pdb=" CD1 LEU D 789 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.69e+01 bond pdb=" CB THR A 605 " pdb=" CG2 THR A 605 " ideal model delta sigma weight residual 1.521 1.386 0.135 3.30e-02 9.18e+02 1.68e+01 bond pdb=" CB THR B 609 " pdb=" CG2 THR B 609 " ideal model delta sigma weight residual 1.521 1.386 0.135 3.30e-02 9.18e+02 1.68e+01 ... (remaining 15349 not shown) Histogram of bond angle deviations from ideal: 93.33 - 102.98: 124 102.98 - 112.63: 8382 112.63 - 122.28: 10027 122.28 - 131.94: 2197 131.94 - 141.59: 42 Bond angle restraints: 20772 Sorted by residual: angle pdb=" C10 79N B 904 " pdb=" C9 79N B 904 " pdb=" C8 79N B 904 " ideal model delta sigma weight residual 128.02 141.59 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C10 79N A1206 " pdb=" C9 79N A1206 " pdb=" C8 79N A1206 " ideal model delta sigma weight residual 128.02 141.59 -13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N SER D 741 " pdb=" CA SER D 741 " pdb=" C SER D 741 " ideal model delta sigma weight residual 113.02 108.75 4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" N SER B 741 " pdb=" CA SER B 741 " pdb=" C SER B 741 " ideal model delta sigma weight residual 113.02 108.75 4.27 1.20e+00 6.94e-01 1.27e+01 angle pdb=" CG ARG J 122 " pdb=" CD ARG J 122 " pdb=" NE ARG J 122 " ideal model delta sigma weight residual 112.00 119.81 -7.81 2.20e+00 2.07e-01 1.26e+01 ... (remaining 20767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.97: 8054 18.97 - 37.94: 666 37.94 - 56.91: 160 56.91 - 75.89: 24 75.89 - 94.86: 10 Dihedral angle restraints: 8914 sinusoidal: 3300 harmonic: 5614 Sorted by residual: dihedral pdb=" CB CYS J 52 " pdb=" SG CYS J 52 " pdb=" SG CYS J 91 " pdb=" CB CYS J 91 " ideal model delta sinusoidal sigma weight residual 93.00 133.51 -40.51 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS I 52 " pdb=" SG CYS I 52 " pdb=" SG CYS I 91 " pdb=" CB CYS I 91 " ideal model delta sinusoidal sigma weight residual 93.00 133.50 -40.50 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" C THR B 744 " pdb=" N THR B 744 " pdb=" CA THR B 744 " pdb=" CB THR B 744 " ideal model delta harmonic sigma weight residual -122.00 -133.36 11.36 0 2.50e+00 1.60e-01 2.07e+01 ... (remaining 8911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1989 0.084 - 0.168: 332 0.168 - 0.252: 65 0.252 - 0.336: 4 0.336 - 0.420: 4 Chirality restraints: 2394 Sorted by residual: chirality pdb=" C1 CYZ B 902 " pdb=" C2 CYZ B 902 " pdb=" C6 CYZ B 902 " pdb=" C8 CYZ B 902 " both_signs ideal model delta sigma weight residual False 2.79 2.37 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" C1 CYZ D 902 " pdb=" C2 CYZ D 902 " pdb=" C6 CYZ D 902 " pdb=" C8 CYZ D 902 " both_signs ideal model delta sigma weight residual False 2.79 2.38 0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CB THR C 605 " pdb=" CA THR C 605 " pdb=" OG1 THR C 605 " pdb=" CG2 THR C 605 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 2391 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP J 111 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" CG ASP J 111 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP J 111 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP J 111 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 111 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" CG ASP I 111 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP I 111 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP I 111 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 403 " -0.039 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO D 404 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 404 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 404 " -0.029 5.00e-02 4.00e+02 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 636 2.70 - 3.25: 16702 3.25 - 3.80: 24893 3.80 - 4.35: 30635 4.35 - 4.90: 52586 Nonbonded interactions: 125452 Sorted by model distance: nonbonded pdb=" O1 79N D 903 " pdb=" O3 79N D 903 " model vdw 2.144 2.440 nonbonded pdb=" O1 79N B 903 " pdb=" O3 79N B 903 " model vdw 2.144 2.440 nonbonded pdb=" O THR I 110 " pdb=" OD1 ASP I 111 " model vdw 2.187 3.040 nonbonded pdb=" O THR J 110 " pdb=" OD1 ASP J 111 " model vdw 2.188 3.040 nonbonded pdb=" OG1 THR A 651 " pdb=" OE2 GLU A1202 " model vdw 2.214 2.440 ... (remaining 125447 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 390 or resid 393 through 398 or resid 400 through 403 or r \ esid 405 through 407 or (resid 412 and (name N or name CA or name C or name O or \ name CB )) or resid 413 through 414 or resid 416 through 422 or resid 424 throu \ gh 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 466 or resid 468 t \ hrough 469 or resid 471 or resid 473 through 522 or (resid 523 and (name N or na \ me CA or name C or