Starting phenix.real_space_refine on Mon Dec 11 10:01:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbd_22116/12_2023/6xbd_22116_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbd_22116/12_2023/6xbd_22116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbd_22116/12_2023/6xbd_22116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbd_22116/12_2023/6xbd_22116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbd_22116/12_2023/6xbd_22116_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbd_22116/12_2023/6xbd_22116_updated.pdb" } resolution = 3.05 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= 0.071 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 2 5.49 5 S 68 5.16 5 C 11140 2.51 5 N 2963 2.21 5 O 3260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 70": "OD1" <-> "OD2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C ASP 136": "OD1" <-> "OD2" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "E GLU 7": "OE1" <-> "OE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E ASP 95": "OD1" <-> "OD2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "G ARG 141": "NH1" <-> "NH2" Residue "G ASP 181": "OD1" <-> "OD2" Residue "G ASP 194": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H GLU 98": "OE1" <-> "OE2" Residue "H GLU 133": "OE1" <-> "OE2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "I GLU 144": "OE1" <-> "OE2" Residue "I ARG 151": "NH1" <-> "NH2" Residue "I ARG 157": "NH1" <-> "NH2" Residue "I ARG 255": "NH1" <-> "NH2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "J ARG 151": "NH1" <-> "NH2" Residue "J ARG 157": "NH1" <-> "NH2" Residue "J ARG 255": "NH1" <-> "NH2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "K ARG 32": "NH1" <-> "NH2" Residue "L GLU 30": "OE1" <-> "OE2" Residue "L ARG 32": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17433 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "B" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1063 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 1 Chain: "C" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1096 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 2 Chain: "E" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1112 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 1 Chain: "F" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1028 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "G" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1926 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "H" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1918 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "I" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "J" Number of atoms: 1996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1996 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 18, 'TRANS': 244} Chain: "K" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "L" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "M" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 821 Classifications: {'peptide': 164} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'TRANS': 163} Unresolved non-hydrogen bonds: 327 Unresolved non-hydrogen angles: 490 Unresolved non-hydrogen dihedrals: 164 Planarities with less than four sites: {'UNK:plan-1': 163} Unresolved non-hydrogen planarities: 163 Chain: "N" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 780 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'TRANS': 155} Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 156 Planarities with less than four sites: {'UNK:plan-1': 156} Unresolved non-hydrogen planarities: 156 Chain: "G" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'PEF': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 9.83, per 1000 atoms: 0.56 Number of scatterers: 17433 At special positions: 0 Unit cell: (128.96, 104.832, 139.776, 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 68 16.00 P 2 15.00 O 3260 8.00 N 2963 7.00 C 11140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.90 Conformation dependent library (CDL) restraints added in 3.0 seconds 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 21 sheets defined 57.5% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 3 through 27 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'B' and resid 5 through 23 Processing helix chain 'B' and resid 143 through 151 Processing helix chain 'C' and resid 5 through 27 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'D' and resid 4 through 26 Processing helix chain 'D' and resid 143 through 151 Processing helix chain 'E' and resid 5 through 30 Processing helix chain 'E' and resid 143 through 151 Processing helix chain 'F' and resid 5 through 28 Processing helix chain 'F' and resid 143 through 150 Processing helix chain 'G' and resid 5 through 30 Processing helix chain 'G' and resid 41 through 51 Processing helix chain 'G' and resid 57 through 80 removed outlier: 3.804A pdb=" N VAL G 77 " --> pdb=" O GLN G 73 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 97 removed outlier: 4.266A pdb=" N GLY G 88 " --> pdb=" O THR G 85 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG G 97 " --> pdb=" O SER G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 125 removed outlier: 3.878A pdb=" N SER G 114 " --> pdb=" O GLY G 110 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 115 " --> pdb=" O ARG G 111 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 135 removed outlier: 3.742A pdb=" N MET G 135 " --> pdb=" O SER G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 174 Proline residue: G 156 - end of helix removed outlier: 3.823A pdb=" N TRP G 168 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 192 Processing helix chain 'G' and resid 196 through 222 Processing helix chain 'G' and resid 228 through 257 removed outlier: 3.754A pdb=" N SER G 232 " --> pdb=" O SER G 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 233 " --> pdb=" O ALA G 229 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG G 237 " --> pdb=" O ARG G 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 31 removed outlier: 3.528A pdb=" N GLY H 10 " --> pdb=" O LEU H 6 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N HIS H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 51 removed outlier: 3.821A pdb=" N ARG H 46 " --> pdb=" O PRO H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 57 through 80 removed outlier: 3.511A pdb=" N PHE H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL H 77 " --> pdb=" O GLN H 73 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N THR H 80 " --> pdb=" O LEU H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 97 removed outlier: 4.321A pdb=" N GLY H 88 " --> pdb=" O THR H 85 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG H 97 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 125 removed outlier: 3.955A pdb=" N SER H 114 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR H 117 " --> pdb=" O GLY H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 134 Processing helix chain 'H' and resid 139 through 142 No H-bonds generated for 'chain 'H' and resid 139 through 142' Processing helix chain 'H' and resid 145 through 174 Proline residue: H 156 - end of helix removed outlier: 3.566A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TRP H 168 " --> pdb=" O ALA H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 192 removed outlier: 3.536A pdb=" N ALA H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 222 Processing helix chain 'H' and resid 228 through 257 removed outlier: 4.137A pdb=" N SER H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG H 237 " --> pdb=" O ARG H 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.730A pdb=" N ILE I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 85 removed outlier: 3.988A pdb=" N LYS I 85 " --> pdb=" O TYR I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 113 Proline residue: I 109 - end of helix Processing helix chain 'I' and resid 118 through 132 Processing helix chain 'I' and resid 135 through 137 No H-bonds generated for 'chain 'I' and resid 135 through 137' Processing helix chain 'I' and resid 142 through 144 No H-bonds generated for 'chain 'I' and resid 142 through 144' Processing helix chain 'I' and resid 147 through 158 removed outlier: 3.861A pdb=" N ARG I 151 " --> pdb=" O GLY I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 193 Processing helix chain 'I' and resid 205 through 210 removed outlier: 4.052A pdb=" N SER I 210 " --> pdb=" O PRO I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 229 through 232 No H-bonds generated for 'chain 'I' and resid 229 through 232' Processing helix chain 'I' and resid 238 through 245 Processing helix chain 'I' and resid 262 through 265 No H-bonds generated for 'chain 'I' and resid 262 through 265' Processing helix chain 'J' and resid 49 through 54 removed outlier: 3.729A pdb=" N ILE J 54 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 85 removed outlier: 3.989A pdb=" N LYS J 85 " --> pdb=" O TYR J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 113 Proline residue: J 109 - end of helix Processing helix chain 'J' and resid 118 through 132 Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 142 through 144 No H-bonds generated for 'chain 'J' and resid 142 through 144' Processing helix chain 'J' and resid 147 through 158 removed outlier: 3.861A pdb=" N ARG J 151 " --> pdb=" O GLY J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 193 Processing helix chain 'J' and resid 205 through 210 removed outlier: 4.054A pdb=" N SER J 210 " --> pdb=" O PRO J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 229 through 232 No H-bonds generated for 'chain 'J' and resid 229 through 232' Processing helix chain 'J' and resid 238 through 245 Processing helix chain 'J' and resid 262 through 265 No H-bonds generated for 'chain 'J' and resid 262 through 265' Processing helix chain 'K' and resid 26 through 29 No H-bonds generated for 'chain 'K' and resid 26 through 29' Processing helix chain 'K' and resid 32 through 36 Processing helix chain 'K' and resid 52 through 68 removed outlier: 3.830A pdb=" N GLN K 68 " --> pdb=" O LEU K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 87 Processing helix chain 'L' and resid 26 through 29 No