Starting phenix.real_space_refine on Wed Apr 10 01:07:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/04_2024/8p3q_17392_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/04_2024/8p3q_17392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/04_2024/8p3q_17392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/04_2024/8p3q_17392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/04_2024/8p3q_17392_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3q_17392/04_2024/8p3q_17392_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.047 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 5 5.49 5 S 125 5.16 5 C 11851 2.51 5 N 2840 2.21 5 O 3226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 422": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A GLU 710": "OE1" <-> "OE2" Residue "A ARG 743": "NH1" <-> "NH2" Residue "A GLU 813": "OE1" <-> "OE2" Residue "A GLU 821": "OE1" <-> "OE2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 486": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "B GLU 524": "OE1" <-> "OE2" Residue "B GLU 550": "OE1" <-> "OE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B GLU 710": "OE1" <-> "OE2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "C GLU 466": "OE1" <-> "OE2" Residue "C GLU 486": "OE1" <-> "OE2" Residue "C GLU 487": "OE1" <-> "OE2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 692": "NH1" <-> "NH2" Residue "C GLU 710": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D GLU 466": "OE1" <-> "OE2" Residue "D GLU 486": "OE1" <-> "OE2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D GLU 570": "OE1" <-> "OE2" Residue "D GLU 710": "OE1" <-> "OE2" Residue "E ARG 99": "NH1" <-> "NH2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F GLU 55": "OE1" <-> "OE2" Residue "F GLU 95": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F GLU 191": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18047 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3059 Classifications: {'peptide': 399} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 10} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 386} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3037 Classifications: {'peptide': 398} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 385} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 3024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3024 Classifications: {'peptide': 396} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 383} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 3025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3025 Classifications: {'peptide': 397} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 13} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 384} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "E" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1364 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1373 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 175} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1369 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 82 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "B" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 85 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "F" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 94 Unusual residues: {'PLM': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.28, per 1000 atoms: 0.57 Number of scatterers: 18047 At special positions: 0 Unit cell: (121.422, 119.977, 135.877, 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 125 16.00 P 5 15.00 O 3226 8.00 N 2840 7.00 C 11851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.04 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.02 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.04 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.02 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " 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: 7.23 Conformation dependent library (CDL) restraints added in 3.0 seconds 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4166 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 24 sheets defined 54.9% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... 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 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 462 through 468 Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 523 through 545 Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 576 through 584 Processing helix chain 'A' and resid 596 through 628 Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 654 through 660 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 741 through 756 Proline residue: A 745 - end of helix Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 789 through 820 removed outlier: 5.106A pdb=" N GLY A 794 " --> pdb=" O SER A 790 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 795 " --> pdb=" O ASN A 791 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) 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 417 through 420 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 545 Processing helix chain 'B' and resid 573 through 584 Processing helix chain 'B' and resid 596 through 623 Processing helix chain 'B' and resid 636 through 641 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 676 removed outlier: 3.564A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 741 through 756 Proline residue: B 745 - end of helix Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 793 through 822 removed outlier: 3.776A pdb=" N ALA B 822 " --> pdb=" O SER B 818 " (cutoff:3.500A) 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 417 through 420 Processing helix chain 'C' and resid 424 through 436 Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 483 through 486 No H-bonds generated for 'chain 'C' and resid 483 through 486' Processing helix chain 'C' and resid 516 through 518 No H-bonds generated for 'chain 'C' and resid 516 through 518' Processing helix chain 'C' and resid 523 through 545 Processing helix chain 'C' and resid 548 through 550 No H-bonds generated for 'chain 'C' and resid 548 through 550' Processing helix chain 'C' and resid 573 through 584 Processing helix chain 'C' and resid 596 through 624 Processing helix chain 'C' and resid 636 through 640 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 665 through 676 removed outlier: 3.927A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.562A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 756 removed outlier: 3.584A pdb=" N THR C 744 " --> pdb=" O SER C 741 " (cutoff:3.500A) Proline residue: C 745 - end of helix removed outlier: 3.501A