name O or name CB )) or resid 524 through 542 or (resid 566 a \ nd (name N or name CA or name C or name O or name CB )) or resid 567 through 581 \ or resid 583 through 635 or resid 637 through 646 or resid 649 through 652 or ( \ resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ through 656 or (resid 657 and (name N or name CA or name C or name O or name CB \ )) or resid 658 through 663 or resid 665 through 670 or resid 672 through 682 or \ resid 684 through 685 or resid 688 through 709 or (resid 710 through 712 and (n \ ame N or name CA or name C or name O or name CB )) or resid 713 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 736 or resid 738 or resid 741 through 747 or (resid 748 and (name N or n \ ame CA or name C or name O or name CB )) or resid 749 through 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB )) or resid 755 through 75 \ 9 or resid 761 through 764 or (resid 765 through 766 and (name N or name CA or n \ ame C or name O or name CB )) or resid 767 through 769 or resid 779 through 783 \ or (resid 784 and (name N or name CA or name C or name O or name CB )) or resid \ 785 through 795 or resid 797 through 811 or (resid 812 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 814 or (resid 815 and (name \ N or name CA or name C or name O or name CB )) or resid 1202 through 1203)) selection = (chain 'B' and (resid 394 or resid 397 through 402 or resid 404 through 407 or r \ esid 409 through 411 or resid 416 through 418 or resid 420 through 426 or resid \ 428 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 435 or resid 437 or resid 440 or resid 442 or resid \ 444 through 445 or resid 447 through 448 or (resid 449 and (name N or name CA or \ name C or name O or name CB )) or resid 450 through 453 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thr \ ough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 470 or resid 472 through 473 or resid 475 or resid 477 thro \ ugh 504 or (resid 505 through 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 or (resid 508 through 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 546 or resid 570 through 585 or \ resid 587 through 593 or (resid 594 and (name N or name CA or name C or name O o \ r name CB )) or resid 595 through 632 or (resid 633 through 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 636 or (resid 637 \ through 639 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 1 through 643 or (resid 644 and (name N or name CA or name C or name O or name C \ B )) or resid 645 through 650 or resid 653 through 655 or (resid 656 through 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 6 \ 67 or (resid 669 through 670 and (name N or name CA or name C or name O or name \ CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or name C or \ name O or name CB )) or resid 676 through 686 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 or resid 692 through 693 or ( \ resid 694 through 697 and (name N or name CA or name C or name O or name CB )) o \ r resid 698 or (resid 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 709 or (resid 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 737 or (resid 738 and (name N or name CA \ or name C or name O or name CB )) or resid 739 through 740 or resid 742 or resi \ d 745 through 760 or (resid 761 and (name N or name CA or name C or name O or na \ me CB )) or resid 762 through 763 or resid 765 through 799 or resid 801 through \ 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 814 through 817 or (resid 818 through 819 and (name N or name CA or name C o \ r name O or name CB )) or resid 901 through 902)) selection = (chain 'C' and (resid 390 or resid 393 through 398 or resid 400 through 403 or r \ esid 405 through 407 or (resid 412 and (name N or name CA or name C or name O or \ name CB )) or resid 413 through 414 or resid 416 through 422 or resid 424 throu \ gh 431 or resid 433 or resid 436 or resid 438 or resid 440 through 441 or resid \ 443 through 450 or resid 452 through 454 or resid 456 through 466 or resid 468 t \ hrough 469 or resid 471 or resid 473 through 522 or (resid 523 and (name N or na \ me CA or name C or name O or name CB )) or resid 524 through 542 or (resid 566 a \ nd (name N or name CA or name C or name O or name CB )) or resid 567 through 581 \ or resid 583 through 635 or resid 637 through 646 or resid 649 through 652 or ( \ resid 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ through 656 or (resid 657 and (name N or name CA or name C or name O or name CB \ )) or resid 658 through 663 or resid 665 through 670 or resid 672 through 682 or \ resid 684 through 685 or resid 688 through 709 or (resid 710 through 712 and (n \ ame N or name CA or name C or name O or name CB )) or resid 713 through 714 or ( \ resid 715 and (name N or name CA or name C or name O or name CB )) or resid 716 \ through 736 or resid 738 or resid 741 through 747 or (resid 748 and (name N or n \ ame CA or name C or name O or name CB )) or resid 749 through 753 or (resid 754 \ and (name N or name CA or name C or name O or name CB )) or resid 755 through 75 \ 9 or resid 761 through 764 or (resid 765 through 766 and (name N or name CA or n \ ame C or name O or name CB )) or resid 767 through 769 or resid 779 through 783 \ or (resid 784 and (name N or name CA or name C or name O or name CB )) or resid \ 785 through 795 or resid 797 through 811 or (resid 812 and (name N or name CA or \ name C or name O or name CB )) or resid 813 through 814 or (resid 815 and (name \ N or name CA or name C or name O or name CB )) or resid 1202 through 1203)) selection = (chain 'D' and (resid 394 or resid 397 through 402 or resid 404 through 407 or r \ esid 409 through 411 or resid 416 through 418 or resid 420 through 426 or resid \ 428 through 430 or (resid 431 and (name N or name CA or name C or name O or name \ CB )) or resid 432 through 435 or resid 437 or resid 440 or resid 442 or resid \ 444 through 445 or resid 447 through 448 or (resid 449 and (name N or name CA or \ name C or name O or name CB )) or resid 450 through 453 or (resid 454 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 460 thr \ ough 465 or (resid 466 and (name N or name CA or name C or name O or name CB )) \ or resid 467 through 470 or resid 472 through 473 or resid 475 or resid 477 thro \ ugh 504 or (resid 505 through 506 and (name N or name CA or name C or name O or \ name CB )) or resid 507 or (resid 508 through 509 and (name N or name CA or name \ C or name O or name CB )) or resid 510 through 546 or resid 570 through 585 or \ resid 587 through 593 or (resid 594 and (name N or name CA or name C or name O o \ r name CB )) or resid 595 through 632 or (resid 633 through 634 and (name N or n \ ame CA or name C or name O or name CB )) or resid 635 through 636 or (resid 637 \ through 639 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 1 through 643 or (resid 644 and (name N or name CA or name C or name O or name C \ B )) or resid 645 through 650 or resid 653 through 655 or (resid 656 through 657 \ and (name N or name CA or name C or name O or name CB )) or resid 658 through 6 \ 67 or (resid 669 through 670 and (name N or name CA or name C or name O or name \ CB )) or resid 671 through 673 or (resid 674 and (name N or name CA or name C or \ name O or name CB )) or resid 676 through 686 or (resid 688 and (name N or name \ CA or name C or name O or name CB )) or resid 689 or resid 692 through 693 or ( \ resid 694 through 697 and (name N or name CA or name C or name O or name CB )) o \ r resid 698 or (resid 699 and (name N or name CA or name C or name O or name CB \ )) or resid 700 through 709 or (resid 710 and (name N or name CA or name C or na \ me O or name CB )) or resid 711 through 737 or (resid 738 and (name N or name CA \ or name C or name O or name CB )) or resid 739 through 740 or resid 742 or resi \ d 745 through 760 or (resid 761 and (name N or name CA or name C or name O or na \ me CB )) or resid 762 through 763 or resid 765 through 799 or resid 801 through \ 812 or (resid 813 and (name N or name CA or name C or name O or name CB )) or re \ sid 814 through 817 or (resid 818 through 819 and (name N or name CA or name C o \ r name O or name CB )) or resid 901 through 902)) } ncs_group { reference = chain 'I' selection = chain 'J' } 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 group one per residue 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: 1.860 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: 8.050 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.440 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 : 0.018 0.146 15354 Z= 1.140 Angle : 1.050 13.568 20772 Z= 0.535 Chirality : 0.068 0.420 2394 Planarity : 0.005 0.058 2544 Dihedral : 15.224 94.856 5306 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 21.43 % 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: -2.00 (0.18), residues: 1926 helix: -0.28 (0.15), residues: 1056 sheet: -2.63 (0.35), residues: 172 loop : -2.55 (0.21), residues: 698 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 284 time to evaluate : 1.517 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 286 average time/residue: 0.2617 time to fit residues: 111.7238 Evaluate side-chains 241 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 239 time to evaluate : 1.549 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1391 time to fit residues: 2.6749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 0.0170 chunk 49 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 174 