Starting phenix.real_space_refine on Mon Apr 8 12:13:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/04_2024/8j8r_36078_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/04_2024/8j8r_36078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/04_2024/8j8r_36078.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/04_2024/8j8r_36078.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/04_2024/8j8r_36078_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8r_36078/04_2024/8j8r_36078_updated.pdb" } resolution = 2.9 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= 0.121 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 9 5.49 5 S 27 5.16 5 C 8522 2.51 5 N 2304 2.21 5 O 2562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 30": "OD1" <-> "OD2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 76": "OD1" <-> "OD2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 13424 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2691 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 317} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2695 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 317} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2693 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 317} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 920 Classifications: {'peptide': 119} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 115} Chain: "E" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 798 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 911 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "U" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 7.61, per 1000 atoms: 0.57 Number of scatterers: 13424 At special positions: 0 Unit cell: (148.664, 141.47, 91.1164, 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 27 16.00 P 9 15.00 O 2562 8.00 N 2304 7.00 C 8522 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.36 Conformation dependent library (CDL) restraints added in 2.2 seconds 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3238 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 10 helices and 36 sheets defined 3.2% alpha, 39.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'B' and resid 100 through 112 removed outlier: 6.707A pdb=" N GLN B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N HIS B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 49 No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'M' and resid 91 through 93 No H-bonds generated for 'chain 'M' and resid 91 through 93' Processing sheet with id= A, first strand: chain 'A' and resid 10 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.395A pdb=" N ARG A 170 " --> pdb=" O PHE A 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.712A pdb=" N ASP A 144 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 145 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'A' and resid 184 through 190 removed outlier: 3.656A pdb=" N SER A 197 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A 224 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.419A pdb=" N VAL A 343 " --> pdb=" O TYR A 209 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 336 through 342 removed outlier: 3.547A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 54 through 60 removed outlier: 6.797A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE A 82 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 10 through 13 Processing sheet with id= J, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.152A pdb=" N ARG B 170 " --> pdb=" O PHE B 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.675A pdb=" N PHE B 76 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP B 144 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= M, first strand: chain 'B' and resid 184 through 189 removed outlier: 3.501A pdb=" N LEU B 200 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 336 through 342 removed outlier: 3.990A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 329 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS B 231 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 54 through 60 removed outlier: 6.806A pdb=" N VAL B 56 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLN B 86 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 58 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ASN B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 60 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ILE B 82 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 10 through 13 Processing sheet with id= Q, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.502A pdb=" N ARG C 170 " --> pdb=" O PHE C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 77 