pdb=" N ALA C 749 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN C 756 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 789 through 819 removed outlier: 5.607A pdb=" N GLY C 794 " --> pdb=" O SER C 790 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL C 795 " --> pdb=" O ASN C 791 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) 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 417 through 420 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 544 Processing helix chain 'D' and resid 573 through 584 removed outlier: 3.646A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 625 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 removed outlier: 3.566A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 755 Proline residue: D 745 - end of helix Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 789 through 822 removed outlier: 5.450A pdb=" N GLY D 794 " --> pdb=" O SER D 790 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL D 795 " --> pdb=" O ASN D 791 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 29 Processing helix chain 'E' and resid 93 through 103 Processing helix chain 'E' and resid 106 through 125 Processing helix chain 'E' and resid 134 through 160 Processing helix chain 'E' and resid 178 through 209 Processing helix chain 'F' and resid 6 through 29 Processing helix chain 'F' and resid 93 through 103 Processing helix chain 'F' and resid 106 through 126 removed outlier: 4.102A pdb=" N GLU F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 159 Processing helix chain 'F' and resid 178 through 208 Processing helix chain 'G' and resid 8 through 29 Processing helix chain 'G' and resid 93 through 103 Processing helix chain 'G' and resid 106 through 126 removed outlier: 3.745A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 161 Processing helix chain 'G' and resid 178 through 209 Processing helix chain 'H' and resid 6 through 29 removed outlier: 3.521A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 11 " --> pdb=" O GLY H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 106 through 125 Processing helix chain 'H' and resid 133 through 160 Processing helix chain 'H' and resid 178 through 209 Processing sheet with id= A, first strand: chain 'A' and resid 395 through 399 Processing sheet with id= B, first strand: chain 'A' and resid 489 through 491 Processing sheet with id= C, first strand: chain 'A' and resid 502 through 505 removed outlier: 3.725A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 646 through 648 Processing sheet with id= E, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.688A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 394 through 399 removed outlier: 6.272A pdb=" N LYS B 439 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 397 " --> pdb=" O LYS B 439 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LYS B 441 " --> pdb=" O VAL B 397 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR B 399 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N THR B 443 " --> pdb=" O THR B 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= H, first strand: chain 'B' and resid 496 through 498 removed outlier: 3.860A pdb=" N MET B 496 " --> pdb=" O TYR B 732 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 720 through 723 removed outlier: 5.248A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 394 through 399 removed outlier: 6.089A pdb=" N LYS C 439 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 397 " --> pdb=" O LYS C 439 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LYS C 441 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR C 399 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR C 443 " --> pdb=" O THR C 399 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= L, first strand: chain 'C' and resid 502 through 505 Processing sheet with id= M, first strand: chain 'C' and resid 646 through 648 removed outlier: 3.674A pdb=" N GLY C 648 " --> pdb=" O ALA C 701 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.589A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= P, first strand: chain 'D' and resid 496 through 498 Processing sheet with id= Q, first strand: chain 'D' and resid 720 through 723 removed outlier: 3.738A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET D 503 " --> pdb=" O TYR D 702 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR D 702 " --> pdb=" O MET D 503 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 11.540A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 489 through 494 removed outlier: 3.684A pdb=" N ILE D 734 " --> pdb=" O SER D 492 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= T, first strand: chain 'F' and resid 36 through 38 Processing sheet with id= U, first strand: chain 'F' and resid 65 through 67 Processing sheet with id= V, first strand: chain 'G' and resid 57 through 61 Processing sheet with id= W, first strand: chain 'G' and resid 65 through 67 Processing sheet with id= X, first strand: chain 'H' and resid 36 through 38 959 hydrogen bonds defined for protein. 2754 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: 6.58 Time building geometry restraints manager: 7.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2800 1.32 - 1.45: 5145 1.45 - 1.58: 10263 1.58 - 1.71: 10 1.71 - 1.84: 202 Bond restraints: 18420 Sorted by residual: bond pdb=" C VAL B 484 " pdb=" N ARG B 485 " ideal model delta sigma weight residual 1.334 1.410 -0.075 1.33e-02 5.65e+03 3.22e+01 bond pdb=" C ALA C 691 " pdb=" N ARG C 692 " ideal model delta sigma weight residual 1.335 1.392 -0.057 1.31e-02 5.83e+03 1.90e+01 bond pdb=" CA SER C 537 " pdb=" CB SER C 537 " ideal model delta sigma weight residual 1.528 1.464 0.065 1.56e-02 4.11e+03 1.74e+01 bond pdb=" C LEU A 742 " pdb=" N ARG A 743 " ideal model delta sigma weight residual 1.335 1.387 -0.053 1.27e-02 6.20e+03 1.71e+01 bond pdb=" CA SER D 537 " pdb=" CB SER D 537 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.55e-02 4.16e+03 1.63e+01 ... (remaining 18415 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.87: 348 105.87 - 113.07: 9337 113.07 - 120.27: 8919 120.27 - 127.46: 6052 127.46 - 134.66: 153 Bond angle restraints: 24809 Sorted by residual: angle pdb=" O VAL B 484 " pdb=" C VAL B 484 " pdb=" N ARG B 485 " ideal model delta sigma weight residual 121.87 131.47 -9.60 1.01e+00 9.80e-01 9.04e+01 angle pdb=" CA ALA B 477 " pdb=" C ALA B 477 " pdb=" N PRO B 478 " ideal model delta sigma weight residual 117.68 122.31 -4.63 7.10e-01 1.98e+00 4.26e+01 angle pdb=" O MET D 674 " pdb=" C MET D 674 " pdb=" N ARG D 675 " ideal model delta sigma weight residual 122.12 128.81 -6.69 1.06e+00 8.90e-01 3.99e+01 