H-bonds generated for 'chain 'L' and resid 26 through 29' Processing helix chain 'L' and resid 32 through 36 Processing helix chain 'L' and resid 52 through 68 removed outlier: 3.831A pdb=" N GLN L 68 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 87 Processing helix chain 'M' and resid 2 through 163 removed outlier: 3.791A pdb=" N UNK M 22 " --> pdb=" O UNK M 18 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N UNK M 33 " --> pdb=" O UNK M 29 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N UNK M 36 " --> pdb=" O UNK M 32 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N UNK M 37 " --> pdb=" O UNK M 33 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N UNK M 41 " --> pdb=" O UNK M 37 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N UNK M 51 " --> pdb=" O UNK M 47 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N UNK M 75 " --> pdb=" O UNK M 71 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N UNK M 80 " --> pdb=" O UNK M 76 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N UNK M 90 " --> pdb=" O UNK M 86 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N UNK M 143 " --> pdb=" O UNK M 139 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N UNK M 150 " --> pdb=" O UNK M 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 38 removed outlier: 3.686A pdb=" N UNK N 10 " --> pdb=" O UNK N 6 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N UNK N 28 " --> pdb=" O UNK N 24 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N UNK N 31 " --> pdb=" O UNK N 27 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N UNK N 32 " --> pdb=" O UNK N 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N UNK N 35 " --> pdb=" O UNK N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 40 through 154 removed outlier: 4.170A pdb=" N UNK N 53 " --> pdb=" O UNK N 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N UNK N 54 " --> pdb=" O UNK N 50 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N UNK N 58 " --> pdb=" O UNK N 54 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N UNK N 86 " --> pdb=" O UNK N 82 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N UNK N 97 " --> pdb=" O UNK N 93 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N UNK N 136 " --> pdb=" O UNK N 132 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N UNK N 142 " --> pdb=" O UNK N 138 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 39 through 45 removed outlier: 3.907A pdb=" N ASP A 70 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU A 85 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL A 68 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU A 87 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY A 66 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 103 Processing sheet with id= C, first strand: chain 'B' and resid 40 through 45 removed outlier: 3.561A pdb=" N ASP B 70 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU B 85 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL B 68 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 58 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN B 110 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N SER B 59 " --> pdb=" O GLN B 110 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU B 112 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 39 through 45 removed outlier: 3.591A pdb=" N ASP C 70 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU C 85 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL C 68 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU C 87 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY C 66 " --> pdb=" O GLU C 87 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL C 58 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 101 through 103 Processing sheet with id= F, first strand: chain 'D' and resid 39 through 45 removed outlier: 6.075A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 98 through 103 removed outlier: 4.084A pdb=" N ASN D 115 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 66 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE D 60 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 40 through 45 removed outlier: 3.610A pdb=" N ASP E 70 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU E 85 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL E 68 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 63 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL E 58 " --> pdb=" O VAL E 65 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 98 through 103 Processing sheet with id= J, first strand: chain 'F' and resid 101 through 103 Processing sheet with id= K, first strand: chain 'F' and resid 66 through 73 removed outlier: 3.637A pdb=" N ARG F 67 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR F 83 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE F 71 " --> pdb=" O ARG F 81 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG F 81 " --> pdb=" O ILE F 71 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 64 through 67 removed outlier: 6.702A pdb=" N VAL I 31 " --> pdb=" O LEU I 8 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 