through 79 removed outlier: 3.834A pdb=" N PHE C 145 " --> pdb=" O ILE C 169 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= T, first strand: chain 'C' and resid 184 through 190 Processing sheet with id= U, first strand: chain 'C' and resid 336 through 342 removed outlier: 3.967A pdb=" N VAL C 336 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA C 240 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS C 251 " --> pdb=" O ALA C 240 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 54 through 60 removed outlier: 6.714A pdb=" N VAL C 56 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N GLN C 86 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 58 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN C 84 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL C 60 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILE C 82 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.557A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 13 through 15 removed outlier: 5.994A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 100 through 102 removed outlier: 3.835A pdb=" N TYR D 112 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.641A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.023A pdb=" N LYS E 104 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= AC, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.650A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 5 through 8 Processing sheet with id= AE, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.241A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA L 85 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 6 through 10 Processing sheet with id= AG, first strand: chain 'M' and resid 13 through 15 removed outlier: 6.084A pdb=" N ARG M 41 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TRP M 50 " --> pdb=" O ARG M 41 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'N' and resid 6 through 8 removed outlier: 3.535A pdb=" N VAL N 20 " --> pdb=" O ILE N 76 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.039A pdb=" N LYS N 104 " --> pdb=" O LEU N 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'N' and resid 86 through 91 removed outlier: 6.048A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 5.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4326 1.34 - 1.46: 3188 1.46 - 1.58: 6151 1.58 - 1.70: 31 1.70 - 1.81: 39 Bond restraints: 13735 Sorted by residual: bond pdb=" OG1 TPO G 360 " pdb=" P TPO G 360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" OG1 TPO V 349 " pdb=" P TPO V 349 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" OG1 TPO U 307 " pdb=" P TPO U 307 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" OG1 TPO G 363 " pdb=" P TPO G 363 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" OG1 TPO U 310 " pdb=" P TPO U 310 " ideal model delta sigma weight residual 1.717 1.610 0.107 2.00e-02 2.50e+03 2.89e+01 ... (remaining 13730 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.76: 464 106.76 - 113.56: 7577 113.56 - 120.36: 4630 120.36 - 127.17: 5861 127.17 - 133.97: 154 Bond angle restraints: 18686 Sorted by residual: angle pdb=" C CYS B 69 " pdb=" N ASP B 70 " pdb=" CA ASP B 70 " ideal model delta sigma weight residual 123.03 115.87 7.16 1.34e+00 5.57e-01 2.85e+01 angle pdb=" C VAL B 71 " pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta sigma weight residual 122.93 115.81 7.12 1.45e+00 4.76e-01 2.41e+01 angle pdb=" CA PRO C 97 " pdb=" N PRO C 97 " pdb=" CD PRO C 97 " ideal model delta sigma weight residual 112.00 105.27 6.73 1.40e+00 5.10e-01 2.31e+01 angle pdb=" N VAL B 71 " pdb=" CA VAL B 71 " pdb=" C VAL B 71 " ideal model delta sigma weight residual 108.81 101.87 6.94 1.62e+00 3.81e-01 1.84e+01 angle pdb=" CB TPO G 363 " pdb=" OG1 TPO G 363 " pdb=" P TPO G 363 " ideal model delta sigma weight residual 119.31 106.51 12.80 3.00e+00 1.11e-01 1.82e+01 ... (remaining 18681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7347 17.79 - 35.58: 638 35.58 - 53.37: 197 53.37 - 71.16: 22 71.16 - 88.95: 23 Dihedral angle restraints: 8227 sinusoidal: 3187 harmonic: 5040 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 59.96 33.04 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" CB CYS M 25 " pdb=" SG CYS M 25 " pdb=" SG CYS M 99 " pdb=" CB CYS M 99 " ideal model delta sinusoidal sigma weight residual 93.00 64.38 28.62 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA ASP B 79 " pdb=" CB ASP B 79 " pdb=" CG ASP B 79 " pdb=" OD1 ASP B 79 " ideal model delta sinusoidal sigma weight residual -30.00 -89.02 59.02 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 8224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1808 0.058 - 0.116: 