angle pdb=" O ALA D 452 " pdb=" C ALA D 452 " pdb=" N ARG D 453 " ideal model delta sigma weight residual 123.41 116.30 7.11 1.17e+00 7.31e-01 3.70e+01 angle pdb=" CA GLU D 678 " pdb=" C GLU D 678 " pdb=" O GLU D 678 " ideal model delta sigma weight residual 119.99 114.87 5.12 8.70e-01 1.32e+00 3.46e+01 ... (remaining 24804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 10106 31.57 - 63.15: 621 63.15 - 94.72: 44 94.72 - 126.29: 5 126.29 - 157.87: 2 Dihedral angle restraints: 10778 sinusoidal: 4237 harmonic: 6541 Sorted by residual: dihedral pdb=" CB CYS H 40 " pdb=" SG CYS H 40 " pdb=" SG CYS H 68 " pdb=" CB CYS H 68 " ideal model delta sinusoidal sigma weight residual 93.00 4.92 88.08 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS F 40 " pdb=" SG CYS F 40 " pdb=" SG CYS F 68 " pdb=" CB CYS F 68 " ideal model delta sinusoidal sigma weight residual 93.00 12.31 80.69 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS G 40 " pdb=" SG CYS G 40 " pdb=" SG CYS G 68 " pdb=" CB CYS G 68 " ideal model delta sinusoidal sigma weight residual -86.00 -13.66 -72.34 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 10775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1670 0.069 - 0.137: 891 0.137 - 0.206: 181 0.206 - 0.275: 19 0.275 - 0.344: 7 Chirality restraints: 2768 Sorted by residual: chirality pdb=" CB VAL B 543 " pdb=" CA VAL B 543 " pdb=" CG1 VAL B 543 " pdb=" CG2 VAL B 543 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CG LEU A 498 " pdb=" CB LEU A 498 " pdb=" CD1 LEU A 498 " pdb=" CD2 LEU A 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CG LEU B 498 " pdb=" CB LEU B 498 " pdb=" CD1 LEU B 498 " pdb=" CD2 LEU B 498 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 2765 not shown) Planarity restraints: 3018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV G1103 " 0.026 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C29 POV G1103 " -0.064 2.00e-02 2.50e+03 pdb="C210 POV G1103 " 0.064 2.00e-02 2.50e+03 pdb="C211 POV G1103 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 541 " 0.028 2.00e-02 2.50e+03 3.15e-02 1.74e+01 pdb=" CG PHE B 541 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE B 541 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 541 " -0.061 2.00e-02 2.50e+03 pdb=" CE1 PHE B 541 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE B 541 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 541 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 485 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C ARG B 485 " 0.064 2.00e-02 2.50e+03 pdb=" O ARG B 485 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU B 486 " -0.022 2.00e-02 2.50e+03 ... (remaining 3015 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6069 2.83 - 3.35: 18498 3.35 - 3.86: 32918 3.86 - 4.38: 39227 4.38 - 4.90: 61033 Nonbonded interactions: 157745 Sorted by model distance: nonbonded pdb=" O ARG A 453 " pdb=" C ASP A 454 " model vdw 2.310 3.270 nonbonded pdb=" O LEU E 63 " pdb=" NH2 ARG E 102 " model vdw 2.363 2.520 nonbonded pdb=" O ARG G 6 " pdb=" N VAL G 8 " model vdw 2.365 2.520 nonbonded pdb=" O ARG D 743 " pdb=" N ASN D 747 " model vdw 2.428 2.520 nonbonded pdb=" O SER E 104 " pdb=" OG SER E 104 " model vdw 2.433 2.440 ... (remaining 157740 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 393 through 593 or (resid 594 and (name N or name CA or na \ me C or name O or name CB )) or resid 595 through 625 or resid 635 through 812 o \ r (resid 813 and (name N or name CA or name C or name O or name CB )) or resid 8 \ 14 through 818 or (resid 819 through 823 and (name N or name CA or name C or nam \ e O or name CB )))) selection = (chain 'B' and (resid 393 through 510 or (resid 511 and (name N or name CA or na \ me C or name O or name CB )) or resid 512 through 551 or (resid 569 and (name N \ or name CA or name C or name O or name CB )) or resid 570 through 593 or (resid \ 594 and (name N or name CA or name C or name O or name CB )) or resid 595 throug \ h 625 or resid 635 through 773 or resid 785 through 823)) selection = (chain 'C' and (resid 393 through 625 or resid 635 through 812 or (resid 813 and \ (name N or name CA or name C or name O or name CB )) or resid 814 through 818 o \ r (resid 819 through 823 and (name N or name CA or name C or name O or name CB ) \ ))) selection = (chain 'D' and (resid 393 through 551 or (resid 569 and (name N or name CA or na \ me C or name O or name CB )) or resid 570 through 593 or (resid 594 and (name N \ or name CA or name C or name O or name CB )) or resid 595 through 625 or resid 6 \ 35 through 773 or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 21 \ 0)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 206 or (resid 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 206 or (resid 207 and (na \ me N or name CA or name C or name O or name CB )) or resid 208 through 210)) } 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.570 Check model and map are aligned: 0.270 Set scattering table: 0.150 Process input model: 49.730 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.090 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 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 : 0.010 0.075 18420 Z= 0.622 Angle : 1.369 9.604 24809 Z= 0.947 Chirality : 0.080 0.344 2768 Planarity : 0.009 0.076 3018 Dihedral : 18.610 157.867 6576 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.98 % Allowed : 5.86 % Favored : 93.15 % Rotamer: Outliers : 9.79 % Allowed : 8.42 % Favored : 81.79 % Cbeta Deviations : 0.10 % 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: -1.51 (0.16), residues: 2235 helix: 0.03 (0.14), residues: 1302 sheet: -2.14 (0.38), residues: 126 loop : -2.49 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.007 TRP A 606 HIS 0.018 0.005 HIS D 435 PHE 0.061 0.007 PHE B 541 TYR 0.038 0.006 TYR D 549 ARG 0.041 0.004 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 325 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7294 (mmt) REVERT: A 481 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8605 (OUTLIER) REVERT: A 503 MET cc_start: 0.7829 (ttm) cc_final: 0.7314 (ptm) REVERT: A 506 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8180 (ttmm) REVERT: A 713 GLU cc_start: 0.9325 (tt0) cc_final: 0.8923 (tp30) REVERT: A 721 MET cc_start: 0.9029 (ttt) cc_final: 0.8661 (tpp) REVERT: B 543 VAL cc_start: 0.9041 (OUTLIER) cc_final: 0.8733 (m) REVERT: B 586 ARG cc_start: 0.9324 (mmm-85) cc_final: 0.8873 (mmm160) REVERT: B 770 LYS cc_start: 0.4185 (OUTLIER) cc_final: 0.3138 (mmmt) REVERT: C 407 MET cc_start: 0.2826 (OUTLIER) cc_final: 0.1439 (ptt) REVERT: C 408 MET cc_start: 0.1356 (mmm) cc_final: 0.0498 (pmm) REVERT: C 414 MET cc_start: 0.5990 (OUTLIER) cc_final: 0.4498 (ptt) REVERT: C 633 ILE cc_start: 0.5540 (OUTLIER) cc_final: 0.5308 (mm) REVERT: C 647 TYR cc_start: 0.3256 (p90) cc_final: 0.2299 (p90) REVERT: C 666 VAL cc_start: 0.4182 (OUTLIER) cc_final: 0.3961 (p) REVERT: C 714 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7927 (mp10) REVERT: C 819 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8450 (ttt-90) REVERT: E 57 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.9025 (p) REVERT: E 69 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8944 (pt) REVERT: E 76 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9151 (mm) REVERT: E 95 GLU cc_start: 0.9414 (mm-30) cc_final: 0.8931 (tp30) REVERT: F 9 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8951 (mt0) REVERT: F 10 MET cc_start: 0.9339 (tpp) cc_final: 0.8998 (mmm) REVERT: F 24 MET cc_start: 0.8564 (tpt) cc_final: 0.7937 (tpp) REVERT: F 69 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8931 (pt) REVERT: F 81 ASP cc_start: 0.9109 (t0) cc_final: 0.8649 (t0) REVERT: F 95 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: F 99 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8646 (mtm180) REVERT: G 37 ARG cc_start: 0.8543 (mtp85) cc_final: 0.8143 (mmm-85) REVERT: G 41 LYS cc_start: 0.8533 (tptp) cc_final: 0.8130 (pptt) REVERT: G 131 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8490 (mmm160) REVERT: G 207 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9132 (pt0) REVERT: H 5 ASP cc_start: 0.6294 (m-30) cc_final: 0.5906 (m-30) REVERT: H 9 GLN cc_start: 0.8586 (mt0) cc_final: 0.8324 (mp-120) REVERT: H 41 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8279 (tptp) REVERT: H 78 LYS cc_start: 0.9146 (ptmt) cc_final: 0.8436 (pttm) REVERT: H 81 ASP cc_start: 0.9296 (t70) cc_final: 0.9060 (t70) REVERT: H 207 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8519 (mm110) outliers start: 178 outliers final: 41 residues processed: 468 average time/residue: 1.4913 time to fit residues: 772.4361 Evaluate side-chains 248 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 190 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 409 LYS Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 654 SER Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 791 ASN Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 817 LYS Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 485 ARG Chi-restraints excluded: chain C residue 486 GLU Chi-restraints excluded: chain C residue 595 SER Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 768 TYR Chi-restraints excluded: chain C residue 819 ARG Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 692 ARG Chi-restraints excluded: chain D residue 759 LEU Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 78 LYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 186 SER Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 40 CYS Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 203 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN A 619 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 HIS C 587 GLN C 709 ASN D 569 ASN D 587 GLN D 619 ASN D 756 GLN D 791 ASN E 132 HIS E 160 ASN E 199 HIS F 60 HIS F 132 HIS F 160 ASN F 205 HIS G 160 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18420 Z= 0.202 Angle : 0.612 10.266 24809 Z= 0.319 Chirality : 0.041 0.188 2768 Planarity : 0.004 0.040 3018 Dihedral : 13.257 111.328 2932 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.18 % Favored : 96.55 % Rotamer: Outliers : 4.95 % Allowed : 17.99 % Favored : 77.06 % 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: 0.46 (0.18), residues: 2235 helix: 1.73 (0.15), residues: 1316 sheet: -2.31 (0.38), residues: 124 loop : -1.75 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 766 HIS 0.006 0.001 HIS D 435 PHE 0.019 0.001 PHE H 127 TYR 0.018 0.002 TYR D 711 ARG 0.006 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 241 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7908 (mmm) cc_final: 0.7488 (mmt) REVERT: A 503 MET cc_start: 0.7822 (ttm) cc_final: 0.7243 (ptm) REVERT: A 587 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7832 (tp-100) REVERT: A 759 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6221 (mt) REVERT: B 408 MET cc_start: 0.6392 (mmm) cc_final: 0.5935 (mpp) REVERT: B 527 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8133 (mtp) REVERT: B 586 ARG cc_start: 0.9071 (mmm-85) cc_final: 0.8724 (mmm160) REVERT: B 770 LYS cc_start: 0.4095 (OUTLIER) cc_final: 0.3190 (mmmt) REVERT: C 407 MET cc_start: 0.2144 (ptt) cc_final: 0.1934 (ptt) REVERT: C 414 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.5732 (ptt) REVERT: C 463 MET cc_start: 0.2830 (mtm) cc_final: 0.1865 (ptp) REVERT: C 496 MET cc_start: 0.3564 (mtt) cc_final: 0.2309 (tpt) REVERT: C 674 MET cc_start: 0.3706 (mtt) cc_final: 0.3471 (mtp) REVERT: C 714 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7898 (mp10) REVERT: D 414 MET cc_start: 0.5225 (OUTLIER) cc_final: 0.4387 (pp-130) REVERT: E 5 ASP cc_start: 0.5819 (OUTLIER) cc_final: 0.5210 (p0) REVERT: E 37 ARG cc_start: 0.9095 (ttm-80) cc_final: 0.8731 (ttm-80) REVERT: E 95 GLU cc_start: 0.9339 (mm-30) cc_final: 0.9020 (tp30) REVERT: E 102 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8480 (tpt90) REVERT: F 6 ARG cc_start: 0.8715 (tpt90) cc_final: 0.8394 (tpt90) REVERT: F 69 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8019 (pt) REVERT: F 81 ASP cc_start: 0.9215 (t0) cc_final: 0.8803 (t0) REVERT: F 95 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8699 (tp30) REVERT: G 37 ARG cc_start: 0.8839 (mtp85) cc_final: 0.8554 (mtp85) REVERT: G 95 GLU cc_start: 0.9178 (tt0) cc_final: 0.8958 (tp30) REVERT: G 99 ARG cc_start: 0.9334 (mtt-85) cc_final: 0.9091 (ptp-110) REVERT: G 207 GLN cc_start: 0.9349 (mm-40) cc_final: 0.9098 (pt0) REVERT: H 5 ASP cc_start: 0.5642 (m-30) cc_final: 0.4887 (m-30) REVERT: H 6 ARG cc_start: 0.8101 (tmm160) cc_final: 0.7893 (tmm160) REVERT: H 9 GLN cc_start: 0.8481 (mt0) cc_final: 0.7979 (mp10) REVERT: H 78 LYS cc_start: 0.9006 (ptmt) cc_final: 0.8315 (pttm) REVERT: H 81 ASP cc_start: 0.9290 (t70) cc_final: 0.9045 (t0) outliers start: 90 outliers final: 26 residues processed: 312 average time/residue: 1.2740 time to fit residues: 446.4779 Evaluate side-chains 219 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 2.