Starting phenix.real_space_refine on Sun Mar 17 15:44:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/03_2024/8p3s_17393_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/03_2024/8p3s_17393.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/8p3s_17393/03_2024/8p3s_17393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/03_2024/8p3s_17393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/03_2024/8p3s_17393_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p3s_17393/03_2024/8p3s_17393_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= 0.049 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 127 5.16 5 C 11954 2.51 5 N 2866 2.21 5 O 3243 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 GLU 710": "OE1" <-> "OE2" Residue "A GLU 813": "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 628": "NH1" <-> "NH2" Residue "B PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 710": "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 627": "OE1" <-> "OE2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D GLU 710": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "F GLU 55": "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 GLU 126": "OE1" <-> "OE2" Residue "H GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18195 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Conformer: "B" Number of residues, atoms: 404, 3081 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 bond proxies already assigned to first conformer: 3125 Chain: "B" Number of atoms: 3077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3077 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3015 Classifications: {'peptide': 395} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 383} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 3100 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3078 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 404, 3078 Classifications: {'peptide': 404} Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 390} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 3122 Chain: "E" 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: "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: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1372 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1359 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 3 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 59 Unusual residues: {'OLC': 1, 'PLM': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 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: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} 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: "B" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N APHE A 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 574 " occ=0.50 residue: pdb=" N APHE A 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 623 " occ=0.50 residue: pdb=" N APHE D 574 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 574 " occ=0.50 residue: pdb=" N APHE D 623 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 623 " occ=0.50 Time building chain proxies: 12.35, per 1000 atoms: 0.68 Number of scatterers: 18195 At special positions: 0 Unit cell: (118.531, 127.204, 137.323, 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 127 16.00 P 5 15.00 O 3243 8.00 N 2866 7.00 C 11954 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=2.02 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=2.02 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=2.05 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 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=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 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: 6.81 Conformation dependent library (CDL) restraints added in 3.8 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4208 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 21 sheets defined 53.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 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 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 543 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 573 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 661 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.678A pdb=" N SER A 676 " --> pdb=" O THR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.531A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 removed outlier: 4.251A pdb=" N THR A 744 " --> pdb=" O SER A 741 " (cutoff:3.500A) Proline residue: A 745 - end of helix Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 789 through 791 No H-bonds generated for 'chain 'A' and resid 789 through 791' Processing helix chain 'A' and resid 793 through 819 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 628 removed outlier: 3.735A pdb=" N ARG B 628 " --> pdb=" O LEU B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 640 Processing helix chain 'B' and resid 654 through 661 Processing helix chain 'B' and resid 665 through 676 removed outlier: 3.675A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 695 Processing helix chain 'B' and resid 706 through 714 removed outlier: 3.542A pdb=" N GLN B 714 " --> pdb=" O GLU B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 758 through 767 Processing helix chain 'B' and resid 793 through 822 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 625 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: 3.732A pdb=" N SER C 676 " --> pdb=" O THR C 