266 0.116 - 0.174: 33 0.174 - 0.232: 1 0.232 - 0.291: 1 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CA VAL B 71 " pdb=" N VAL B 71 " pdb=" C VAL B 71 " pdb=" CB VAL B 71 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB TPO V 352 " pdb=" CA TPO V 352 " pdb=" OG1 TPO V 352 " pdb=" CG2 TPO V 352 " both_signs ideal model delta sigma weight residual False 2.48 2.29 0.19 2.00e-01 2.50e+01 9.42e-01 chirality pdb=" CA CYS B 69 " pdb=" N CYS B 69 " pdb=" C CYS B 69 " pdb=" CB CYS B 69 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 2106 not shown) Planarity restraints: 2391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG C 96 " -0.051 5.00e-02 4.00e+02 7.40e-02 8.75e+00 pdb=" N PRO C 97 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 97 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 97 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 84 " 0.011 2.00e-02 2.50e+03 1.71e-02 5.13e+00 pdb=" CG PHE E 84 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 84 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE E 84 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 84 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE E 84 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 84 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 91 " -0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO C 92 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 92 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 92 " -0.028 5.00e-02 4.00e+02 ... (remaining 2388 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 925 2.74 - 3.28: 12484 3.28 - 3.82: 21277 3.82 - 4.36: 25210 4.36 - 4.90: 46035 Nonbonded interactions: 105931 Sorted by model distance: nonbonded pdb=" OD1 ASP B 205 " pdb=" OH TYR B 209 " model vdw 2.199 2.440 nonbonded pdb=" N GLU C 177 " pdb=" OE1 GLU C 177 " model vdw 2.216 2.520 nonbonded pdb=" N ASN C 93 " pdb=" OD1 ASN C 93 " model vdw 2.250 2.520 nonbonded pdb=" OD2 ASP A 136 " pdb=" NH1 ARG A 286 " model vdw 2.253 2.520 nonbonded pdb=" O THR C 222 " pdb=" OG1 THR C 222 " model vdw 2.262 2.440 ... (remaining 105926 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 7 through 69 or (resid 70 and (name N or name CA or name C \ or name O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 157 or (resid 158 and \ (name N or name CA or name C or name O or name CB )) or resid 159 through 160 or \ (resid 161 through 162 and (name N or name CA or name C or name O or name CB )) \ or resid 163 through 191 or (resid 192 and (name N or name CA or name C or name \ O or name CB )) or resid 193 through 307 or (resid 308 and (name N or name CA o \ r name C or name O or name CB )) or resid 309 through 311 or (resid 312 through \ 314 and (name N or name CA or name C or name O or name CB )) or resid 315 throug \ h 350)) selection = (chain 'B' and (resid 7 through 48 or (resid 49 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 75 or (resid 76 and (n \ ame N or name CA or name C or name O or name CB )) or resid 77 through 110 or (r \ esid 111 and (name N or name CA or name C or name O or name CB )) or resid 112 t \ hrough 157 or (resid 158 and (name N or name CA or name C or name O or name CB ) \ ) or resid 159 through 160 or (resid 161 through 162 and (name N or name CA or n \ ame C or name O or name CB )) or resid 163 through 307 or (resid 308 and (name N \ or name CA or name C or name O or name CB )) or resid 309 through 350)) selection = (chain 'C' and (resid 7 through 48 or (resid 49 through 51 and (name N or name C \ A or name C or name O or name CB )) or resid 52 or (resid 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 65 or (resid 66 and (n \ ame N or name CA or name C or name O or name CB )) or resid 67 through 69 or (re \ sid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 thro \ ugh 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or \ resid 77 through 110 or (resid 111 and (name N or name CA or name C or name O or \ name CB )) or resid 112 through 311 or (resid 312 through 314 and (name N or na \ me CA or name C or name O or name CB )) or resid 315 through 350)) } ncs_group { reference = (chain 'D' and (resid 5 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 106 or (resid 107 and (name N or na \ me CA or name C or name O or name CB )) or resid 108 through 122)) selection = (chain 'H' and (resid 5 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 through 122)) selection = (chain 'M' and (resid 5 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 122)) } ncs_group { reference = (chain 'E' and (resid 1 through 30 or resid 33 through 107)) selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.950 Check model and map are aligned: 