Starting phenix.real_space_refine on Sun Apr 7 20:54:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/04_2024/8gp3_34188_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/04_2024/8gp3_34188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/04_2024/8gp3_34188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/04_2024/8gp3_34188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/04_2024/8gp3_34188_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gp3_34188/04_2024/8gp3_34188_updated.pdb" } resolution = 4.8 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= -0.000 sd= 0.008 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 10 5.49 5 S 38 5.16 5 C 7275 2.51 5 N 1938 2.21 5 O 2233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 200": "OE1" <-> "OE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 166": "OE1" <-> "OE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11494 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2797 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "V" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 89 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "B" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2805 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 52 Chain: "U" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 89 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "H" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1496 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 191} Chain breaks: 2 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1363 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "M" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 6.59, per 1000 atoms: 0.57 Number of scatterers: 11494 At special positions: 0 Unit cell: (107.116, 197.55, 99.214, 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 38 16.00 P 10 15.00 O 2233 8.00 N 1938 7.00 C 7275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 150 " - pdb=" SG CYS I 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.03 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: 4.71 Conformation dependent library (CDL) restraints added in 2.4 seconds 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 28 sheets defined 4.9% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.614A pdb=" N ARG A 103 " --> pdb=" O ARG A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.644A pdb=" N ARG B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 165 through 167 No H-bonds generated for 'chain 'H' and resid 165 through 167' Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'I' and resid 165 through 167 No H-bonds generated for 'chain 'I' and resid 165 through 167' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.855A pdb=" N LYS L 127 " --> pdb=" O ASP L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing helix chain 'M' and resid 123 through 128 removed outlier: 3.875A pdb=" N LYS M 127 " --> pdb=" O ASP M 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 184 through 189 Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.520A pdb=" N THR A 19 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.812A pdb=" N ARG A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 163 through 168 removed outlier: 3.619A pdb=" N ILE A 168 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 145 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 63 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG A 76 " --> pdb=" O TYR A 63 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 140 through 142 removed outlier: 4.506A pdb=" N CYS A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 183 through 188 removed outlier: 3.562A pdb=" N TYR A 272 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 343 through 349 removed outlier: 3.526A pdb=" N VAL A 343 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 349 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 322 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 235 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A 254 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE A 241 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N GLN A 248 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 9 through 12 Processing sheet with id= H, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.852A pdb=" N ARG B 169 " --> pdb=" O PHE B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.938A pdb=" N