87 through 90 removed outlier: 6.566A pdb=" N LEU I 165 " --> pdb=" O SER I 88 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU I 90 " --> pdb=" O LEU I 165 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N MET I 167 " --> pdb=" O LEU I 90 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 16 through 18 removed outlier: 7.106A pdb=" N ARG I 18 " --> pdb=" O CYS I 22 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N CYS I 22 " --> pdb=" O ARG I 18 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 215 through 219 removed outlier: 3.659A pdb=" N ALA I 225 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ALA I 219 " --> pdb=" O ILE I 223 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE I 223 " --> pdb=" O ALA I 219 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 64 through 67 removed outlier: 6.701A pdb=" N VAL J 31 " --> pdb=" O LEU J 8 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 87 through 90 removed outlier: 6.565A pdb=" N LEU J 165 " --> pdb=" O SER J 88 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU J 90 " --> pdb=" O LEU J 165 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N MET J 167 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'J' and resid 16 through 18 removed outlier: 7.106A pdb=" N ARG J 18 " --> pdb=" O CYS J 22 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N CYS J 22 " --> pdb=" O ARG J 18 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 215 through 219 removed outlier: 3.659A pdb=" N ALA J 225 " --> pdb=" O ILE J 217 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA J 219 " --> pdb=" O ILE J 223 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE J 223 " --> pdb=" O ALA J 219 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 41 through 43 removed outlier: 6.995A pdb=" N THR K 73 " --> pdb=" O ILE K 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'L' and resid 41 through 43 removed outlier: 6.996A pdb=" N THR L 73 " --> pdb=" O ILE L 42 " (cutoff:3.500A) No H-bonds generated for sheet with id= U 960 hydrogen bonds defined for protein. 2787 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: 4.67 Time building geometry restraints manager: 7.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2931 1.31 - 1.43: 4166 1.43 - 1.56: 10475 1.56 - 1.68: 6 1.68 - 1.81: 124 Bond restraints: 17702 Sorted by residual: bond pdb=" O4P PEF G 301 " pdb=" P PEF G 301 " ideal model delta sigma weight residual 1.639 1.509 0.130 2.00e-02 2.50e+03 4.20e+01 bond pdb=" O4P PEF G 302 " pdb=" P PEF G 302 " ideal model delta sigma weight residual 1.639 1.510 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C10 PEF G 302 " pdb=" O2 PEF G 302 " ideal model delta sigma weight residual 1.330 1.442 -0.112 2.00e-02 2.50e+03 3.16e+01 bond pdb=" C10 PEF G 301 " pdb=" O2 PEF G 301 " ideal model delta sigma weight residual 1.330 1.441 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C30 PEF G 302 " pdb=" O3 PEF G 302 " ideal model delta sigma weight residual 1.333 1.407 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 17697 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.87: 490 106.87 - 113.66: 10201 113.66 - 120.45: 6793 120.45 - 127.24: 6467 127.24 - 134.04: 157 Bond angle restraints: 24108 Sorted by residual: angle pdb=" N ALA G 192 " pdb=" CA ALA G 192 " pdb=" C ALA G 192 " ideal model delta sigma weight residual 111.14 122.24 -11.10 1.08e+00 8.57e-01 1.06e+02 angle pdb=" N VAL G 193 " pdb=" CA VAL G 193 " pdb=" C VAL G 193 " ideal model delta sigma weight residual 109.34 124.43 -15.09 2.08e+00 2.31e-01 5.26e+01 angle pdb=" N ALA H 192 " pdb=" CA ALA H 192 " pdb=" C ALA H 192 " ideal model delta sigma weight residual 111.36 118.91 -7.55 1.09e+00 8.42e-01 4.80e+01 angle pdb=" N GLN H 190 " pdb=" CA GLN H 190 " pdb=" C GLN H 190 " ideal model delta sigma weight residual 111.14 118.52 -7.38 1.08e+00 8.57e-01 4.67e+01 angle pdb=" N SER A 56 " pdb=" CA SER A 56 " pdb=" C SER A 56 " ideal model delta sigma weight residual 109.72 101.47 8.25 1.25e+00 6.40e-01 4.35e+01 ... (remaining 24103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.70: 10022 19.70 - 39.41: 508 39.41 - 59.11: 65 59.11 - 78.82: 10 78.82 - 98.52: 7 Dihedral angle restraints: 10612 sinusoidal: 3725 harmonic: 6887 Sorted by residual: dihedral pdb=" CA GLU E 37 " pdb=" C GLU E 37 " pdb=" N PRO E 38 " pdb=" CA PRO E 38 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" C12 PEF G 301 " pdb=" C10 PEF G 301 " pdb=" C11 PEF G 301 " pdb=" O4 PEF G 301 " ideal model delta sinusoidal sigma weight residual -21.28 77.24 -98.52 1 3.00e+01 1.11e-03 1.22e+01 dihedral pdb=" C12 PEF G 301 " pdb=" C10 PEF G 301 " pdb=" C11 PEF G 301 " pdb=" O2 PEF G 301 " ideal model delta sinusoidal sigma weight residual 159.53 -102.97 -97.50 1 3.00e+01 1.11e-03 1.21e+01 ... (remaining 10609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2761 0.081 - 0.163: 180 0.163 - 0.244: 6 0.244 - 0.326: 5 0.326 - 0.407: 4 Chirality restraints: 2956 Sorted by residual: chirality pdb=" CA ALA G 192 " pdb=" N ALA G 192 " pdb=" C ALA G 192 " pdb=" CB ALA G 192 " both_signs ideal model