672 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.539A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 755 removed outlier: 4.308A pdb=" N THR C 744 " --> pdb=" O SER C 741 " (cutoff:3.500A) Proline residue: C 745 - end of helix Processing helix chain 'C' and resid 758 through 767 Processing helix chain 'C' and resid 793 through 820 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: 3.619A pdb=" N TRP D 578 " --> pdb=" O BPHE D 574 " (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 676 removed outlier: 3.678A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 695 Processing helix chain 'D' and resid 706 through 714 removed outlier: 3.545A pdb=" N GLN D 714 " --> pdb=" O GLU D 710 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 755 Processing helix chain 'D' and resid 758 through 767 Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 793 through 822 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 161 removed outlier: 3.503A pdb=" N ALA E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 209 Processing helix chain 'F' and resid 6 through 27 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.506A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.900A 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: 4.091A 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: 3.944A pdb=" N MET H 10 " --> pdb=" O ARG H 6 " (cutoff:3.500A) removed outlier: 3.981A 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 134 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 720 through 723 removed outlier: 4.099A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 494 through 498 removed outlier: 6.656A pdb=" N TYR A 732 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER A 497 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS A 730 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 395 through 399 Processing sheet with id= F, first strand: chain 'B' and resid 489 through 491 Processing sheet with id= G, first strand: chain 'B' and resid 720 through 723 removed outlier: 4.036A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS B 505 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N TYR B 700 " --> pdb=" O LYS B 505 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA B 646 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU B 703 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 648 " --> pdb=" O LEU B 703 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N GLU B 705 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 494 through 498 removed outlier: 6.624A pdb=" N TYR B 732 " --> pdb=" O PHE B 495 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 497 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS B 730 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 395 through 399 Processing sheet with id= J, first strand: chain 'C' and resid 489 through 491 Processing sheet with id= K, first strand: chain 'C' and resid 720 through 723 removed outlier: 4.036A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.617A pdb=" N TYR C 732 " --> pdb=" O PHE C 495 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER C 497 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LYS C 730 " --> pdb=" O SER C 497 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 395 through 399 Processing sheet with id= N, first strand: chain 'D' and resid 489 through 491 Processing sheet with id= O, first strand: chain 'D' and resid 496 through 498 removed outlier: 3.833A pdb=" N MET D 496 " --> pdb=" O TYR D 732 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 720 through 723 removed outlier: 4.070A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS D 505 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TYR D 700 " --> pdb=" O LYS D 505 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA D 646 " --> pdb=" O ALA D 701 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU D 703 " --> pdb=" O ALA D 646 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY D 648 " --> pdb=" O LEU D 703 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N GLU D 705 " --> pdb=" O GLY D 648 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 34 through 38 Processing sheet with id= R, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.794A pdb=" N LYS F 78 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 174 through 176 Processing sheet with id= T, first strand: chain 'H' and resid 36 through 38 Processing sheet with id= U, first strand: chain 'H' and resid 65 through 67 963 hydrogen bonds defined for protein. 2810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 7.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2816 1.31 - 1.44: 5174 1.44 - 1.57: 10374 1.57 - 1.71: 10 1.71 - 1.84: 206 Bond restraints: 18580 Sorted by residual: bond pdb=" C PRO B 512 " pdb=" O PRO B 512 " ideal model delta sigma weight residual 1.233 1.178 0.055 1.13e-02 7.83e+03 2.34e+01 bond pdb=" N VAL D 488 " pdb=" CA VAL D 488 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.94e+01 bond pdb=" N VAL C 488 " pdb=" CA VAL C 488 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.86e+01 bond pdb=" C LYS A 506 " pdb=" O LYS A 506 " ideal model delta sigma weight residual 1.238 1.183 0.055 1.28e-02 6.10e+03 1.84e+01 bond pdb=" N VAL B 488 " pdb=" CA VAL B 488 " ideal model delta sigma weight residual 1.456 1.497 -0.041 9.50e-03 1.11e+04 1.83e+01 ... (remaining 18575 not shown) Histogram of bond angle deviations from ideal: 96.64 - 104.25: 250 104.25 - 