ASP B 143 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 60 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 61 " --> pdb=" O ASP B 78 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASP B 78 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR B 63 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ARG B 76 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 140 through 142 removed outlier: 4.553A pdb=" N CYS B 140 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 183 through 188 removed outlier: 3.555A pdb=" N TYR B 272 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 343 through 349 removed outlier: 3.533A pdb=" N VAL B 343 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 349 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 322 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 235 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.920A pdb=" N LEU H 21 " --> pdb=" O MET H 86 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET H 86 " --> pdb=" O LEU H 21 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 117 through 119 removed outlier: 5.882A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.586A pdb=" N LEU H 134 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY H 149 " --> pdb=" O LEU H 134 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 161 through 164 removed outlier: 3.581A pdb=" N VAL H 208 " --> pdb=" O VAL H 217 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.914A pdb=" N LEU I 21 " --> pdb=" O MET I 86 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N MET I 86 " --> pdb=" O LEU I 21 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU I 23 " --> pdb=" O LEU I 84 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 117 through 119 removed outlier: 5.906A pdb=" N ARG I 41 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TRP I 50 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR I 62 " --> pdb=" O SER I 53 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 130 through 134 removed outlier: 3.584A pdb=" N LEU I 134 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY I 149 " --> pdb=" O LEU I 134 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 161 through 164 removed outlier: 3.576A pdb=" N VAL I 208 " --> pdb=" O VAL I 217 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 11 through 14 removed outlier: 6.349A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ALA L 14 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU L 106 " --> pdb=" O ALA L 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'L' and resid 20 through 25 Processing sheet with id= W, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.794A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.767A pdb=" N VAL L 134 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 11 through 14 removed outlier: 6.439A pdb=" N LYS M 104 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ALA M 14 " --> pdb=" O LYS M 104 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU M 106 " --> pdb=" O ALA M 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'M' and resid 20 through 25 Processing sheet with id= AA, first strand: chain 'M' and resid 86 through 91 removed outlier: 3.823A pdb=" N ILE M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'M' and resid 115 through 119 removed outlier: 3.770A pdb=" N VAL M 134 " --> pdb=" O PHE M 119 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYR M 174 " --> pdb=" O ASN M 139 " (cutoff:3.500A) 340 hydrogen bonds defined for protein. 897 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: 3.39 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3469 1.33 - 1.45: 1783 1.45 - 1.57: 6426 1.57 - 1.69: 34 1.69 - 1.81: 48 Bond restraints: 11760 Sorted by residual: bond pdb=" O3P SEP U 346 " pdb=" P SEP U 346 " ideal model delta sigma weight residual 1.610 1.505 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" O2P SEP V 344 " pdb=" P SEP V 344 " ideal model delta sigma weight residual 1.610 1.513 0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" O1P SEP U 346 " pdb=" P SEP U 346 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O3P SEP V 344 " pdb=" P SEP V 344 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" O1P SEP V 344 " pdb=" P SEP V 344 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 11755 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 420 106.29 - 113.22: 6461 113.22 - 120.15: 3750 