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 20 GLN I 105 HIS ** I 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN J 105 HIS ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 15354 Z= 0.203 Angle : 0.557 8.606 20772 Z= 0.288 Chirality : 0.043 0.211 2394 Planarity : 0.004 0.043 2544 Dihedral : 11.347 88.102 2384 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.15 (0.20), residues: 1926 helix: 1.60 (0.16), residues: 1060 sheet: -2.55 (0.34), residues: 158 loop : -1.61 (0.24), residues: 708 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 277 time to evaluate : 1.582 Fit side-chains outliers start: 10 outliers final: 2 residues processed: 279 average time/residue: 0.2703 time to fit residues: 111.1449 Evaluate side-chains 247 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 245 time to evaluate : 1.569 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1285 time to fit residues: 2.6630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 188 optimal weight: 0.0370 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 HIS I 197 ASN J 83 HIS J 197 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 15354 Z= 0.268 Angle : 0.545 8.616 20772 Z= 0.282 Chirality : 0.042 0.165 2394 Planarity : 0.004 0.040 2544 Dihedral : 10.924 85.411 2384 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.54 (0.20), residues: 1926 helix: 1.86 (0.16), residues: 1062 sheet: -2.30 (0.35), residues: 154 loop : -1.37 (0.24), residues: 710 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 1.732 Fit side-chains outliers start: 28 outliers final: 10 residues processed: 293 average time/residue: 0.2530 time to fit residues: 112.3879 Evaluate side-chains 268 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 258 time to evaluate : 1.689 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1369 time to fit residues: 4.7275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 185 optimal weight: 6.9990 chunk 91 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 756 GLN D 756 GLN I 83 HIS I 105 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 15354 Z= 0.222 Angle : 0.536 9.964 20772 Z= 0.271 Chirality : 0.041 0.159 2394 Planarity : 0.004 0.042 2544 Dihedral : 10.401 83.589 2384 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.73 (0.20), residues: 1926 helix: 1.92 (0.16), residues: 1064 sheet: -2.02 (0.39), residues: 128 loop : -1.22 (0.23), residues: 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 272 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 11 residues processed: 286 average time/residue: 0.2430 time to fit residues: 106.0068 Evaluate side-chains 269 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 258 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1373 time to fit residues: 4.9236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.0870 chunk 105 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN I 105 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 15354 Z= 0.342 Angle : 0.589 9.202 20772 Z= 0.297 Chirality : 0.043 0.149 2394 Planarity : 0.004 0.037 2544 Dihedral : 10.763 85.325 2384 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.49 (0.20), residues: 1926 helix: 1.74 (0.16), residues: 1046 sheet: -2.25 (0.34), residues: 158 loop : -1.18 (0.23), residues: 722 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 279 time to evaluate : 1.483 Fit side-chains outliers start: 23 outliers final: 8 residues processed: 291 average time/residue: 0.2563 time to fit residues: 113.9728 Evaluate side-chains 269 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 261 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1850 time to fit residues: 5.8360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 185 optimal weight: 0.0470 chunk 154 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN J 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 15354 Z= 0.191 Angle : 0.516 11.102 20772 Z= 0.263 Chirality : 0.040 0.159 2394 Planarity : 0.004 0.042 2544 Dihedral : 10.273 84.302 2384 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.82 (0.20), residues: 1926 helix: 2.02 (0.17), residues: 1044 sheet: -2.20 (0.33), residues: 172 loop : -0.97 (0.24), residues: 710 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 276 time to evaluate : 1.699 Fit side-chains outliers start: 19 outliers final: 15 residues processed: 283 average time/residue: 0.2779 time to fit residues: 118.5206 Evaluate side-chains 268 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 253 time to evaluate : 1.778 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1536 time to fit residues: 6.4304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 135 optimal weight: 0.6980 chunk 156 optimal weight: 0.0000 chunk 103 optimal weight: 5.9990 chunk 185 optimal weight: 0.3980 