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 527 MET Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 675 ARG Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 692 ARG Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 137 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 202 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN D 619 ASN F 9 GLN F 160 ASN G 160 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18420 Z= 0.387 Angle : 0.641 10.467 24809 Z= 0.332 Chirality : 0.043 0.200 2768 Planarity : 0.004 0.046 3018 Dihedral : 11.812 89.811 2841 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.47 % Favored : 95.26 % Rotamer: Outliers : 5.45 % Allowed : 19.25 % Favored : 75.30 % 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 (0.18), residues: 2235 helix: 1.94 (0.15), residues: 1319 sheet: -2.64 (0.39), residues: 118 loop : -1.54 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 766 HIS 0.007 0.001 HIS G 60 PHE 0.024 0.002 PHE D 495 TYR 0.018 0.002 TYR B 523 ARG 0.008 0.001 ARG C 660 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 182 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.8120 (mmm) cc_final: 0.7735 (mmt) REVERT: A 495 PHE cc_start: 0.7455 (p90) cc_final: 0.7206 (p90) REVERT: A 496 MET cc_start: 0.6908 (mmm) cc_final: 0.6587 (mmm) REVERT: A 503 MET cc_start: 0.7641 (ttm) cc_final: 0.6945 (ptm) REVERT: A 587 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8289 (tp-100) REVERT: A 759 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6662 (mt) REVERT: B 586 ARG cc_start: 0.9262 (mmm-85) cc_final: 0.8853 (mmm160) REVERT: C 414 MET cc_start: 0.7289 (mtm) cc_final: 0.5783 (ptt) REVERT: C 463 MET cc_start: 0.2497 (mtm) cc_final: 0.1130 (ptp) REVERT: C 496 MET cc_start: 0.3741 (mtt) cc_final: 0.2887 (tpt) REVERT: C 647 TYR cc_start: 0.2400 (p90) cc_final: 0.1839 (p90) REVERT: C 670 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6755 (pmm) REVERT: C 714 GLN cc_start: 0.8097 (mm-40) cc_final: 0.7629 (mp10) REVERT: D 408 MET cc_start: 0.4749 (tpp) cc_final: 0.4182 (tpp) REVERT: D 414 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5116 (pp-130) REVERT: E 5 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5519 (p0) REVERT: E 37 ARG cc_start: 0.9099 (ttm-80) cc_final: 0.8741 (ttm-80) REVERT: E 95 GLU cc_start: 0.9352 (mm-30) cc_final: 0.9115 (tm-30) REVERT: F 6 ARG cc_start: 0.8601 (tpt90) cc_final: 0.8395 (tpt90) REVERT: F 10 MET cc_start: 0.9264 (mmm) cc_final: 0.9029 (mmm) REVERT: F 69 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8640 (pt) REVERT: F 81 ASP cc_start: 0.9208 (t0) cc_final: 0.8840 (t0) REVERT: F 95 GLU cc_start: 0.9162 (tp30) cc_final: 0.8829 (tp30) REVERT: G 56 GLU cc_start: 0.8856 (tp30) cc_final: 0.8647 (tp30) REVERT: G 99 ARG cc_start: 0.9385 (mtt-85) cc_final: 0.9154 (ptp-110) REVERT: H 5 ASP cc_start: 0.6181 (m-30) cc_final: 0.5485 (m-30) REVERT: H 9 GLN cc_start: 0.8865 (mt0) cc_final: 0.8511 (mp10) REVERT: H 78 LYS cc_start: 0.8904 (ptmt) cc_final: 0.8405 (ptpt) REVERT: H 203 ASP cc_start: 0.9425 (OUTLIER) cc_final: 0.9197 (t0) outliers start: 99 outliers final: 49 residues processed: 262 average time/residue: 1.2979 time to fit residues: 381.6261 Evaluate side-chains 219 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 163 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 587 GLN Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain C residue 670 MET Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 60 HIS Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 73 PHE Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 106 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN D 569 ASN D 619 ASN F 60 HIS F 160 ASN F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18420 Z= 0.169 Angle : 0.539 9.797 24809 Z= 0.278 Chirality : 0.039 0.172 2768 Planarity : 0.004 0.045 3018 Dihedral : 10.670 87.805 2823 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.22 % Favored : 96.55 % Rotamer: Outliers : 4.29 % Allowed : 20.41 % Favored : 75.30 % 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: 1.25 (0.19), residues: 2235 helix: 2.36 (0.15), residues: 1321 sheet: -2.23 (0.43), residues: 105 loop : -1.43 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 766 HIS 0.004 0.001 HIS F 205 PHE 0.023 0.001 PHE D 495 TYR 0.014 0.001 TYR D 732 ARG 0.007 0.001 ARG G 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 196 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7709 (mpp) cc_final: 0.7506 (mpp) REVERT: A 503 MET cc_start: 0.7490 (ttm) cc_final: 0.6957 (ptm) REVERT: B 408 MET cc_start: 0.6520 (mmm) cc_final: 0.6226 (mpp) REVERT: B 463 MET cc_start: -0.2047 (ptp) cc_final: -0.2557 (ptp) REVERT: B 586 ARG cc_start: 0.9246 (mmm-85) cc_final: 0.8823 (mmm160) REVERT: C 407 MET cc_start: 0.1528 (OUTLIER) cc_final: 0.0765 (ppp) REVERT: C 414 MET cc_start: 0.7440 (mtm) cc_final: 0.5893 (ptt) REVERT: C 463 MET cc_start: 0.2025 (mtm) cc_final: 0.1622 (ptp) REVERT: C 496 MET cc_start: 0.3638 (mtt) cc_final: 0.2797 (tpt) REVERT: C 647 TYR cc_start: 0.1821 (p90) cc_final: 0.1253 (p90) REVERT: C 670 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.7000 (ptp) REVERT: C 675 ARG cc_start: 0.4096 (OUTLIER) cc_final: 0.3750 (mtt90) REVERT: C 714 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7573 (mp10) REVERT: D 408 MET cc_start: 0.4995 (tpp) cc_final: 0.4754 (tpp) REVERT: D 414 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.4819 (pp-130) REVERT: D 590 ASP cc_start: 0.8456 (m-30) cc_final: 0.8235 (t0) REVERT: E 5 ASP cc_start: 0.5776 (OUTLIER) cc_final: 0.5277 (p0) REVERT: E 37 ARG cc_start: 0.9136 (ttm-80) cc_final: 0.8824 (ttm-80) REVERT: E 95 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9133 (tm-30) REVERT: E 99 ARG cc_start: 0.9134 (mtt180) cc_final: 0.8883 (mtm180) REVERT: F 6 ARG cc_start: 0.8537 (tpt90) cc_final: 0.8288 (tpt90) REVERT: F 10 MET cc_start: 0.9262 (mmm) cc_final: 0.9049 (mmm) REVERT: F 69 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8611 (pt) REVERT: F 81 ASP cc_start: 0.9131 (t0) cc_final: 0.8766 (t0) REVERT: F 95 GLU cc_start: 0.9152 (tp30) cc_final: 0.8775 (tp30) REVERT: G 58 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8550 (mmp) REVERT: G 60 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.8577 (p90) REVERT: H 5 ASP cc_start: 0.6039 (m-30) cc_final: 0.5519 (m-30) REVERT: H 9 GLN cc_start: 0.8824 (mt0) cc_final: 0.8566 (mp10) REVERT: H 78 LYS cc_start: 0.9146 (ptmt) cc_final: 0.8763 (pttm) REVERT: H 203 ASP cc_start: 0.9444 (t0) cc_final: 0.9231 (t0) outliers start: 78 outliers final: 27 residues processed: 257 average time/residue: 1.2842 time to fit residues: 370.9345 Evaluate side-chains 201 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 670 MET Chi-restraints excluded: chain C residue 675 ARG Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain D residue 414 MET Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 68 CYS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 128 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 161 optimal weight: 0.0050 chunk 89 optimal weight: 20.0000 chunk 184 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 110 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 overall best weight: 2.