120.15 - 127.09: 5280 127.09 - 134.02: 132 Bond angle restraints: 16043 Sorted by residual: angle pdb=" CA PHE B 75 " pdb=" C PHE B 75 " pdb=" N ARG B 76 " ideal model delta sigma weight residual 115.51 110.14 5.37 1.24e+00 6.50e-01 1.88e+01 angle pdb=" N VAL M 30 " pdb=" CA VAL M 30 " pdb=" C VAL M 30 " ideal model delta sigma weight residual 113.20 109.05 4.15 9.60e-01 1.09e+00 1.87e+01 angle pdb=" N VAL L 30 " pdb=" CA VAL L 30 " pdb=" C VAL L 30 " ideal model delta sigma weight residual 113.20 109.39 3.81 9.60e-01 1.09e+00 1.57e+01 angle pdb=" N GLY A 291 " pdb=" CA GLY A 291 " pdb=" C GLY A 291 " ideal model delta sigma weight residual 111.36 115.74 -4.38 1.17e+00 7.31e-01 1.40e+01 angle pdb=" C CYS A 59 " pdb=" N ALA A 60 " pdb=" CA ALA A 60 " ideal model delta sigma weight residual 122.59 116.75 5.84 1.57e+00 4.06e-01 1.39e+01 ... (remaining 16038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 6446 17.30 - 34.61: 520 34.61 - 51.91: 71 51.91 - 69.21: 21 69.21 - 86.52: 15 Dihedral angle restraints: 7073 sinusoidal: 2629 harmonic: 4444 Sorted by residual: dihedral pdb=" CA HIS B 362 " pdb=" C HIS B 362 " pdb=" N ARG B 363 " pdb=" CA ARG B 363 " ideal model delta harmonic sigma weight residual -180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.78e+00 dihedral pdb=" CA HIS A 362 " pdb=" C HIS A 362 " pdb=" N ARG A 363 " pdb=" CA ARG A 363 " ideal model delta harmonic sigma weight residual 180.00 -164.65 -15.35 0 5.00e+00 4.00e-02 9.42e+00 dihedral pdb=" N SEP V 344 " pdb=" CA SEP V 344 " pdb=" CB SEP V 344 " pdb=" OG SEP V 344 " ideal model delta sinusoidal sigma weight residual 60.00 3.37 56.63 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 7070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1339 0.040 - 0.079: 298 0.079 - 0.119: 182 0.119 - 0.158: 9 0.158 - 0.198: 4 Chirality restraints: 1832 Sorted by residual: chirality pdb=" CA ARG A 62 " pdb=" N ARG A 62 " pdb=" C ARG A 62 " pdb=" CB ARG A 62 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" CA LEU B 68 " pdb=" N LEU B 68 " pdb=" C LEU B 68 " pdb=" CB LEU B 68 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CB THR A 6 " pdb=" CA THR A 6 " pdb=" OG1 THR A 6 " pdb=" CG2 THR A 6 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.11e-01 ... (remaining 1829 not shown) Planarity restraints: 2055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 61 " 0.020 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C PHE A 61 " -0.071 2.00e-02 2.50e+03 pdb=" O PHE A 61 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG A 62 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 75 " 0.019 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C PHE B 75 " -0.070 2.00e-02 2.50e+03 pdb=" O PHE B 75 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG B 76 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 67 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ASP B 67 " -0.067 2.00e-02 2.50e+03 pdb=" O ASP B 67 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 68 " 0.023 2.00e-02 2.50e+03 ... (remaining 2052 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 221 2.66 - 3.22: 10596 3.22 - 3.78: 17616 3.78 - 4.34: 22460 4.34 - 4.90: 36834 Nonbonded interactions: 87727 Sorted by model distance: nonbonded pdb=" NE2 GLN L 90 " pdb=" O GLN L 91 " model vdw 2.102 2.520 nonbonded pdb=" NE2 GLN M 90 " pdb=" O GLN M 91 " model vdw 2.201 2.520 nonbonded pdb=" O ILE B 31 " pdb=" NH2 ARG B 307 " model vdw 2.207 2.520 nonbonded pdb=" O3P SEP V 346 " pdb=" OG SER L 31 " model vdw 2.230 2.440 nonbonded pdb=" O ASP M 83 " pdb=" OH TYR M 87 " model vdw 2.237 2.440 ... (remaining 87722 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 6 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 133 or (resid 134 and (name N or na \ me CA or name C or name O or name CB )) or resid 135 through 368)) selection = (chain 'B' and (resid 6 through 176 or (resid 177 and (name N or name CA or name \ C or name O or name CB )) or resid 178 through 311 or (resid 312 and (name N or \ name CA or name C or name O or name CB )) or resid 313 through 358 or (resid 35 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 360 through \ 368)) } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = (chain 'L' and (resid 1 through 3 or (resid 4 and (name N or name CA or name C o \ r name O or name CB )) or resid 5 through 190)) selection = chain 'M' } ncs_group { reference = 