delta sigma weight residual False 2.48 2.08 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA GLN H 190 " pdb=" N GLN H 190 " pdb=" C GLN H 190 " pdb=" CB GLN H 190 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA VAL G 193 " pdb=" N VAL G 193 " pdb=" C VAL G 193 " pdb=" CB VAL G 193 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2953 not shown) Planarity restraints: 3075 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 185 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.29e+00 pdb=" C PHE G 185 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE G 185 " -0.012 2.00e-02 2.50e+03 pdb=" N TRP G 186 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 163 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C VAL H 163 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL H 163 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA H 164 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 163 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL G 163 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL G 163 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA G 164 " -0.009 2.00e-02 2.50e+03 ... (remaining 3072 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 226 2.66 - 3.22: 17381 3.22 - 3.78: 26304 3.78 - 4.34: 35881 4.34 - 4.90: 58642 Nonbonded interactions: 138434 Sorted by model distance: nonbonded pdb=" O GLY G 183 " pdb=" OG SER G 187 " model vdw 2.104 2.440 nonbonded pdb=" OG SER K 6 " pdb=" OG SER K 17 " model vdw 2.224 2.440 nonbonded pdb=" OG SER L 6 " pdb=" OG SER L 17 " model vdw 2.224 2.440 nonbonded pdb=" O SER G 55 " pdb=" OG SER G 55 " model vdw 2.286 2.440 nonbonded pdb=" OH TYR L 82 " pdb=" O ARG L 97 " model vdw 2.294 2.440 ... (remaining 138429 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 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 121 or resid 124 through 152)) selection = (chain 'B' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 121 or resid 124 through 152)) selection = (chain 'C' and (resid 4 through 25 or resid 37 through 121 or resid 124 through \ 152)) selection = (chain 'D' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 152)) selection = (chain 'E' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 25 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 121 or resid 124 through 152)) selection = (chain 'F' and (resid 4 through 25 or resid 37 through 121 or resid 124 through \ 152)) } ncs_group { reference = (chain 'G' and resid 5 through 259) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and (resid 9 through 164 and (name N or name CA or name C or name O o \ r name CB ))) selection = chain 'N' } 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: 6.950 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 47.560 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.110 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 0.130 17702 Z= 0.221 Angle : 0.661 15.551 24108 Z= 0.353 Chirality : 0.045 0.407 2956 Planarity : 0.003 0.036 3075 Dihedral : 12.080 98.524 6164 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.17), residues: 2046 helix: -0.41 (0.16), residues: 876 sheet: -3.38 (0.25), residues: 283 loop : -2.24 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 195 HIS 0.002 0.001 HIS I 122 PHE 0.017 0.001 PHE G 185 TYR 0.010 0.001 TYR F 40 ARG 0.002 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 1.852 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 414 average time/residue: 0.3888 time to fit residues: 222.6497 Evaluate side-chains 330 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 330 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 70 optimal weight: 30.0000 chunk 111 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 chunk 212 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN C 88 GLN C 110 GLN D 2 GLN G 40 HIS I 226 HIS I 230 GLN J 57 GLN J 191 ASN J 226 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17702 Z= 0.195 Angle : 0.576 6.900 24108 Z= 0.282 Chirality : 0.040 0.148 2956 Planarity : 0.004 0.034 3075 Dihedral : 6.563 62.491 2619 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.13 % Allowed : 10.12 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 2046 helix: 0.84 (0.17), residues: 893 sheet: -2.78 (0.26), residues: 312 loop : -1.70 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 216 HIS 0.004 0.001 HIS A 92 PHE 0.019 0.001 PHE G 185 TYR 0.014 0.001 TYR D 40 ARG 0.006 0.000 ARG I 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 346 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 354 average time/residue: 0.3825 time to fit residues: 190.1091 Evaluate side-chains 328 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 318 time to evaluate : 1.786 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2218 time to fit residues: 6.0529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 212 optimal weight: 30.0000 chunk 229 optimal weight: 30.0000 chunk 189 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 170 optimal weight: 0.0370 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 HIS C 110 GLN D 2 GLN G 40 HIS I 175 GLN I 