0.220 Set scattering table: 0.170 Process input model: 38.590 Find NCS groups from input model: 0.990 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:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.004 0.110 13735 Z= 0.290 Angle : 0.636 12.797 18686 Z= 0.307 Chirality : 0.044 0.291 2109 Planarity : 0.004 0.074 2391 Dihedral : 15.504 88.948 4971 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.26 % Allowed : 18.24 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % 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: 0.97 (0.22), residues: 1687 helix: 1.80 (0.82), residues: 36 sheet: 1.51 (0.20), residues: 790 loop : -0.24 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 106 HIS 0.006 0.001 HIS B 160 PHE 0.039 0.001 PHE E 84 TYR 0.026 0.001 TYR C 48 ARG 0.009 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 192 time to evaluate : 1.651 Fit side-chains outliers start: 33 outliers final: 33 residues processed: 224 average time/residue: 0.9679 time to fit residues: 244.3102 Evaluate side-chains 218 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 185 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain M residue 53 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain N residue 21 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 42 optimal weight: 0.0170 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN B 131 GLN B 218 ASN B 220 HIS B 281 ASN C 262 GLN D 6 GLN H 80 ASN M 38 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.0811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13735 Z= 0.173 Angle : 0.544 8.394 18686 Z= 0.283 Chirality : 0.044 0.155 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.893 58.972 1946 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.77 % Allowed : 17.08 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % 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: 0.94 (0.21), residues: 1687 helix: 1.91 (0.82), residues: 36 sheet: 1.47 (0.19), residues: 808 loop : -0.28 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 106 HIS 0.005 0.001 HIS B 160 PHE 0.029 0.002 PHE E 84 TYR 0.012 0.001 TYR H 107 ARG 0.005 0.000 ARG M 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 194 time to evaluate : 1.622 Fit side-chains REVERT: B 316 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7939 (mt) REVERT: C 30 ASP cc_start: 0.8413 (t0) cc_final: 0.8088 (t0) REVERT: C 163 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.6980 (p0) REVERT: D 92 GLU cc_start: 0.7624 (pm20) cc_final: 0.7221 (pm20) outliers start: 55 outliers final: 34 residues processed: 233 average time/residue: 0.9169 time to fit residues: 241.4897 Evaluate side-chains 217 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain V residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 163 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN B 220 HIS H 80 ASN L 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13735 Z= 0.284 Angle : 0.585 8.036 18686 Z= 0.306 Chirality : 0.045 0.161 2109 Planarity : 0.004 0.053 2391 Dihedral : 5.674 56.048 1927 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.94 % Allowed : 16.94 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % 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: 0.78 (0.21), residues: 1687 helix: 1.79 (0.81), residues: 36 sheet: 1.34 (0.19), residues: 807 loop : -0.35 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 106 HIS 0.006 0.001 HIS B 112 PHE 0.036 0.002 PHE E 84 TYR 0.019 0.001 TYR C 48 ARG 0.006 0.000 ARG M 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 197 time to evaluate : 1.536 Fit side-chains REVERT: A 228 THR cc_start: 0.6783 (m) cc_final: 0.6511 (t) REVERT: A 327 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8358 (tttt) REVERT: B 222 THR cc_start: 0.7912 (m) cc_final: 0.7514 (p) REVERT: C 163 ASN cc_start: 0.7795 (OUTLIER) cc_final: 0.7122 (p0) REVERT: D 92 GLU cc_start: 0.7707 (pm20) cc_final: 0.7348 (pm20) REVERT: L 93 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8829 (tmtm) REVERT: M 83 TYR cc_start: 0.8079 (m-80) cc_final: 0.7871 (m-80) outliers start: 72 outliers final: 48 residues processed: 248 average time/residue: 0.8383 time to fit residues: 235.1599 Evaluate side-chains 239 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 189 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 353 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.0010 chunk 113 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN B 220 HIS H 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13735 Z= 0.233 Angle : 0.559 8.841 18686 Z= 0.290 Chirality : 0.044 0.156 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.523 58.517 1924 