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=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 23.150 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 34.470 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 0.105 11760 Z= 0.249 Angle : 0.654 11.832 16043 Z= 0.361 Chirality : 0.044 0.198 1832 Planarity : 0.004 0.041 2055 Dihedral : 13.226 86.515 4191 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: 0.13 (0.22), residues: 1480 helix: 0.93 (0.75), residues: 46 sheet: 0.69 (0.21), residues: 582 loop : -0.35 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 36 HIS 0.002 0.001 HIS A 210 PHE 0.020 0.001 PHE I 105 TYR 0.021 0.001 TYR L 50 ARG 0.003 0.000 ARG B 307 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 30 PHE cc_start: 0.9010 (p90) cc_final: 0.8702 (p90) REVERT: H 80 ASN cc_start: 0.9041 (m-40) cc_final: 0.8733 (m-40) REVERT: H 93 ASP cc_start: 0.7814 (m-30) cc_final: 0.7279 (m-30) REVERT: I 30 PHE cc_start: 0.9095 (p90) cc_final: 0.8794 (p90) REVERT: I 93 ASP cc_start: 0.7775 (m-30) cc_final: 0.7237 (m-30) REVERT: M 50 TYR cc_start: 0.9744 (p90) cc_final: 0.9422 (p90) REVERT: M 166 GLU cc_start: 0.9744 (tp30) cc_final: 0.9433 (tp30) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2046 time to fit residues: 22.9537 Evaluate side-chains 51 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 20.0000 chunk 112 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 174 HIS M 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11760 Z= 0.241 Angle : 0.589 11.315 16043 Z= 0.293 Chirality : 0.041 0.136 1832 Planarity : 0.004 0.036 2055 Dihedral : 7.449 84.831 1670 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: -0.06 (0.21), residues: 1480 helix: 0.44 (0.74), residues: 46 sheet: 0.43 (0.20), residues: 616 loop : -0.38 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 36 HIS 0.006 0.001 HIS B 210 PHE 0.013 0.002 PHE B 27 TYR 0.016 0.002 TYR L 50 ARG 0.004 0.001 ARG M 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.405 Fit side-chains REVERT: H 80 ASN cc_start: 0.8845 (m-40) cc_final: 0.8480 (m-40) REVERT: H 93 ASP cc_start: 0.8125 (m-30) cc_final: 0.7580 (m-30) REVERT: I 93 ASP cc_start: 0.8113 (m-30) cc_final: 0.7575 (m-30) REVERT: M 166 GLU cc_start: 0.9763 (tp30) cc_final: 0.9470 (tp30) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1820 time to fit residues: 18.5633 Evaluate side-chains 44 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 133 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 30 HIS ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN B 30 HIS ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 11760 Z= 0.459 Angle : 0.830 10.438 16043 Z= 0.422 Chirality : 0.047 0.186 1832 Planarity : 0.006 0.048 2055 Dihedral : 8.496 83.220 1670 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 28.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.34 % Rotamer: Outliers : 0.16 % Allowed : 9.97 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1480 helix: -0.22 (0.74), residues: 44 sheet: -0.19 (0.20), residues: 632 loop : -1.15 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP L 36 HIS 0.021 0.003 HIS A 210 PHE 0.017 0.003 PHE M 99 TYR 0.022 0.003 TYR A 321 ARG 0.009 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 5 MET cc_start: 0.5972 (tmm) cc_final: 0.5741 (tmm) REVERT: L 49 ILE cc_start: 0.9483 (mm) cc_final: 0.9179 (tt) REVERT: M 50 TYR cc_start: 0.9547 (p90) cc_final: 0.9168 (p90) outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 0.1716 time to fit residues: 14.6305 Evaluate side-chains 36 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 64 optimal weight: 0.0570 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11760 Z= 0.158 Angle : 0.592 16.591 16043 Z= 0.283 Chirality : 0.044 0.150 1832 Planarity : 0.004 0.045 2055 Dihedral : 7.652 82.710 1670 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: -0.55 (0.21), residues: 1480 helix: -0.05 (0.73), residues: 46 sheet: 0.14 (0.20), residues: 628 loop : -0.75 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.002 0.001 HIS B 295 PHE 0.024 0.001 PHE I 105 TYR 0.013 0.001 TYR M 88 ARG 0.003 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 1.443 Fit side-chains revert: symmetry clash REVERT: A 229 LYS cc_start: 0.9621 (mmmt) cc_final: 0.9362 (mmmt) REVERT: B 229 LYS cc_start: 0.9623 (mmmt) cc_final: 0.9365 (mmmt) REVERT: B 249 TYR cc_start: 0.8539 (p90) cc_final: 0.8044 (p90) REVERT: H 48 LEU cc_start: 0.9271 (mt) cc_final: 0.8915 (tp) REVERT: I 105 PHE cc_start: 0.9094 (m-80) cc_final: 0.8615 (m-10) REVERT: L 49 ILE cc_start: 0.9355 (mm) cc_final: 0.9131 (tp) REVERT: M 166 GLU cc_start: 0.9778 (tp30) cc_final: 0.9526 (tp30) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2031 time to fit residues: 18.6880 Evaluate side-chains 45 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 0.0050 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 128 optimal weight: 0.0370 chunk 36 optimal weight: 10.0000 overall best weight: 2.