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17702 Z= 0.301 Angle : 0.585 7.696 24108 Z= 0.286 Chirality : 0.041 0.145 2956 Planarity : 0.004 0.039 3075 Dihedral : 6.118 58.708 2619 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.79 % Allowed : 12.80 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 2046 helix: 1.20 (0.18), residues: 908 sheet: -2.51 (0.26), residues: 319 loop : -1.42 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 195 HIS 0.009 0.001 HIS I 113 PHE 0.015 0.001 PHE G 185 TYR 0.016 0.001 TYR G 222 ARG 0.007 0.000 ARG I 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 330 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 343 average time/residue: 0.3764 time to fit residues: 180.7802 Evaluate side-chains 323 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 312 time to evaluate : 2.113 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1949 time to fit residues: 6.1675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 213 optimal weight: 30.0000 chunk 226 optimal weight: 10.0000 chunk 111 optimal weight: 0.0970 chunk 202 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN C 110 GLN D 2 GLN I 230 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17702 Z= 0.237 Angle : 0.558 7.492 24108 Z= 0.274 Chirality : 0.040 0.141 2956 Planarity : 0.004 0.038 3075 Dihedral : 5.863 58.735 2619 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.55 % Allowed : 15.12 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 2046 helix: 1.47 (0.18), residues: 896 sheet: -2.39 (0.28), residues: 298 loop : -1.24 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 195 HIS 0.003 0.001 HIS I 113 PHE 0.014 0.001 PHE G 185 TYR 0.017 0.001 TYR G 222 ARG 0.005 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 322 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 337 average time/residue: 0.3770 time to fit residues: 177.9918 Evaluate side-chains 325 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 311 time to evaluate : 1.856 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1780 time to fit residues: 6.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 203 optimal weight: 40.0000 chunk 57 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN C 110 GLN D 2 GLN I 230 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17702 Z= 0.224 Angle : 0.543 7.461 24108 Z= 0.266 Chirality : 0.039 0.139 2956 Planarity : 0.003 0.038 3075 Dihedral : 5.644 59.733 2619 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.95 % Allowed : 17.26 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.20), residues: 2046 helix: 1.69 (0.18), residues: 895 sheet: -2.31 (0.28), residues: 312 loop : -1.00 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 195 HIS 0.002 0.000 HIS L 60 PHE 0.013 0.001 PHE G 185 TYR 0.016 0.001 TYR G 222 ARG 0.006 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 337 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 342 average time/residue: 0.3770 time to fit residues: 180.6270 Evaluate side-chains 322 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 317 time to evaluate : 2.001 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2377 time to fit residues: 4.4137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 3.9990 chunk 203 optimal weight: 50.0000 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 GLN D 2 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17702 Z= 0.239 Angle : 0.555 7.615 24108 Z= 0.273 Chirality : 0.040 0.140 2956 Planarity : 0.004 0.038 3075 Dihedral : 5.532 57.479 2619 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.73 % Allowed : 17.50 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 2046 helix: 1.79 (0.18), residues: 896 sheet: -2.22 (0.28), residues: 316 loop : -0.92 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 195 HIS 0.003 0.001 HIS L 60 PHE 0.018 0.001 PHE C 118 TYR 0.018 0.001 TYR G 222 ARG 0.007 0.000 ARG I 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 318 time to evaluate : 1.979 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 336 average time/residue: 0.3776 time to fit residues: 177.8728 Evaluate side-chains 323 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 310 time to evaluate : 1.965 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1592 time to fit residues: 6.4928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 40.0000 chunk 25 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 225 optimal weight: 30.0000 chunk 141 optimal weight: 0.1980 chunk 137 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 HIS I 230 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17702 Z= 0.186 Angle : 0.542 7.128 24108 Z= 0.266 Chirality : 0.039 0.141 2956 Planarity : 0.003 0.039 3075 Dihedral : 5.347 57.770 2619 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.13 % Allowed : 18.10 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 2046 helix: 1.95 (0.18), residues: 895 sheet: -2.18 (0.28), residues: 316 loop : -0.81 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 195 HIS 0.002 0.000 HIS A 92 PHE 0.023 0.001 PHE C 118 TYR 0.017 0.001 TYR G 222 ARG 0.012 