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 569 ASN D 619 ASN F 160 ASN G 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18420 Z= 0.372 Angle : 0.633 12.546 24809 Z= 0.326 Chirality : 0.042 0.240 2768 Planarity : 0.004 0.046 3018 Dihedral : 10.803 89.591 2812 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.34 % Favored : 95.44 % Rotamer: Outliers : 5.28 % Allowed : 20.52 % Favored : 74.20 % 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: 1.12 (0.18), residues: 2235 helix: 2.22 (0.15), residues: 1323 sheet: -2.36 (0.39), residues: 123 loop : -1.39 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 766 HIS 0.005 0.001 HIS E 60 PHE 0.023 0.002 PHE D 495 TYR 0.022 0.002 TYR C 711 ARG 0.009 0.001 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 167 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.7018 (mpp) REVERT: A 495 PHE cc_start: 0.6853 (p90) cc_final: 0.6382 (p90) REVERT: A 503 MET cc_start: 0.7613 (ttm) cc_final: 0.7138 (ptm) REVERT: B 408 MET cc_start: 0.6685 (mmm) cc_final: 0.6345 (mpp) REVERT: B 586 ARG cc_start: 0.9293 (mmm-85) cc_final: 0.8810 (mmm160) REVERT: C 414 MET cc_start: 0.7427 (mtm) cc_final: 0.5871 (ptt) REVERT: C 463 MET cc_start: 0.1589 (mtm) cc_final: 0.1250 (ptp) REVERT: C 496 MET cc_start: 0.3892 (mtt) cc_final: 0.2667 (tpt) REVERT: C 670 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6532 (ptp) REVERT: C 714 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7705 (mp10) REVERT: D 414 MET cc_start: 0.6269 (mtm) cc_final: 0.5193 (pp-130) REVERT: D 569 ASN cc_start: 0.8157 (m-40) cc_final: 0.7625 (p0) REVERT: D 736 THR cc_start: 0.4698 (OUTLIER) cc_final: 0.4186 (t) REVERT: E 5 ASP cc_start: 0.6094 (OUTLIER) cc_final: 0.5743 (p0) REVERT: E 37 ARG cc_start: 0.9230 (ttm-80) cc_final: 0.8952 (ttm-80) REVERT: E 95 GLU cc_start: 0.9341 (mm-30) cc_final: 0.9120 (tm-30) REVERT: E 102 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8240 (tpt90) REVERT: E 174 TYR cc_start: 0.8828 (p90) cc_final: 0.8612 (p90) REVERT: F 10 MET cc_start: 0.9371 (mmm) cc_final: 0.9099 (mmm) REVERT: F 81 ASP cc_start: 0.9146 (t0) cc_final: 0.8773 (t0) REVERT: F 95 GLU cc_start: 0.9089 (tp30) cc_final: 0.8729 (tp30) REVERT: G 56 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8649 (tp30) REVERT: G 58 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8665 (mmp) REVERT: H 5 ASP cc_start: 0.6261 (m-30) cc_final: 0.5648 (m-30) REVERT: H 9 GLN cc_start: 0.8929 (mt0) cc_final: 0.8648 (mp10) REVERT: H 78 LYS cc_start: 0.9002 (ptmt) cc_final: 0.8701 (pttm) REVERT: H 203 ASP cc_start: 0.9412 (t0) cc_final: 0.9184 (t0) outliers start: 96 outliers final: 46 residues processed: 238 average time/residue: 1.2459 time to fit residues: 335.7717 Evaluate side-chains 209 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 156 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 670 MET Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain D residue 506 LYS Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 153 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 192 MET Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 67 CYS Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 96 TYR Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 188 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 216 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN E 160 ASN F 205 HIS H 149 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18420 Z= 0.269 Angle : 0.589 13.154 24809 Z= 0.304 Chirality : 0.041 0.194 2768 Planarity : 0.004 0.044 3018 Dihedral : 10.468 88.935 2806 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.67 % Favored : 96.11 % Rotamer: Outliers : 5.06 % Allowed : 21.18 % Favored : 73.76 % 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: 1.29 (0.19), residues: 2235 helix: 2.35 (0.15), residues: 1321 sheet: -2.22 (0.46), residues: 101 loop : -1.34 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A 766 HIS 0.004 0.001 HIS F 205 PHE 0.021 0.001 PHE D 495 TYR 0.020 0.001 TYR C 711 ARG 0.007 0.001 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 174 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7892 (mpp) cc_final: 0.7426 (mpp) REVERT: A 503 MET cc_start: 0.7586 (ttm) cc_final: 0.7155 (ptm) REVERT: A 759 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6509 (mp) REVERT: B 586 ARG cc_start: 0.9248 (mmm-85) cc_final: 0.8783 (mmm160) REVERT: C 414 MET cc_start: 0.7656 (mtm) cc_final: 0.6170 (ptt) REVERT: C 496 MET cc_start: 0.3887 (mtt) cc_final: 0.2701 (tpt) REVERT: C 714 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7711 (mp10) REVERT: D 408 MET cc_start: 0.4622 (tpp) cc_final: 0.4164 (tpp) REVERT: D 414 MET cc_start: 0.6271 (mtm) cc_final: 0.5297 (pp-130) REVERT: D 736 THR cc_start: 0.4718 (OUTLIER) cc_final: 0.3992 (t) REVERT: E 95 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9131 (tm-30) REVERT: E 102 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8231 (tpt90) REVERT: E 174 TYR cc_start: 0.8822 (p90) cc_final: 0.8618 (p90) REVERT: F 10 MET cc_start: 0.9352 (mmm) cc_final: 0.9108 (mmm) REVERT: F 81 ASP cc_start: 0.9100 (t0) cc_final: 0.8725 (t0) REVERT: F 95 GLU cc_start: 0.9101 (tp30) cc_final: 0.8700 (tp30) REVERT: G 56 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8639 (tp30) REVERT: G 58 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8682 (mmp) REVERT: G 60 HIS cc_start: 0.8812 (OUTLIER) cc_final: 0.8483 (p90) REVERT: H 9 GLN cc_start: 0.8888 (mt0) cc_final: 0.8558 (mp10) REVERT: H 203 ASP cc_start: 0.9453 (t0) cc_final: 0.9240 (t0) outliers start: 92 outliers final: 49 residues processed: 247 average time/residue: 1.1842 time to fit residues: 332.2126 Evaluate side-chains 214 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 159 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 623 PHE Chi-restraints excluded: chain D residue 736 THR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 73 PHE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 123 optimal weight: 30.0000 chunk 158 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 135 optimal weight: 0.0670 chunk 131 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 overall best weight: 2.