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN B 181 GLN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11760 Z= 0.255 Angle : 0.609 16.385 16043 Z= 0.296 Chirality : 0.042 0.156 1832 Planarity : 0.004 0.041 2055 Dihedral : 7.725 83.146 1670 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: -0.67 (0.21), residues: 1480 helix: -0.09 (0.71), residues: 46 sheet: -0.00 (0.20), residues: 636 loop : -0.79 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 113 HIS 0.008 0.002 HIS I 38 PHE 0.020 0.002 PHE H 105 TYR 0.023 0.002 TYR L 50 ARG 0.004 0.001 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.415 Fit side-chains REVERT: A 215 SER cc_start: 0.8788 (m) cc_final: 0.8522 (p) REVERT: A 229 LYS cc_start: 0.9620 (mmmt) cc_final: 0.9399 (mmmt) REVERT: B 215 SER cc_start: 0.8832 (m) cc_final: 0.8545 (p) REVERT: B 229 LYS cc_start: 0.9632 (mmmt) cc_final: 0.9400 (mmmt) REVERT: I 105 PHE cc_start: 0.9196 (m-80) cc_final: 0.8738 (m-10) REVERT: L 49 ILE cc_start: 0.9418 (mm) cc_final: 0.9122 (tt) REVERT: M 50 TYR cc_start: 0.9604 (p90) cc_final: 0.9363 (p90) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.2167 time to fit residues: 17.7986 Evaluate side-chains 39 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 128 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 118 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 11 optimal weight: 0.0020 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11760 Z= 0.228 Angle : 0.596 16.047 16043 Z= 0.290 Chirality : 0.042 0.149 1832 Planarity : 0.004 0.039 2055 Dihedral : 7.651 82.349 1670 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.53 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: -0.71 (0.21), residues: 1480 helix: -0.13 (0.71), residues: 46 sheet: -0.03 (0.20), residues: 616 loop : -0.81 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 39 HIS 0.007 0.001 HIS H 38 PHE 0.019 0.002 PHE M 99 TYR 0.022 0.002 TYR M 50 ARG 0.004 0.000 ARG H 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 229 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9401 (mmmt) REVERT: A 289 LEU cc_start: 0.9600 (tp) cc_final: 0.9334 (tp) REVERT: B 215 SER cc_start: 0.8910 (m) cc_final: 0.8619 (p) REVERT: I 105 PHE cc_start: 0.9232 (m-80) cc_final: 0.8876 (m-10) REVERT: L 49 ILE cc_start: 0.9445 (mm) cc_final: 0.9170 (tt) REVERT: M 50 TYR cc_start: 0.9571 (p90) cc_final: 0.9326 (p90) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.2219 time to fit residues: 17.7265 Evaluate side-chains 39 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 120 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 86 optimal weight: 0.0020 chunk 65 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 overall best weight: 2.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11760 Z= 0.316 Angle : 0.675 16.443 16043 Z= 0.334 Chirality : 0.043 0.149 1832 Planarity : 0.005 0.041 2055 Dihedral : 7.998 81.797 1670 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 23.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.21), residues: 1480 helix: -0.15 (0.73), residues: 44 sheet: -0.24 (0.20), residues: 620 loop : -0.99 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 39 HIS 0.011 0.002 HIS I 38 PHE 0.020 0.002 PHE H 105 TYR 0.021 0.002 TYR M 50 ARG 0.005 0.001 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.428 Fit side-chains revert: symmetry clash REVERT: A 289 LEU cc_start: 0.9573 (tp) cc_final: 0.9262 (tp) REVERT: A 306 LEU cc_start: 0.8778 (pt) cc_final: 0.8564 (pt) REVERT: I 105 PHE cc_start: 0.9316 (m-80) cc_final: 0.8897 (m-10) REVERT: L 49 ILE cc_start: 0.9473 (mm) cc_final: 0.9187 (tt) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2059 time to fit residues: 15.7578 Evaluate side-chains 35 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 0.0980 chunk 129 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 