111.86: 8431 111.86 - 119.48: 8645 119.48 - 127.09: 7556 127.09 - 134.71: 156 Bond angle restraints: 25038 Sorted by residual: angle pdb=" O LYS A 506 " pdb=" C LYS A 506 " pdb=" N PRO A 507 " ideal model delta sigma weight residual 121.32 110.49 10.83 1.15e+00 7.56e-01 8.88e+01 angle pdb=" N ASP C 590 " pdb=" CA ASP C 590 " pdb=" C ASP C 590 " ideal model delta sigma weight residual 113.88 104.62 9.26 1.23e+00 6.61e-01 5.67e+01 angle pdb=" N PRO B 512 " pdb=" CA PRO B 512 " pdb=" C PRO B 512 " ideal model delta sigma weight residual 110.80 100.86 9.94 1.51e+00 4.39e-01 4.33e+01 angle pdb=" C LYS A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.84 111.94 7.90 1.25e+00 6.40e-01 4.00e+01 angle pdb=" N PRO B 632 " pdb=" CA PRO B 632 " pdb=" CB PRO B 632 " ideal model delta sigma weight residual 103.25 96.64 6.61 1.05e+00 9.07e-01 3.97e+01 ... (remaining 25033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.03: 10376 29.03 - 58.07: 435 58.07 - 87.10: 52 87.10 - 116.14: 8 116.14 - 145.17: 2 Dihedral angle restraints: 10873 sinusoidal: 4263 harmonic: 6610 Sorted by residual: 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 23.57 69.43 1 1.00e+01 1.00e-02 6.23e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 68 " pdb=" CB CYS E 68 " ideal model delta sinusoidal sigma weight residual 93.00 35.60 57.40 1 1.00e+01 1.00e-02 4.43e+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 93.00 43.29 49.71 1 1.00e+01 1.00e-02 3.39e+01 ... (remaining 10870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2587 0.173 - 0.347: 197 0.347 - 0.520: 8 0.520 - 0.693: 0 0.693 - 0.866: 1 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CB VAL A 626 " pdb=" CA VAL A 626 " pdb=" CG1 VAL A 626 " pdb=" CG2 VAL A 626 " both_signs ideal model delta sigma weight residual False -2.63 -1.76 -0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CG LEU A 483 " pdb=" CB LEU A 483 " pdb=" CD1 LEU A 483 " pdb=" CD2 LEU A 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.04e+00 chirality pdb=" CG LEU D 483 " pdb=" CB LEU D 483 " pdb=" CD1 LEU D 483 " pdb=" CD2 LEU D 483 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.64e+00 ... (remaining 2790 not shown) Planarity restraints: 3050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 628 " 0.693 9.50e-02 1.11e+02 3.11e-01 5.88e+01 pdb=" NE ARG B 628 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B 628 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 628 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 628 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA BPHE D 574 " 0.033 2.00e-02 2.50e+03 6.76e-02 4.56e+01 pdb=" C BPHE D 574 " -0.117 2.00e-02 2.50e+03 pdb=" O BPHE D 574 " 0.044 2.00e-02 2.50e+03 pdb=" N ASN D 575 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 675 " -0.601 9.50e-02 1.11e+02 2.70e-01 4.44e+01 pdb=" NE ARG D 675 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG D 675 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG D 675 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 675 " -0.021 2.00e-02 2.50e+03 ... (remaining 3047 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2415 2.75 - 3.29: 18764 3.29 - 3.83: 30163 3.83 - 4.36: 37997 4.36 - 4.90: 62855 Nonbonded interactions: 152194 Sorted by model distance: nonbonded pdb=" O LYS E 129 " pdb=" OG1 THR E 130 " model vdw 2.216 2.440 nonbonded pdb=" O GLU B 627 " pdb=" N MET B 629 " model vdw 2.254 2.520 nonbonded pdb=" O SER E 104 " pdb=" N ILE E 106 " model vdw 2.271 2.520 nonbonded pdb=" O GLU H 70 " pdb=" OE1 GLU H 70 " model vdw 2.279 3.040 nonbonded pdb=" OG SER A 592 " pdb=" OD2 ASP B 590 " model vdw 2.287 2.440 ... (remaining 152189 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 506 or resid 510 through 573 or resid 575 thro \ ugh 593 or (resid 594 and (name N or name CA or name C or name O or name CB )) o \ r resid 595 through 622 or resid 624 through 626 or (resid 633 through 634 and ( \ name N or name CA or name C or name O or name CB )) 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 or (resid 819 through 823 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'B' and (resid 393 through 506 or resid 510 through 549 or (resid 550 and \ (name N or name CA or name C or name O or name CB )) or resid 551 or (resid 569 \ and (name N or name CA or name C or name O or name CB )) or resid 570 through 5 \ 73 or resid 575 or (resid 576 and (name N or name CA or name C or name O or name \ CB )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C o \ r name O or name CB )) or resid 595 through 622 or resid 624 through 626 or (res \ id 633 through 634 and (name N or name CA or name C or name O or name CB )) or r \ esid 635 through 773 or (resid 784 and (name N or name CA or name C or name O or \ name CB )) or resid 785 through 823)) selection = (chain 'C' and (resid 393 through 573 or resid 575 or (resid 576 and (name N or \ name CA or name C or name O or name CB )) or resid 577 through 622 or resid 624 \ through 626 or (resid 633 through 634 and (name N or name CA or name C or name O \ or name CB )) 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 or (resid 819 through 82 \ 3 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 393 through 506 or resid 510 through 551 or (resid 569 and \ (name N or name CA or name C or name O or name CB )) or resid 570 through 573 o \ r resid 575 or (resid 576 and (name N or name CA or name C or name O or name CB \ )) or resid 577 through 593 or (resid 594 and (name N or name CA or name