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS D 619 ASN E 160 ASN F 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18420 Z= 0.314 Angle : 0.626 13.109 24809 Z= 0.317 Chirality : 0.041 0.195 2768 Planarity : 0.004 0.043 3018 Dihedral : 10.432 89.076 2804 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.21 % Favored : 95.57 % Rotamer: Outliers : 4.95 % Allowed : 21.67 % Favored : 73.38 % 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: 1.23 (0.19), residues: 2235 helix: 2.27 (0.15), residues: 1322 sheet: -2.46 (0.45), residues: 101 loop : -1.27 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 460 HIS 0.003 0.001 HIS E 60 PHE 0.023 0.002 PHE D 495 TYR 0.020 0.002 TYR C 711 ARG 0.008 0.001 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 169 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7806 (mpp) cc_final: 0.7262 (mpp) REVERT: A 503 MET cc_start: 0.7630 (ttm) cc_final: 0.7230 (ptm) REVERT: B 407 MET cc_start: 0.7372 (ppp) cc_final: 0.6921 (ppp) REVERT: B 408 MET cc_start: 0.6780 (mpp) cc_final: 0.4422 (pp-130) REVERT: B 496 MET cc_start: 0.3414 (ptp) cc_final: 0.1470 (ppp) REVERT: B 503 MET cc_start: 0.6778 (pp-130) cc_final: 0.6063 (ppp) REVERT: B 586 ARG cc_start: 0.9221 (mmm-85) cc_final: 0.8755 (mmm160) REVERT: C 414 MET cc_start: 0.7633 (mtm) cc_final: 0.6197 (ptt) REVERT: C 463 MET cc_start: 0.3347 (mpp) cc_final: 0.1432 (ttp) REVERT: C 496 MET cc_start: 0.4093 (mtt) cc_final: 0.2890 (tpt) REVERT: C 714 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7711 (mp10) REVERT: D 408 MET cc_start: 0.4707 (tpp) cc_final: 0.4397 (tpp) REVERT: D 414 MET cc_start: 0.6360 (mtm) cc_final: 0.5439 (pmm) REVERT: E 5 ASP cc_start: 0.6203 (OUTLIER) cc_final: 0.5496 (p0) REVERT: E 102 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8553 (tpt90) REVERT: E 174 TYR cc_start: 0.8779 (p90) cc_final: 0.8566 (p90) REVERT: F 10 MET cc_start: 0.9363 (mmm) cc_final: 0.9074 (mmm) REVERT: F 81 ASP cc_start: 0.9082 (t0) cc_final: 0.8684 (t0) REVERT: F 95 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8564 (tm-30) REVERT: G 56 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8661 (tp30) REVERT: G 58 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8717 (mmp) REVERT: G 60 HIS cc_start: 0.8828 (OUTLIER) cc_final: 0.8450 (p90) REVERT: H 9 GLN cc_start: 0.8897 (mt0) cc_final: 0.8578 (mp10) REVERT: H 203 ASP cc_start: 0.9433 (OUTLIER) cc_final: 0.9229 (t0) outliers start: 90 outliers final: 46 residues processed: 240 average time/residue: 1.1400 time to fit residues: 314.0121 Evaluate side-chains 214 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 161 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 795 VAL Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 812 ILE Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 200 MET Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 28 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 60 HIS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 137 SER Chi-restraints excluded: chain H residue 150 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.9980 chunk 86 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 137 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN E 160 ASN ** F 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 HIS H 79 GLN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18420 Z= 0.172 Angle : 0.594 10.919 24809 Z= 0.299 Chirality : 0.040 0.194 2768 Planarity : 0.003 0.042 3018 Dihedral : 9.901 87.317 2801 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.31 % Favored : 96.47 % Rotamer: Outliers : 3.47 % Allowed : 23.10 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.51 (0.19), residues: 2235 helix: 2.52 (0.15), residues: 1319 sheet: -2.40 (0.46), residues: 98 loop : -1.19 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 766 HIS 0.004 0.001 HIS F 205 PHE 0.023 0.001 PHE D 623 TYR 0.020 0.001 TYR C 711 ARG 0.007 0.000 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 179 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7152 (mpp) REVERT: A 503 MET cc_start: 0.7779 (ttm) cc_final: 0.7405 (ptm) REVERT: A 659 PHE cc_start: 0.8522 (m-80) cc_final: 0.8080 (t80) REVERT: B 407 MET cc_start: 0.7299 (ppp) cc_final: 0.6833 (ppp) REVERT: B 408 MET cc_start: 0.6517 (mpp) cc_final: 0.4430 (pp-130) REVERT: B 496 MET cc_start: 0.2147 (ptp) cc_final: 0.1118 (ppp) REVERT: B 586 ARG cc_start: 0.9192 (mmm-85) cc_final: 0.8697 (mmm160) REVERT: C 414 MET cc_start: 0.7334 (mtm) cc_final: 0.6165 (ptt) REVERT: C 463 MET cc_start: 0.3209 (mpp) cc_final: 0.1554 (ttp) REVERT: C 496 MET cc_start: 0.4069 (mtt) cc_final: 0.2905 (tpt) REVERT: C 714 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7616 (mp10) REVERT: D 414 MET cc_start: 0.6577 (mtm) cc_final: 0.5537 (pmm) REVERT: D 545 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7902 (mtp180) REVERT: D 569 ASN cc_start: 0.8507 (p0) cc_final: 0.8250 (p0) REVERT: E 5 ASP cc_start: 0.6025 (OUTLIER) cc_final: 0.5398 (p0) REVERT: E 41 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7394 (pttm) REVERT: E 102 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8224 (tpt90) REVERT: E 174 TYR cc_start: 0.8714 (p90) cc_final: 0.8487 (p90) REVERT: F 10 MET cc_start: 0.9280 (mmm) cc_final: 0.9044 (mmm) REVERT: F 81 ASP cc_start: 0.9073 (t0) cc_final: 0.8671 (t0) REVERT: F 95 GLU cc_start: 0.9079 (tp30) cc_final: 0.8715 (tp30) REVERT: G 6 ARG cc_start: 0.8018 (mmp-170) cc_final: 0.7780 (mmp-170) REVERT: G 58 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8459 (mmp) REVERT: H 9 GLN cc_start: 0.8828 (mt0) cc_final: 0.8495 (mp10) outliers start: 63 outliers final: 28 residues processed: 227 average time/residue: 1.2315 time to fit residues: 316.8642 Evaluate side-chains 201 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 77 CYS Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 61 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 160 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18420 Z= 0.187 Angle : 0.627 12.635 24809 Z= 0.312 Chirality : 0.040 0.190 2768 Planarity : 0.003 0.041 3018 Dihedral : 9.646 87.005 2800 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.31 % Favored : 96.47 % Rotamer: Outliers : 2.97 % Allowed : 23.82 % Favored : 73.21 % 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: 1.55 (0.19), residues: 2235 helix: 2.55 (0.15), residues: 1316 sheet: -2.25 (0.45), residues: 109 loop : -1.15 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 766 HIS 0.004 0.001 HIS G 60 PHE 0.022 0.001 PHE D 495 TYR 0.019 0.001 TYR C 711 ARG 0.009 0.000 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 179 time to evaluate : 1.