GLN B 210 HIS L 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11760 Z= 0.155 Angle : 0.577 15.920 16043 Z= 0.275 Chirality : 0.043 0.157 1832 Planarity : 0.004 0.042 2055 Dihedral : 7.332 80.887 1670 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: -0.51 (0.21), residues: 1480 helix: -0.42 (0.73), residues: 46 sheet: 0.23 (0.21), residues: 572 loop : -0.70 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 106 HIS 0.004 0.001 HIS B 210 PHE 0.010 0.001 PHE L 140 TYR 0.012 0.001 TYR M 88 ARG 0.003 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.9580 (tp) cc_final: 0.9315 (tp) REVERT: L 49 ILE cc_start: 0.9357 (mm) cc_final: 0.9136 (tp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.2152 time to fit residues: 19.1173 Evaluate side-chains 41 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.0060 chunk 124 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 chunk 40 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 87 optimal weight: 0.0870 chunk 140 optimal weight: 4.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11760 Z= 0.139 Angle : 0.557 15.260 16043 Z= 0.261 Chirality : 0.042 0.142 1832 Planarity : 0.004 0.041 2055 Dihedral : 7.108 80.597 1670 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: -0.34 (0.21), residues: 1480 helix: -0.22 (0.75), residues: 46 sheet: 0.39 (0.20), residues: 612 loop : -0.68 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 39 HIS 0.004 0.001 HIS A 210 PHE 0.031 0.001 PHE I 105 TYR 0.025 0.001 TYR M 50 ARG 0.004 0.000 ARG I 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.9530 (tp) cc_final: 0.9232 (tp) REVERT: L 49 ILE cc_start: 0.9372 (mm) cc_final: 0.9170 (tp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2164 time to fit residues: 19.0977 Evaluate side-chains 40 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 117 optimal weight: 0.0000 chunk 12 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.0040 chunk 125 optimal weight: 20.0000 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11760 Z= 0.138 Angle : 0.539 13.988 16043 Z= 0.254 Chirality : 0.042 0.145 1832 Planarity : 0.004 0.042 2055 Dihedral : 6.933 80.008 1670 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: -0.23 (0.21), residues: 1480 helix: -0.13 (0.76), residues: 46 sheet: 0.54 (0.21), residues: 612 loop : -0.68 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 39 HIS 0.006 0.001 HIS A 210 PHE 0.011 0.001 PHE L 99 TYR 0.013 0.001 TYR L 92 ARG 0.003 0.000 ARG I 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2960 Ramachandran restraints generated. 1480 Oldfield, 0 Emsley, 1480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 1.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 LEU cc_start: 0.9526 (tp) cc_final: 0.9233 (tp) REVERT: I 105 PHE cc_start: 0.9223 (m-10) cc_final: 0.8967 (m-10) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2037 time to fit residues: 18.2585 Evaluate side-chains 40 residues out of total 1322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.0170 chunk 108 optimal weight: 0.1980 chunk 17 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 6 optimal weight: 0.0970 overall best weight: 0.8620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.030783 restraints weight = 103940.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.031943 restraints weight = 64625.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.032768 restraints weight = 47051.358| |-----------------------------------------------------------------------------| r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2656 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2656 r_free = 0.2656 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2656 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11760 Z= 0.148 Angle : 0.535 13.747 16043 Z= 0.253 Chirality : 0.042 0.167 1832 Planarity : 0.004 0.042 2055 Dihedral : 6.885 79.763 1670 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.14 % 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: -0.19 (0.21), residues: 1480 helix: -0.08 (0.75), residues: 46 sheet: 0.56 (0.20), residues: 624 loop : -0.66 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP L 36 HIS 0.006 0.001 HIS A 210 PHE 0.010 0.001 PHE M 99 TYR 0.032 0.001 TYR L 50 ARG 0.003 0.000 ARG I 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2291.66 seconds wall clock time: 43 minutes 34.88 seconds (2614.88 seconds total)