C or na \ me O or name CB )) or resid 595 through 622 or resid 624 through 626 or resid 63 \ 3 through 773 or (resid 784 and (name N or name CA or name C or name O or name C \ B )) or resid 785 through 823)) } ncs_group { reference = (chain 'E' and (resid 5 through 84 or resid 93 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thro \ ugh 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 210)) selection = (chain 'F' and (resid 5 through 42 or resid 55 through 84 or resid 93 through 20 \ 3 or (resid 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 through 206 or (resid 207 and (name N or name CA or name C or name O or na \ me CB )) or resid 208 through 210)) selection = (chain 'G' and (resid 5 through 84 or resid 93 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 or ( \ resid 206 through 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 210)) selection = (chain 'H' and (resid 5 through 42 or resid 55 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB )) or resid 96 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=0.50 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.460 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 51.750 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4965 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 : 0.012 0.064 18580 Z= 0.812 Angle : 1.458 11.189 25038 Z= 1.036 Chirality : 0.107 0.866 2793 Planarity : 0.015 0.311 3050 Dihedral : 15.799 145.169 6629 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.53 % Allowed : 4.26 % Favored : 95.21 % Rotamer: Outliers : 1.80 % Allowed : 3.66 % Favored : 94.54 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 20.69 % 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: -0.32 (0.17), residues: 2268 helix: 0.97 (0.14), residues: 1332 sheet: -1.68 (0.37), residues: 107 loop : -1.98 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP B 578 HIS 0.011 0.003 HIS E 60 PHE 0.021 0.005 PHE A 517 TYR 0.034 0.005 TYR B 469 ARG 0.016 0.002 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 365 time to evaluate : 1.963 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 591 ILE cc_start: 0.8820 (tp) cc_final: 0.8549 (pt) REVERT: B 585 MET cc_start: 0.8907 (mmt) cc_final: 0.8300 (mmt) REVERT: E 81 ASP cc_start: 0.8323 (t0) cc_final: 0.7968 (p0) REVERT: E 92 ASP cc_start: 0.7509 (t0) cc_final: 0.7065 (p0) REVERT: E 207 GLN cc_start: 0.8904 (mm110) cc_final: 0.8653 (tm-30) REVERT: F 24 MET cc_start: 0.9162 (tpt) cc_final: 0.8905 (tpt) REVERT: F 61 SER cc_start: 0.9389 (t) cc_final: 0.9060 (p) REVERT: F 65 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.7997 (mtm110) REVERT: F 81 ASP cc_start: 0.8811 (t0) cc_final: 0.8584 (t70) REVERT: F 98 LEU cc_start: 0.8486 (tt) cc_final: 0.8235 (mm) REVERT: F 126 GLU cc_start: 0.9529 (mt-10) cc_final: 0.9191 (tm-30) REVERT: G 13 THR cc_start: 0.9374 (t) cc_final: 0.9027 (p) REVERT: G 81 ASP cc_start: 0.9230 (p0) cc_final: 0.8832 (t0) REVERT: G 84 PRO cc_start: 0.5605 (Cg_exo) cc_final: 0.5203 (Cg_endo) REVERT: G 99 ARG cc_start: 0.9299 (mtt-85) cc_final: 0.8961 (mtm180) REVERT: H 6 ARG cc_start: 0.8404 (tmt-80) cc_final: 0.8176 (tmm160) REVERT: H 10 MET cc_start: 0.9034 (tpp) cc_final: 0.8704 (tpp) REVERT: H 13 THR cc_start: 0.9102 (m) cc_final: 0.8697 (t) REVERT: H 35 TYR cc_start: 0.8828 (m-80) cc_final: 0.8553 (m-80) REVERT: H 61 SER cc_start: 0.9502 (t) cc_final: 0.8932 (p) REVERT: H 70 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8495 (pp20) REVERT: H 74 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8999 (ttmm) outliers start: 33 outliers final: 8 residues processed: 392 average time/residue: 1.3922 time to fit residues: 605.5424 Evaluate side-chains 203 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain D residue 628 ARG Chi-restraints excluded: chain D residue 743 ARG Chi-restraints excluded: chain D residue 746 VAL Chi-restraints excluded: chain E residue 12 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 191 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 206 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 160 ASN F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN H 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4996 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 18580 Z= 0.209 Angle : 0.622 16.770 25038 Z= 0.323 Chirality : 0.043 0.224 2793 Planarity : 0.004 0.040 3050 Dihedral : 11.485 105.553 2841 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.57 % Favored : 97.25 % Rotamer: Outliers : 2.40 % Allowed : 13.65 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.13 (0.18), residues: 2268 helix: 2.16 (0.15), residues: 1326 sheet: -1.37 (0.36), residues: 159 loop : -1.32 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 460 HIS 0.004 0.001 HIS G 60 PHE 0.031 0.001 PHE A 658 TYR 0.015 0.001 TYR D 711 ARG 0.009 0.001 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 232 time to evaluate : 1.855 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: C 496 MET cc_start: -0.0213 (mtp) cc_final: -0.0851 (mtp) REVERT: C 674 MET cc_start: 0.0193 (ptm) cc_final: -0.0243 (ptp) REVERT: D 503 MET cc_start: 0.4614 (tpt) cc_final: 0.4177 (tpt) REVERT: D 545 ARG cc_start: 0.8255 (mtm180) cc_final: 0.8037 (ptm160) REVERT: E 58 MET cc_start: 0.8402 (mmp) cc_final: 0.8106 (tpt) REVERT: E 81 ASP cc_start: 0.8384 (t0) cc_final: 0.7833 (p0) REVERT: E 160 ASN cc_start: 0.8873 (m-40) cc_final: 0.8637 (m110) REVERT: E 207 GLN cc_start: 0.8947 (mm110) cc_final: 0.8710 (tm-30) REVERT: F 24 MET cc_start: 0.9129 (tpt) cc_final: 0.8904 (tpt) REVERT: F 61 SER cc_start: 0.9379 (t) cc_final: 0.9038 (p) REVERT: F 65 ARG cc_start: 0.8247 (mtm-85) cc_final: 0.7850 (mtm110) REVERT: F 78 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8440 (ptmm) REVERT: F 81 ASP cc_start: 0.8887 (t0) cc_final: 0.8658 (t70) REVERT: F 98 LEU cc_start: 0.8737 (tt) cc_final: 0.8390 (mm) REVERT: F 126 GLU cc_start: 0.9541 (mt-10) cc_final: 0.9218 (tm-30) REVERT: G 81 ASP cc_start: 0.9243 (p0) cc_final: 0.8774 (t0) REVERT: G 203 ASP cc_start: 0.9096 (m-30) cc_final: 0.8625 (m-30) REVERT: H 6 ARG cc_start: 0.8599 (tmt-80) cc_final: 0.8247 (tmm160) REVERT: H 34 LEU cc_start: 0.9025 (tp) cc_final: 0.8637 (tp) REVERT: H 61 SER cc_start: 0.9239 (t) cc_final: 0.8328 (p) REVERT: H 70 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8750 (pp20) outliers start: 44 outliers final: 11 residues processed: 259 average time/residue: 1.3692 time to fit residues: 394.1427 Evaluate side-chains 195 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 78 LYS Chi-restraints excluded: chain F residue 120 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 183 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 HIS ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18580 Z= 0.254 Angle : 0.591 13.320 25038 Z= 0.307 Chirality : 0.042 0.185 2793 Planarity : 0.004 0.045 3050 Dihedral : 10.490 85.182 2829 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.70 % Favored : 97.12 % Rotamer: Outliers : 3.17 % Allowed : 14.64 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.38 (0.18), residues: 2268 helix: 2.35 (0.14), residues: 1318 sheet: -1.22 (0.37), residues: 162 loop : -1.16 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 766 HIS 0.004 0.001 HIS G 60 PHE 0.022 0.001 PHE A 658 TYR 0.031 0.002 TYR A 405 ARG 0.012 0.001 ARG D 743 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 199 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 674 MET cc_start: -0.0119 (ptm) cc_final: -0.0583 (ptp) REVERT: E 135 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8478 (pt) REVERT: E 207 GLN cc_start: 0.9003 (mm110) cc_final: 0.8773 (tm-30) REVERT: F 61 SER cc_start: 0.9267 (t) cc_final: 0.8905 (p) REVERT: F 65 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7813 (mtm110) REVERT: F 81 ASP cc_start: 0.8883 (t0) cc_final: 0.8679 (t70) REVERT: G 81 ASP cc_start: 0.9335 (p0) cc_final: 0.8839 (t0) REVERT: H 6 ARG cc_start: 0.8673 (tmt-80) cc_final: 0.8256 (tmm160) REVERT: H 34 LEU cc_start: 0.9173 (tp) cc_final: 0.8734 (tp) REVERT: H 61 SER cc_start: 0.9520 (t) cc_final: 0.8807 (p) REVERT: H 70 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8940 (pp20) outliers start: 58 outliers final: 18 residues processed: 236 average time/residue: 1.2436 time to fit residues: 330.4573 Evaluate side-chains 191 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain D residue 496 MET Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 204 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 0.0670 chunk 138 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 108 optimal weight: 40.0000 chunk 196 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN D 461 ASN D 508 GLN E 205 HIS F 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5050 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18580 Z= 0.211 Angle : 0.591 13.752 25038 Z= 0.299 Chirality : 0.042 0.229 2793 Planarity : 0.004 0.043 3050 Dihedral : 10.104 87.423 2828 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.53 % Favored : 97.30 % Rotamer: Outliers : 3.11 % Allowed : 15.78 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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 (0.18), residues: 2268 helix: 2.47 (0.14), residues: 1320 sheet: -1.00 (0.37), residues: 166 loop : -1.08 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 460 HIS 0.006 0.001 HIS B 412 PHE 0.015 0.001 PHE H 73 TYR 0.022 0.001 TYR A 424 ARG 0.009 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 185 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.5144 (mmm) cc_final: 0.4735 (mmm) REVERT: A 503 MET cc_start: 0.4203 (OUTLIER) cc_final: 0.3741 (tpt) REVERT: A 633 ILE cc_start: 0.5220 (mm) cc_final: 0.4872 (mp) REVERT: B 586 ARG cc_start: 0.9382 (mmm-85) cc_final: 0.9093 (mmm160) REVERT: C 674 MET cc_start: -0.0150 (ptm) cc_final: -0.0602 (ptp) REVERT: D 503 MET cc_start: 0.5567 (OUTLIER) cc_final: 0.5269 (tpt) REVERT: E 135 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8331 (pt) REVERT: E 207 GLN cc_start: 0.9022 (mm110) cc_final: 0.8792 (tm-30) REVERT: F 61 SER cc_start: 0.9239 (t) cc_final: 0.8868 (p) REVERT: F 65 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.7785 (mtm110) REVERT: F 81 ASP cc_start: 0.8796 (t0) cc_final: 0.8577 (t70) REVERT: G 81 ASP cc_start: 0.9287 (p0) cc_final: 0.8830 (t0) REVERT: G 99 ARG cc_start: 0.9534 (tpp80) cc_final: 0.9255 (tpp80) REVERT: G 200 MET cc_start: 0.9183 (ptp) cc_final: 0.8982 (ptp) REVERT: H 6 ARG cc_start: 0.8659 (tmt-80) cc_final: 0.8204 (tmm160) REVERT: H 61 SER cc_start: 0.9445 (t) cc_final: 0.8726 (p) REVERT: H 70 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8935 (pp20) outliers start: 57 outliers final: 18 residues processed: 223 average time/residue: 1.1875 time to fit residues: 300.6306 Evaluate side-chains 190 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 182 optimal weight: 0.0970 chunk 124 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 112 optimal weight: 30.0000 chunk 196 optimal weight: 0.0470 chunk 55 optimal weight: 4.9990 overall best weight: 1.