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 327 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 337 average time/residue: 0.3708 time to fit residues: 176.3330 Evaluate side-chains 326 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 317 time to evaluate : 1.994 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2220 time to fit residues: 5.6878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 0.6980 chunk 153 optimal weight: 0.0170 chunk 111 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 205 optimal weight: 40.0000 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 GLN D 2 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 HIS I 230 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17702 Z= 0.212 Angle : 0.548 7.195 24108 Z= 0.270 Chirality : 0.039 0.150 2956 Planarity : 0.004 0.039 3075 Dihedral : 5.291 56.927 2619 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.65 % Allowed : 18.69 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 2046 helix: 2.07 (0.18), residues: 893 sheet: -2.11 (0.27), residues: 318 loop : -0.77 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP G 195 HIS 0.002 0.000 HIS L 60 PHE 0.023 0.001 PHE C 118 TYR 0.018 0.001 TYR G 222 ARG 0.006 0.000 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 322 time to evaluate : 2.010 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 328 average time/residue: 0.3841 time to fit residues: 177.3098 Evaluate side-chains 316 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 311 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1527 time to fit residues: 4.0185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 30.0000 chunk 197 optimal weight: 0.0170 chunk 210 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 209 optimal weight: 30.0000 chunk 138 optimal weight: 5.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 HIS I 57 GLN I 230 GLN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17702 Z= 0.370 Angle : 0.617 8.268 24108 Z= 0.303 Chirality : 0.042 0.143 2956 Planarity : 0.004 0.040 3075 Dihedral : 5.551 59.806 2619 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.83 % Allowed : 18.81 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 2046 helix: 1.87 (0.18), residues: 896 sheet: -1.99 (0.28), residues: 314 loop : -0.83 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 195 HIS 0.004 0.001 HIS A 92 PHE 0.024 0.001 PHE C 118 TYR 0.023 0.002 TYR G 222 ARG 0.008 0.001 ARG C 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 316 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 324 average time/residue: 0.4043 time to fit residues: 183.7218 Evaluate side-chains 312 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 305 time to evaluate : 1.914 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2250 time to fit residues: 5.2840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 50.0000 chunk 135 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 233 optimal weight: 50.0000 chunk 214 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 143 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17702 Z= 0.278 Angle : 0.594 7.892 24108 Z= 0.293 Chirality : 0.040 0.141 2956 Planarity : 0.004 0.040 3075 Dihedral : 5.490 58.253 2619 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.30 % Allowed : 19.46 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 2046 helix: 1.94 (0.18), residues: 896 sheet: -1.97 (0.28), residues: 312 loop : -0.80 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 195 HIS 0.004 0.001 HIS J 262 PHE 0.024 0.001 PHE C 118 TYR 0.019 0.001 TYR G 222 ARG 0.007 0.000 ARG I 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4092 Ramachandran restraints generated. 2046 Oldfield, 0 Emsley, 2046 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 314 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 316 average time/residue: 0.3757 time to fit residues: 166.1984 Evaluate side-chains 304 residues out of total 1719 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 302 time to evaluate : 1.822 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1547 time to fit residues: 2.9588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 2 GLN ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 230 GLN J 26 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.084427 restraints weight = 29888.562| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.81 r_work: 0.3009 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17702 Z= 0.184 Angle : 0.560 7.225 24108 Z= 0.276 Chirality : 0.039 0.139 2956 Planarity : 0.004 0.040 3075 Dihedral : 5.289 59.154 2619 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.18 % Allowed : 19.82 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 2046 helix: 2.09 (0.18), residues: 905 sheet: -1.96 (0.28), residues: 318 loop : -0.68 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 195 HIS 0.004 0.001 HIS J 262 PHE 0.022 0.001 PHE C 118 TYR 0.016 0.001 TYR G 222 ARG 0.007 0.000 ARG C 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4225.82 seconds wall clock time: 76 minutes 53.07 seconds (4613.07 seconds total)