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.7508 (ttm) cc_final: 0.7161 (ptm) REVERT: B 407 MET cc_start: 0.7265 (ppp) cc_final: 0.6808 (ppp) REVERT: B 408 MET cc_start: 0.6621 (mpp) cc_final: 0.4576 (pp-130) REVERT: B 496 MET cc_start: 0.2144 (ptp) cc_final: 0.1123 (ppp) REVERT: B 503 MET cc_start: 0.6611 (pp-130) cc_final: 0.5875 (ppp) REVERT: C 414 MET cc_start: 0.7290 (mtm) cc_final: 0.6148 (ptt) REVERT: C 463 MET cc_start: 0.3212 (mpp) cc_final: 0.1616 (ttp) REVERT: C 496 MET cc_start: 0.4130 (mtt) cc_final: 0.2701 (mmp) REVERT: C 714 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7616 (mp10) REVERT: D 408 MET cc_start: 0.4848 (tpp) cc_final: 0.4349 (tpp) REVERT: D 414 MET cc_start: 0.6689 (mtm) cc_final: 0.5706 (pmm) REVERT: D 496 MET cc_start: -0.1017 (pp-130) cc_final: -0.1654 (ppp) REVERT: D 545 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7802 (mtp180) REVERT: D 569 ASN cc_start: 0.8471 (p0) cc_final: 0.8188 (p0) REVERT: E 5 ASP cc_start: 0.6038 (OUTLIER) cc_final: 0.5435 (p0) REVERT: E 102 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8243 (tpt90) REVERT: F 10 MET cc_start: 0.9288 (mmm) cc_final: 0.9034 (mmm) REVERT: F 81 ASP cc_start: 0.9080 (t0) cc_final: 0.8702 (t0) REVERT: F 95 GLU cc_start: 0.9089 (tp30) cc_final: 0.8461 (tm-30) REVERT: G 6 ARG cc_start: 0.8075 (mmp-170) cc_final: 0.7815 (mmp-170) REVERT: G 58 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8460 (mmp) REVERT: G 136 LEU cc_start: 0.8976 (tp) cc_final: 0.8756 (tp) REVERT: G 140 ILE cc_start: 0.9247 (mp) cc_final: 0.9041 (mp) REVERT: H 9 GLN cc_start: 0.8825 (mt0) cc_final: 0.8510 (mp10) outliers start: 54 outliers final: 35 residues processed: 223 average time/residue: 1.2303 time to fit residues: 313.6472 Evaluate side-chains 209 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 170 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain D residue 545 ARG Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 153 ILE Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 147 optimal weight: 9.9990 chunk 223 optimal weight: 1.9990 chunk 205 optimal weight: 0.5980 chunk 177 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN F 160 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18420 Z= 0.229 Angle : 0.654 11.942 24809 Z= 0.324 Chirality : 0.041 0.200 2768 Planarity : 0.004 0.041 3018 Dihedral : 9.668 87.371 2800 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.53 % Favored : 96.24 % Rotamer: Outliers : 2.64 % Allowed : 24.09 % Favored : 73.27 % 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: 1.54 (0.19), residues: 2235 helix: 2.52 (0.15), residues: 1316 sheet: -2.17 (0.46), residues: 107 loop : -1.13 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP D 766 HIS 0.006 0.001 HIS G 60 PHE 0.021 0.001 PHE D 495 TYR 0.018 0.001 TYR C 711 ARG 0.007 0.000 ARG A 586 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4470 Ramachandran restraints generated. 2235 Oldfield, 0 Emsley, 2235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 169 time to evaluate : 2.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.7509 (ttm) cc_final: 0.7165 (ptm) REVERT: A 670 MET cc_start: 0.7155 (mmp) cc_final: 0.6197 (mmm) REVERT: B 408 MET cc_start: 0.6617 (mpp) cc_final: 0.4588 (pp-130) REVERT: B 414 MET cc_start: 0.6663 (mmm) cc_final: 0.5561 (ttt) REVERT: B 496 MET cc_start: 0.2193 (ptp) cc_final: 0.0859 (ppp) REVERT: B 503 MET cc_start: 0.6675 (pp-130) cc_final: 0.5964 (ppp) REVERT: C 414 MET cc_start: 0.7312 (mtm) cc_final: 0.6201 (ptt) REVERT: C 463 MET cc_start: 0.3226 (mpp) cc_final: 0.1447 (ttp) REVERT: C 496 MET cc_start: 0.4152 (mtt) cc_final: 0.2758 (tpt) REVERT: C 714 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7624 (mp10) REVERT: D 408 MET cc_start: 0.4724 (tpp) cc_final: 0.4463 (tpp) REVERT: D 414 MET cc_start: 0.6686 (mtm) cc_final: 0.5736 (pmm) REVERT: D 496 MET cc_start: -0.1144 (pp-130) cc_final: -0.1404 (ppp) REVERT: D 732 TYR cc_start: 0.3476 (m-80) cc_final: 0.2232 (m-80) REVERT: E 5 ASP cc_start: 0.6051 (OUTLIER) cc_final: 0.5667 (p0) REVERT: E 56 GLU cc_start: 0.8815 (tp30) cc_final: 0.8612 (tp30) REVERT: E 102 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8224 (tpt90) REVERT: F 10 MET cc_start: 0.9298 (mmm) cc_final: 0.9036 (mmm) REVERT: F 81 ASP cc_start: 0.9003 (t0) cc_final: 0.8631 (t0) REVERT: F 95 GLU cc_start: 0.9102 (tp30) cc_final: 0.8449 (tm-30) REVERT: G 6 ARG cc_start: 0.8094 (mmp-170) cc_final: 0.7821 (mmp-170) REVERT: G 56 GLU cc_start: 0.8839 (tp30) cc_final: 0.8570 (tp30) REVERT: G 58 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8661 (mmp) REVERT: H 9 GLN cc_start: 0.8807 (mt0) cc_final: 0.8506 (mp10) outliers start: 48 outliers final: 33 residues processed: 209 average time/residue: 1.2069 time to fit residues: 285.5809 Evaluate side-chains 201 residues out of total 1919 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 165 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 502 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 673 TYR Chi-restraints excluded: chain D residue 597 SER Chi-restraints excluded: chain D residue 609 THR Chi-restraints excluded: chain E residue 5 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 102 ARG Chi-restraints excluded: chain E residue 205 HIS Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 196 LEU Chi-restraints excluded: chain G residue 58 MET Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain G residue 207 GLN Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 73 PHE Chi-restraints excluded: chain H residue 128 TYR Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 182 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 0.0000 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN ** D 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 ASN ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.160544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085674 restraints weight = 35376.387| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 3.52 r_work: 0.3083 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18420 Z= 0.209 Angle : 0.657 12.975 24809 Z= 0.322 Chirality : 0.041 0.191 2768 Planarity : 0.003 0.040 3018 Dihedral : 9.494 87.352 2800 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.58 % Favored : 96.20 % Rotamer: Outliers : 2.48 % Allowed : 24.48 % Favored : 73.05 % 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: 1.56 (0.19), residues: 2235 helix: 2.53 (0.15), residues: 1318 sheet: -2.17 (0.46), residues: 107 loop : -1.10 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 766 HIS 0.004 0.001 HIS G 60 PHE 0.021 0.001 PHE D 495 TYR 0.018 0.001 TYR C 711 ARG 0.007 0.001 ARG E 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6893.78 seconds wall clock time: 124 minutes 47.21 seconds (7487.21 seconds total)