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN D 435 HIS D 461 ASN E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5077 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18580 Z= 0.259 Angle : 0.602 13.419 25038 Z= 0.304 Chirality : 0.042 0.206 2793 Planarity : 0.004 0.039 3050 Dihedral : 9.954 88.621 2828 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 3.22 % Allowed : 16.71 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.57 (0.18), residues: 2268 helix: 2.48 (0.14), residues: 1314 sheet: -1.03 (0.39), residues: 149 loop : -1.05 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 460 HIS 0.005 0.001 HIS G 60 PHE 0.023 0.001 PHE H 127 TYR 0.025 0.001 TYR B 647 ARG 0.011 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 185 time to evaluate : 1.968 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 633 ILE cc_start: 0.4917 (mm) cc_final: 0.4614 (mp) REVERT: C 674 MET cc_start: -0.0146 (ptm) cc_final: -0.0595 (ptp) REVERT: D 401 LEU cc_start: 0.2807 (OUTLIER) cc_final: 0.2508 (mp) REVERT: D 503 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.5161 (tpp) REVERT: E 66 THR cc_start: 0.9146 (t) cc_final: 0.8895 (t) REVERT: E 69 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7543 (pp) REVERT: E 70 GLU cc_start: 0.7831 (pp20) cc_final: 0.7596 (pp20) REVERT: E 135 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8470 (pt) REVERT: E 174 TYR cc_start: 0.8577 (p90) cc_final: 0.8374 (p90) REVERT: E 207 GLN cc_start: 0.9054 (mm110) cc_final: 0.8836 (tm-30) REVERT: F 61 SER cc_start: 0.9281 (t) cc_final: 0.8910 (p) REVERT: F 65 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7735 (mtm110) REVERT: F 81 ASP cc_start: 0.8800 (t0) cc_final: 0.8588 (t70) REVERT: F 92 ASP cc_start: 0.6856 (m-30) cc_final: 0.6508 (t70) REVERT: G 81 ASP cc_start: 0.9281 (p0) cc_final: 0.8821 (t0) REVERT: G 99 ARG cc_start: 0.9556 (tpp80) cc_final: 0.9252 (tpp80) REVERT: G 205 HIS cc_start: 0.8732 (OUTLIER) cc_final: 0.8406 (t-90) REVERT: H 6 ARG cc_start: 0.8716 (tmt-80) cc_final: 0.8202 (tmm160) REVERT: H 61 SER cc_start: 0.9520 (t) cc_final: 0.8833 (p) outliers start: 59 outliers final: 28 residues processed: 224 average time/residue: 1.1551 time to fit residues: 294.2711 Evaluate side-chains 203 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 591 ILE Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 200 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 73 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 128 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 435 HIS E 205 HIS G 149 ASN ** G 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5102 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18580 Z= 0.302 Angle : 0.623 12.586 25038 Z= 0.314 Chirality : 0.043 0.207 2793 Planarity : 0.004 0.041 3050 Dihedral : 9.920 89.282 2828 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.59 % Rotamer: Outliers : 3.06 % Allowed : 17.42 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.52 (0.18), residues: 2268 helix: 2.43 (0.14), residues: 1311 sheet: -1.21 (0.40), residues: 150 loop : -1.00 (0.22), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 460 HIS 0.005 0.001 HIS G 60 PHE 0.028 0.002 PHE A 658 TYR 0.017 0.001 TYR C 647 ARG 0.011 0.001 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 180 time to evaluate : 2.108 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 633 ILE cc_start: 0.5109 (mm) cc_final: 0.4797 (mp) REVERT: B 586 ARG cc_start: 0.9368 (mmm-85) cc_final: 0.9135 (mtp180) REVERT: C 674 MET cc_start: -0.0155 (ptm) cc_final: -0.0548 (ptp) REVERT: D 503 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5445 (tpp) REVERT: E 66 THR cc_start: 0.9219 (t) cc_final: 0.8982 (t) REVERT: E 69 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7632 (pp) REVERT: E 70 GLU cc_start: 0.7864 (pp20) cc_final: 0.7632 (pp20) REVERT: E 135 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8493 (pt) REVERT: E 207 GLN cc_start: 0.9054 (mm110) cc_final: 0.8832 (tm-30) REVERT: F 65 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7794 (mtm110) REVERT: F 81 ASP cc_start: 0.8830 (t0) cc_final: 0.8628 (t70) REVERT: F 92 ASP cc_start: 0.6464 (m-30) cc_final: 0.6173 (t0) REVERT: G 81 ASP cc_start: 0.9264 (p0) cc_final: 0.8807 (t0) REVERT: G 99 ARG cc_start: 0.9560 (tpp80) cc_final: 0.9270 (tpp80) REVERT: G 205 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8451 (t-90) REVERT: H 6 ARG cc_start: 0.8696 (tmt-80) cc_final: 0.8158 (tmm160) REVERT: H 61 SER cc_start: 0.9519 (t) cc_final: 0.8819 (p) REVERT: H 74 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8905 (mttt) REVERT: H 205 HIS cc_start: 0.8606 (OUTLIER) cc_final: 0.7640 (m-70) outliers start: 56 outliers final: 28 residues processed: 222 average time/residue: 1.2044 time to fit residues: 302.7775 Evaluate side-chains 199 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 135 ILE Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 205 HIS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 211 optimal weight: 0.5980 chunk 24 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 184 optimal weight: 3.9990 chunk 122 optimal weight: 30.0000 chunk 218 optimal weight: 1.9990 chunk 136 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5062 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18580 Z= 0.189 Angle : 0.592 13.189 25038 Z= 0.296 Chirality : 0.041 0.228 