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.83 % Allowed : 17.56 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % 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: 0.70 (0.21), residues: 1687 helix: 1.80 (0.81), residues: 36 sheet: 1.26 (0.19), residues: 808 loop : -0.39 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 106 HIS 0.005 0.001 HIS B 112 PHE 0.029 0.002 PHE M 105 TYR 0.016 0.001 TYR H 107 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 192 time to evaluate : 1.659 Fit side-chains REVERT: A 228 THR cc_start: 0.6801 (m) cc_final: 0.6547 (t) REVERT: B 222 THR cc_start: 0.7879 (m) cc_final: 0.7514 (p) REVERT: C 30 ASP cc_start: 0.8410 (t0) cc_final: 0.8114 (t0) REVERT: C 163 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7179 (p0) REVERT: D 92 GLU cc_start: 0.7689 (pm20) cc_final: 0.7312 (pm20) REVERT: H 49 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7025 (tm-30) REVERT: H 86 MET cc_start: 0.7830 (mtp) cc_final: 0.6611 (mtp) REVERT: L 93 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8806 (tmtm) outliers start: 85 outliers final: 55 residues processed: 256 average time/residue: 0.8729 time to fit residues: 253.4026 Evaluate side-chains 242 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 184 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 93 LYS Chi-restraints excluded: chain M residue 31 ASN Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 353 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 160 HIS B 218 ASN B 220 HIS C 262 GLN D 31 ASN H 80 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.062 13735 Z= 0.595 Angle : 0.758 9.374 18686 Z= 0.401 Chirality : 0.052 0.229 2109 Planarity : 0.006 0.056 2391 Dihedral : 6.313 59.226 1924 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 6.52 % Allowed : 18.59 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % 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: 0.20 (0.21), residues: 1687 helix: 1.30 (0.81), residues: 36 sheet: 0.93 (0.19), residues: 803 loop : -0.72 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 106 HIS 0.009 0.002 HIS B 160 PHE 0.068 0.003 PHE M 105 TYR 0.016 0.002 TYR C 48 ARG 0.007 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 185 time to evaluate : 1.644 Fit side-chains REVERT: A 228 THR cc_start: 0.6952 (m) cc_final: 0.6648 (t) REVERT: B 207 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: B 226 THR cc_start: 0.7953 (p) cc_final: 0.7751 (m) REVERT: C 163 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7241 (p0) REVERT: C 195 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: D 49 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: D 76 ASP cc_start: 0.7789 (p0) cc_final: 0.7460 (p0) REVERT: D 92 GLU cc_start: 0.7701 (pm20) cc_final: 0.7376 (pm20) REVERT: E 46 LYS cc_start: 0.8151 (mttm) cc_final: 0.7709 (mptt) REVERT: H 49 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7207 (tm-30) outliers start: 95 outliers final: 62 residues processed: 259 average time/residue: 0.9160 time to fit residues: 267.9414 Evaluate side-chains 244 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 177 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 295 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 77 THR Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 353 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 160 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS B 86 GLN B 218 ASN B 220 HIS B 262 GLN ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN C 296 HIS H 80 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13735 Z= 0.181 Angle : 0.558 9.894 18686 Z= 0.287 Chirality : 0.044 0.156 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.645 56.243 1924 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.66 % Allowed : 21.12 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % 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: 0.39 (0.21), residues: 1687 helix: 1.52 (0.83), residues: 36 sheet: 1.02 (0.19), residues: 807 loop : -0.55 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 106 HIS 0.004 0.001 HIS B 112 PHE 0.026 0.002 PHE M 105 TYR 0.015 0.001 TYR H 107 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 193 time to evaluate : 1.574 Fit side-chains REVERT: A 77 ARG cc_start: 0.8411 (ttt90) cc_final: 0.8206 (ttt90) REVERT: A 228 THR cc_start: 0.6902 (m) cc_final: 0.6627 (t) REVERT: B 222 THR cc_start: 0.7951 (m) cc_final: 0.7604 (p) REVERT: C 30 ASP cc_start: 0.8376 (t0) cc_final: 0.8104 (t0) REVERT: C 163 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7312 (p0) REVERT: C 195 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7083 (m-30) REVERT: D 92 GLU cc_start: 0.7735 (pm20) cc_final: 