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 15354 Z= 0.197 Angle : 0.521 10.423 20772 Z= 0.262 Chirality : 0.040 0.158 2394 Planarity : 0.004 0.041 2544 Dihedral : 10.010 83.401 2384 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.90 (0.20), residues: 1926 helix: 2.03 (0.17), residues: 1050 sheet: -2.08 (0.34), residues: 172 loop : -0.89 (0.24), residues: 704 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 269 time to evaluate : 1.728 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 275 average time/residue: 0.2726 time to fit residues: 112.9002 Evaluate side-chains 263 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 258 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1460 time to fit residues: 3.7406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 145 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 756 GLN I 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 15354 Z= 0.282 Angle : 0.569 10.210 20772 Z= 0.286 Chirality : 0.042 0.162 2394 Planarity : 0.004 0.060 2544 Dihedral : 10.282 85.841 2384 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.76 (0.20), residues: 1926 helix: 1.91 (0.16), residues: 1048 sheet: -2.07 (0.35), residues: 162 loop : -0.99 (0.24), residues: 716 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 263 time to evaluate : 1.563 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 276 average time/residue: 0.2471 time to fit residues: 104.0344 Evaluate side-chains 271 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 257 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1318 time to fit residues: 5.6724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 chunk 172 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 171 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 15354 Z= 0.259 Angle : 0.546 10.022 20772 Z= 0.277 Chirality : 0.042 0.161 2394 Planarity : 0.004 0.042 2544 Dihedral : 10.076 86.501 2384 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.76 (0.20), residues: 1926 helix: 1.93 (0.16), residues: 1048 sheet: -2.08 (0.34), residues: 180 loop : -0.98 (0.24), residues: 698 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 263 time to evaluate : 1.616 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 268 average time/residue: 0.2447 time to fit residues: 100.4142 Evaluate side-chains 266 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 257 time to evaluate : 1.618 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1437 time to fit residues: 4.5203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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: 0.7240 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 15354 Z= 0.265 Angle : 0.553 10.109 20772 Z= 0.280 Chirality : 0.042 0.165 2394 Planarity : 0.004 0.042 2544 Dihedral : 9.869 86.794 2384 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.75 (0.20), residues: 1926 helix: 1.90 (0.16), residues: 1048 sheet: -1.89 (0.36), residues: 172 loop : -1.01 (0.24), residues: 706 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3852 Ramachandran restraints generated. 1926 Oldfield, 0 Emsley, 1926 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 1.695 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 264 average time/residue: 0.2679 time to fit residues: 108.2237 Evaluate side-chains 260 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 258 time to evaluate : 1.594 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1481 time to fit residues: 2.7228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 140 optimal weight: 0.4980 chunk 22 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 chunk 28 optimal weight: 0.0050 chunk 133 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 198 HIS J 198 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.208393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.179834 restraints weight = 18126.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179054 restraints weight = 37143.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180776 restraints weight = 28583.647| |-----------------------------------------------------------------------------| r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 15354 Z= 0.188 Angle : 0.522 10.746 20772 Z= 0.265 Chirality : 0.040 0.167 2394 Planarity : 0.004 0.061 2544 Dihedral : 9.417 85.575 2384 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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: 0.96 (0.20), residues: 1926 helix: 2.07 (0.17), residues: 1046 sheet: -1.76 (0.36), residues: 172 loop : -0.93 (0.24), residues: 708 =============================================================================== Job complete usr+sys time: 2831.30 seconds wall clock time: 52 minutes 36.07 seconds (3156.07 seconds total)