2793 Planarity : 0.003 0.041 3050 Dihedral : 9.352 89.032 2828 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.62 % Favored : 97.21 % Rotamer: Outliers : 2.79 % Allowed : 17.91 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.71 (0.18), residues: 2268 helix: 2.59 (0.14), residues: 1312 sheet: -0.84 (0.42), residues: 136 loop : -1.02 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 460 HIS 0.006 0.001 HIS G 60 PHE 0.028 0.001 PHE H 127 TYR 0.017 0.001 TYR A 768 ARG 0.010 0.000 ARG A 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 186 time to evaluate : 1.973 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 633 ILE cc_start: 0.4767 (mm) cc_final: 0.4416 (mp) REVERT: B 721 MET cc_start: 0.5727 (ptm) cc_final: 0.5527 (ptm) REVERT: C 674 MET cc_start: -0.0222 (ptm) cc_final: -0.0463 (ptp) REVERT: D 503 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.5323 (tpp) REVERT: E 69 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7686 (pp) REVERT: E 70 GLU cc_start: 0.7829 (pp20) cc_final: 0.7624 (pp20) REVERT: E 128 TYR cc_start: 0.7151 (t80) cc_final: 0.6927 (t80) REVERT: F 65 ARG cc_start: 0.8252 (mtm-85) cc_final: 0.7772 (mtm110) REVERT: F 81 ASP cc_start: 0.8801 (t0) cc_final: 0.8599 (t70) REVERT: F 92 ASP cc_start: 0.6633 (m-30) cc_final: 0.6319 (t0) REVERT: G 58 MET cc_start: 0.8521 (tpt) cc_final: 0.7732 (mmm) REVERT: G 81 ASP cc_start: 0.9216 (p0) cc_final: 0.8766 (t0) REVERT: G 99 ARG cc_start: 0.9488 (tpp80) cc_final: 0.9151 (tpp80) REVERT: H 6 ARG cc_start: 0.8544 (tmt-80) cc_final: 0.8052 (tmm160) REVERT: H 61 SER cc_start: 0.9402 (t) cc_final: 0.8546 (p) REVERT: H 205 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.7602 (m-70) outliers start: 51 outliers final: 23 residues processed: 224 average time/residue: 1.2432 time to fit residues: 313.6331 Evaluate side-chains 196 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 743 ARG Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 CYS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 135 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 65 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 chunk 108 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 171 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS ** G 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS H 160 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18580 Z= 0.168 Angle : 0.609 13.535 25038 Z= 0.301 Chirality : 0.041 0.215 2793 Planarity : 0.003 0.046 3050 Dihedral : 8.914 88.823 2828 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.66 % Favored : 97.16 % Rotamer: Outliers : 2.51 % Allowed : 18.35 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % 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: 1.82 (0.18), residues: 2268 helix: 2.69 (0.14), residues: 1310 sheet: -0.70 (0.43), residues: 131 loop : -0.98 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 460 HIS 0.006 0.001 HIS G 60 PHE 0.025 0.001 PHE A 658 TYR 0.014 0.001 TYR C 647 ARG 0.011 0.000 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 1.954 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 586 ARG cc_start: 0.9226 (mmm-85) cc_final: 0.8694 (tmm160) REVERT: A 633 ILE cc_start: 0.4718 (mm) cc_final: 0.4371 (mp) REVERT: B 503 MET cc_start: 0.4778 (ppp) cc_final: 0.4434 (ppp) REVERT: C 674 MET cc_start: -0.0280 (ptm) cc_final: -0.0504 (ptp) REVERT: E 69 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7696 (pp) REVERT: E 128 TYR cc_start: 0.7161 (t80) cc_final: 0.6925 (t80) REVERT: F 56 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8587 (tt0) REVERT: F 65 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7784 (mtm110) REVERT: F 92 ASP cc_start: 0.6667 (m-30) cc_final: 0.6347 (t0) REVERT: G 58 MET cc_start: 0.8549 (tpt) cc_final: 0.7760 (mmm) REVERT: G 81 ASP cc_start: 0.9204 (p0) cc_final: 0.8773 (t0) REVERT: G 99 ARG cc_start: 0.9498 (tpp80) cc_final: 0.9112 (tpp80) REVERT: G 126 GLU cc_start: 0.9014 (tt0) cc_final: 0.8785 (tp30) REVERT: H 6 ARG cc_start: 0.8582 (tmt-80) cc_final: 0.8043 (tmm160) REVERT: H 61 SER cc_start: 0.9332 (t) cc_final: 0.8458 (p) REVERT: H 205 HIS cc_start: 0.8527 (OUTLIER) cc_final: 0.7534 (m-70) outliers start: 46 outliers final: 22 residues processed: 221 average time/residue: 1.2102 time to fit residues: 302.4858 Evaluate side-chains 199 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 812 ILE Chi-restraints excluded: chain C residue 647 TYR Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 203 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 88 optimal weight: 0.0970 chunk 160 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 HIS G 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5072 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18580 Z= 0.212 Angle : 0.647 13.265 25038 Z= 0.318 Chirality : 0.041 0.210 2793 Planarity : 0.003 0.046 3050 Dihedral : 8.835 86.416 2828 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.84 % Favored : 96.99 % Rotamer: Outliers : 1.91 % Allowed : 19.22 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.77 (0.18), residues: 2268 helix: 2.62 (0.14), residues: 1312 sheet: -0.78 (0.44), residues: 126 loop : -0.97 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 460 HIS 0.004 0.001 HIS B 412 PHE 0.028 0.001 PHE H 127 TYR 0.019 0.001 TYR A 768 ARG 0.011 0.000 ARG C 586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.3347 (mmp) cc_final: 0.2925 (mmt) REVERT: A 586 ARG cc_start: 0.9241 (mmm-85) cc_final: 0.8772 (tmm160) REVERT: B 503 MET cc_start: 0.4998 (ppp) cc_final: 0.4459 (ppp) REVERT: C 708 MET cc_start: 0.1541 (OUTLIER) cc_final: 0.1155 (mtm) REVERT: E 207 GLN cc_start: 0.9233 (tt0) cc_final: 0.8937 (tm-30) REVERT: F 65 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7797 (mtm110) REVERT: F 92 ASP cc_start: 0.6674 (m-30) cc_final: 0.6354 (t0) REVERT: G 81 ASP cc_start: 0.9226 (p0) cc_final: 0.8760 (t0) REVERT: G 99 ARG cc_start: 0.9493 (tpp80) cc_final: 0.9104 (tpp80) REVERT: G 126 GLU cc_start: 0.9013 (tt0) cc_final: 0.8781 (tp30) REVERT: H 6 ARG cc_start: 0.8599 (tmt-80) cc_final: 0.8049 (tmm160) REVERT: H 61 SER cc_start: 0.9481 (t) cc_final: 0.8647 (p) REVERT: H 205 HIS cc_start: 0.8545 (OUTLIER) cc_final: 0.7549 (m-70) outliers start: 35 outliers final: 21 residues processed: 205 average time/residue: 1.2367 time to fit residues: 286.8831 Evaluate side-chains 191 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 807 MET Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 659 PHE Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 131 optimal weight: 0.1980 chunk 102 optimal weight: 0.9990 chunk 149 optimal weight: 0.2980 chunk 226 optimal weight: 0.9980 chunk 208 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 143 optimal weight: 30.0000 chunk 191 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 HIS E 205 HIS G 149 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: 0.5050 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18580 Z= 0.174 Angle : 0.651 13.596 25038 Z= 0.315 Chirality : 0.041 0.193 2793 Planarity : 0.003 0.043 3050 Dihedral : 8.548 85.926 2828 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.66 % Favored : 97.16 % Rotamer: Outliers : 1.47 % Allowed : 19.88 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.18), residues: 2268 helix: 2.70 (0.14), residues: 1310 sheet: -0.65 (0.44), residues: 124 loop : -0.97 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 460 HIS 0.004 0.001 HIS G 60 PHE 0.029 0.001 PHE B 659 TYR 0.020 0.001 TYR E 128 ARG 0.010 0.000 ARG C 586 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 178 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 MET cc_start: 0.3324 (mmp) cc_final: 0.2888 (mmt) REVERT: A 586 ARG cc_start: 0.9208 (mmm-85) cc_final: 0.8806 (tmm160) REVERT: B 408 MET cc_start: 0.4698 (tpp) cc_final: 0.4373 (tpp) REVERT: B 463 MET cc_start: 0.0894 (mmp) cc_final: 0.0619 (mmm) REVERT: B 503 MET cc_start: 0.5005 (ppp) cc_final: 0.4573 (ppp) REVERT: B 590 ASP cc_start: 0.8799 (m-30) cc_final: 0.8516 (p0) REVERT: C 708 MET cc_start: 0.1558 (OUTLIER) cc_final: 0.1157 (mtm) REVERT: E 174 TYR cc_start: 0.8692 (p90) cc_final: 0.8448 (p90) REVERT: E 207 GLN cc_start: 0.9233 (tt0) cc_final: 0.8936 (tm-30) REVERT: F 56 GLU cc_start: 0.8765 (tt0) cc_final: 0.8532 (mm-30) REVERT: F 65 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.7788 (mtm110) REVERT: G 56 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8644 (mm-30) REVERT: G 81 ASP cc_start: 0.9207 (p0) cc_final: 0.8767 (t0) REVERT: G 99 ARG cc_start: 0.9483 (tpp80) cc_final: 0.9092 (tpp80) REVERT: G 126 GLU cc_start: 0.9002 (tt0) cc_final: 0.8776 (tp30) REVERT: H 6 ARG cc_start: 0.8436 (tmt-80) cc_final: 0.7883 (tmm160) REVERT: H 34 LEU cc_start: 0.9025 (tp) cc_final: 0.8502 (tp) REVERT: H 61 SER cc_start: 0.9393 (t) cc_final: 0.8496 (p) REVERT: H 205 HIS cc_start: 0.8522 (OUTLIER) cc_final: 0.7513 (m-70) outliers start: 27 outliers final: 19 residues processed: 201 average time/residue: 1.2124 time to fit residues: 275.0202 Evaluate side-chains 186 residues out of total 1932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 707 THR Chi-restraints excluded: chain C residue 708 MET Chi-restraints excluded: chain D residue 527 MET Chi-restraints excluded: chain D residue 544 SER Chi-restraints excluded: chain D residue 631 SER Chi-restraints excluded: chain D residue 764 ASN Chi-restraints excluded: chain E residue 40 CYS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 205 HIS Chi-restraints excluded: chain G residue 77 CYS Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 205 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 55 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 180 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 158 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 HIS G 149 ASN G 205 HIS ** H 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.153788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.087365 restraints weight = 77485.210| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 5.36 r_work: 0.3032 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3031 r_free = 0.3031 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3031 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18580 Z= 0.187 Angle : 0.659 14.828 25038 Z= 0.318 Chirality : 0.041 0.183 2793 Planarity : 0.004 0.045 3050 Dihedral : 8.518 85.660 2828 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.75 % Favored : 97.07 % Rotamer: Outliers : 1.42 % Allowed : 20.21 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.18), residues: 2268 helix: 2.66 (0.14), residues: 1311 sheet: -0.60 (0.46), residues: 118 loop : -0.93 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 460 HIS 0.004 0.001 HIS G 60 PHE 0.027 0.001 PHE H 127 TYR 0.038 0.001 TYR E 128 ARG 0.010 0.001 ARG C 586 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6284.50 seconds wall clock time: 112 minutes 56.99 seconds (6776.99 seconds total)