0.7388 (pm20) REVERT: H 49 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: H 86 MET cc_start: 0.7754 (mtp) cc_final: 0.6649 (mtp) outliers start: 68 outliers final: 48 residues processed: 249 average time/residue: 0.9048 time to fit residues: 254.4867 Evaluate side-chains 236 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 185 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 0.4980 chunk 90 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 159 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 98 optimal weight: 0.2980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN B 220 HIS C 262 GLN C 296 HIS H 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13735 Z= 0.286 Angle : 0.594 8.648 18686 Z= 0.309 Chirality : 0.045 0.163 2109 Planarity : 0.004 0.053 2391 Dihedral : 5.519 55.165 1921 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.56 % Allowed : 20.64 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % 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: 0.33 (0.21), residues: 1687 helix: 1.51 (0.82), residues: 36 sheet: 0.96 (0.19), residues: 805 loop : -0.56 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 106 HIS 0.005 0.001 HIS B 112 PHE 0.042 0.002 PHE E 84 TYR 0.015 0.001 TYR H 107 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 188 time to evaluate : 1.631 Fit side-chains REVERT: A 77 ARG cc_start: 0.8434 (ttt90) cc_final: 0.8221 (ttt90) REVERT: A 228 THR cc_start: 0.6917 (m) cc_final: 0.6646 (t) REVERT: B 222 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7663 (p) REVERT: C 163 ASN cc_start: 0.7797 (OUTLIER) cc_final: 0.7397 (p0) REVERT: C 195 ASP cc_start: 0.7347 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: D 49 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: D 92 GLU cc_start: 0.7718 (pm20) cc_final: 0.7370 (pm20) REVERT: H 49 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7114 (tm-30) outliers start: 81 outliers final: 60 residues processed: 252 average time/residue: 0.9018 time to fit residues: 256.7380 Evaluate side-chains 249 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 184 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 49 GLU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 353 SER Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 109 optimal weight: 0.0170 chunk 79 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 HIS B 218 ASN B 220 HIS B 262 GLN C 296 HIS H 80 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13735 Z= 0.168 Angle : 0.543 11.982 18686 Z= 0.277 Chirality : 0.044 0.151 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.199 51.959 1921 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.32 % Allowed : 22.02 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1687 helix: 1.65 (0.83), residues: 36 sheet: 1.05 (0.19), residues: 807 loop : -0.48 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 106 HIS 0.007 0.001 HIS B 160 PHE 0.024 0.001 PHE B 269 TYR 0.015 0.001 TYR H 107 ARG 0.005 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 191 time to evaluate : 1.642 Fit side-chains REVERT: A 77 ARG cc_start: 0.8415 (ttt90) cc_final: 0.8189 (ttt90) REVERT: B 86 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: B 207 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7572 (tm-30) REVERT: B 222 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7651 (p) REVERT: B 330 VAL cc_start: 0.6774 (m) cc_final: 0.6546 (m) REVERT: C 30 ASP cc_start: 0.8317 (t0) cc_final: 0.8014 (t0) REVERT: C 163 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7475 (p0) REVERT: C 195 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: C 260 ASP cc_start: 0.7142 (m-30) cc_final: 0.6790 (m-30) REVERT: D 92 GLU cc_start: 0.7713 (pm20) cc_final: 0.7355 (pm20) REVERT: H 46 LYS cc_start: 0.7347 (tptp) cc_final: 0.7144 (tptp) REVERT: H 49 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7074 (tm-30) outliers start: 63 outliers final: 48 residues processed: 238 average time/residue: 0.9270 time to fit residues: 248.3503 Evaluate side-chains 239 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 185 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain N residue 107 ILE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 0.0770 chunk 134 optimal weight: 2.9990 chunk 141 optimal weight: 0.0770 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 HIS B 220 HIS B 262 GLN C 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13735 Z= 0.163 Angle : 0.536 11.001 18686 Z= 0.273 Chirality : 0.043 0.149 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.037 50.066 1921 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.18 % Allowed : 22.70 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1687 helix: 1.78 (0.83), residues: 36 sheet: 1.10 (0.19), residues: 807 loop : -0.43 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 106 HIS 0.004 0.001 HIS B 112 PHE 0.044 0.002 PHE E 84 TYR 0.022 0.001 TYR B 85 ARG 0.004 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 188 time to evaluate : 1.638 Fit side-chains REVERT: A 77 ARG cc_start: 0.8403 (ttt90) cc_final: 0.8179 (ttt90) REVERT: B 207 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: B 222 THR cc_start: 0.7988 (OUTLIER) cc_final: 0.7657 (p) REVERT: B 330 VAL cc_start: 0.6759 (m) cc_final: 0.6542 (m) REVERT: C 30 ASP cc_start: 0.8290 (t0) cc_final: 0.8010 (t0) REVERT: C 163 ASN cc_start: 0.7760 (OUTLIER) cc_final: 0.7535 (p0) REVERT: C 195 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6879 (m-30) REVERT: D 92 GLU cc_start: 0.7663 (pm20) cc_final: 0.7296 (pm20) REVERT: H 22 ARG cc_start: 0.7740 (ttt-90) cc_final: 0.7230 (ttp-170) REVERT: H 49 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: H 86 MET cc_start: 0.7668 (mtp) cc_final: 0.6446 (mtp) REVERT: M 49 GLU cc_start: 0.8696 (tt0) cc_final: 0.8463 (tm-30) outliers start: 61 outliers final: 47 residues processed: 236 average time/residue: 0.9160 time to fit residues: 244.4193 Evaluate side-chains 235 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 183 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 190 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 0.0270 chunk 80 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN ** B 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS B 262 GLN C 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13735 Z= 0.201 Angle : 0.553 10.050 18686 Z= 0.283 Chirality : 0.044 0.148 2109 Planarity : 0.004 0.052 2391 Dihedral : 5.070 49.014 1921 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.12 % Allowed : 22.91 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % 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: 0.52 (0.21), residues: 1687 helix: 1.75 (0.83), residues: 36 sheet: 1.08 (0.19), residues: 807 loop : -0.43 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 106 HIS 0.010 0.001 HIS B 160 PHE 0.026 0.002 PHE M 105 TYR 0.014 0.001 TYR H 107 ARG 0.004 0.000 ARG A 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3374 Ramachandran restraints generated. 1687 Oldfield, 0 Emsley, 1687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 189 time to evaluate : 1.622 Fit side-chains REVERT: A 77 ARG cc_start: 0.8411 (ttt90) cc_final: 0.8181 (ttt90) REVERT: B 207 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: B 222 THR cc_start: 0.8024 (m) cc_final: 0.7623 (p) REVERT: B 330 VAL cc_start: 0.6763 (m) cc_final: 0.6539 (m) REVERT: C 30 ASP cc_start: 0.8328 (t0) cc_final: 0.8041 (t0) REVERT: C 163 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7494 (p0) REVERT: C 195 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6890 (m-30) REVERT: D 92 GLU cc_start: 0.7668 (pm20) cc_final: 0.7306 (pm20) REVERT: H 49 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: M 49 GLU cc_start: 0.8702 (tt0) cc_final: 0.8488 (tm-30) outliers start: 60 outliers final: 49 residues processed: 237 average time/residue: 0.9118 time to fit residues: 243.5887 Evaluate side-chains 236 residues out of total 1507 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 183 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 ASN Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 32 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 120 THR Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 4.9990 chunk 40 optimal weight: 0.0010 chunk 121 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 131 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN B 190 HIS B 220 HIS B 262 GLN C 296 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111438 restraints weight = 19257.983| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.71 r_work: 0.3232 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13735 Z= 0.175 Angle : 0.538 10.374 18686 Z= 0.274 Chirality : 0.043 0.147 2109 Planarity : 0.004 0.052 2391 Dihedral : 4.989 46.170 1921 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.66 % Allowed : 22.50 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.06 % 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: 0.56 (0.21), residues: 1687 helix: 1.79 (0.83), residues: 36 sheet: 1.10 (0.19), residues: 807 loop : -0.41 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 106 HIS 0.003 0.001 HIS B 112 PHE 0.038 0.002 PHE E 84 TYR 0.013 0.001 TYR H 107 ARG 0.004 0.000 ARG H 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4709.65 seconds wall clock time: 87 minutes 21.32 seconds (5241.32 seconds total)