Starting phenix.real_space_refine on Fri Feb 23 10:43:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvj_16265/02_2024/8bvj_16265.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvj_16265/02_2024/8bvj_16265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvj_16265/02_2024/8bvj_16265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvj_16265/02_2024/8bvj_16265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvj_16265/02_2024/8bvj_16265.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvj_16265/02_2024/8bvj_16265.pdb" } resolution = 4.5 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= 0.002 sd= 0.013 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: 6 Type Number sf(0) Gaussians P 55 5.49 5 S 54 5.16 5 C 12131 2.51 5 N 3409 2.21 5 O 3633 1.98 5 H 18901 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 18": "OE1" <-> "OE2" Residue "S GLU 18": "OE1" <-> "OE2" Residue "S TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 18": "OE1" <-> "OE2" Residue "W GLU 37": "OE1" <-> "OE2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 66": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "I GLU 37": "OE1" <-> "OE2" Residue "I PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 197": "OE1" <-> "OE2" Residue "G ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 197": "OE1" <-> "OE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38183 Number of models: 1 Model: "" Number of chains: 23 Chain: "R" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1085 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "T" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1104 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "J" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1111 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "L" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1025 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "N" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1107 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "P" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1104 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "X" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1021 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "Y" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1103 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "S" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1111 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "U" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1008 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain: "V" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1084 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "W" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1126 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 4, 'TRANS': 63} Chain: "K" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1119 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "M" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1104 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain: "D" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1112 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 5, 'TRANS': 61} Chain: "E" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1141 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "F" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1140 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 5, 'TRANS': 63} Chain: "I" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1097 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 4, 'TRANS': 61} Chain: "Q" Number of atoms: 4163 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 261, 4149 Classifications: {'peptide': 261} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 248} Conformer: "B" Number of residues, atoms: 261, 4149 Classifications: {'peptide': 261} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 248} bond proxies already assigned to first conformer: 4188 Chain: "B" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1788 Classifications: {'RNA': 55} Modifications used: {'rna2p_pur': 25, 'rna2p_pyr': 7, 'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna2p': 31, 'rna3p': 23} Chain breaks: 3 Chain: "G" Number of atoms: 4162 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 260, 4148 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Conformer: "B" Number of residues, atoms: 260, 4148 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} bond proxies already assigned to first conformer: 4186 Chain: "C" Number of atoms: 4184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Conformer: "B" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} bond proxies already assigned to first conformer: 4209 Chain: "A" Number of atoms: 4184 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} Conformer: "B" Number of residues, atoms: 262, 4170 Classifications: {'peptide': 262} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 249} bond proxies already assigned to first conformer: 4209 Time building chain proxies: 23.18, per 1000 atoms: 0.61 Number of scatterers: 38183 At special positions: 0 Unit cell: (99.6, 146.91, 152.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 55 15.00 O 3633 8.00 N 3409 7.00 C 12131 6.00 H 18901 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS Q 32 " - pdb=" SG CYS Q 146 " 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: 31.60 Conformation dependent library (CDL) restraints added in 5.2 seconds 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 19 sheets defined 27.7% alpha, 25.0% beta 5 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 17.48 Creating SS restraints... Processing helix chain 'R' and resid 7 through 18 Processing helix chain 'T' and resid 7 through 19 Processing helix chain 'J' and resid 7 through 19 Processing helix chain 'L' and resid 7 through 18 removed outlier: 3.640A pdb=" N TYR L 11 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG L 16 " --> pdb=" O LEU L 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 18 Processing helix chain 'P' and resid 7 through 18 removed outlier: 3.645A pdb=" N GLU P 18 " --> pdb=" O THR P 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 19 Processing helix chain 'Y' and resid 7 through 18 Processing helix chain 'S' and resid 7 through 19 Processing helix chain 'U' and resid 9 through 18 Processing helix chain 'V' and resid 7 through 19 Processing helix chain 'W' and resid 7 through 18 removed outlier: 3.503A pdb=" N TYR W 11 " --> pdb=" O LEU W 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 19 removed outlier: 3.665A pdb=" N TYR K 11 " --> pdb=" O LEU K 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 7 through 18 Processing helix chain 'D' and resid 7 through 19 Processing helix chain 'E' and resid 7 through 18 Processing helix chain 'F' and resid 7 through 19 Processing helix chain 'I' and resid 7 through 19 Processing helix chain 'Q' and resid 10 through 18 removed outlier: 3.540A pdb=" N ALA Q 14 " --> pdb=" O GLY Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 26 Processing helix chain 'Q' and resid 39 through 44 Processing helix chain 'Q' and resid 85 through 90 Processing helix chain 'Q' and resid 115 through 137 Processing helix chain 'Q' and resid 154 through 158 Processing helix chain 'Q' and resid 160 through 165 Processing helix chain 'Q' and resid 171 through 183 Processing helix chain 'Q' and resid 190 through 195 Processing helix chain 'Q' and resid 207 through 214 removed outlier: 3.751A pdb=" N GLU Q 211 " --> pdb=" O SER Q 207 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 230 removed outlier: 3.924A pdb=" N ARG Q 230 " --> pdb=" O GLY Q 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 227 through 230' Processing helix chain 'G' and resid 10 through 17 Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 85 through 90 Processing helix chain 'G' and resid 115 through 135 Processing helix chain 'G' and resid 154 through 158 Processing helix chain 'G' and resid 160 through 165 removed outlier: 3.527A pdb=" N CYS G 164 " --> pdb=" O ASN G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 183 Processing helix chain 'G' and resid 190 through 195 Processing helix chain 'G' and resid 207 through 214 Processing helix chain 'G' and resid 228 through 230 No H-bonds generated for 'chain 'G' and resid 228 through 230' Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.555A pdb=" N GLY C 66 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 115 through 137 Processing helix chain 'C' and resid 154 through 158 Processing helix chain 'C' and resid 160 through 165 removed outlier: 3.562A pdb=" N CYS C 164 " --> pdb=" O ASN C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 183 Processing helix chain 'C' and resid 189 through 195 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 225 through 230 removed outlier: 3.935A pdb=" N ARG C 230 " --> pdb=" O PRO C 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 18 Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.761A pdb=" N TRP A 22 " --> pdb=" O GLY A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.547A pdb=" N LEU A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.784A pdb=" N CYS A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.733A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A 230 " --> pdb=" O PRO A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing sheet with id=AA1, first strand: chain 'R' and resid 22 through 26 removed outlier: 3.565A pdb=" N THR R 61 " --> pdb=" O TYR R 25 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER R 60 " --> pdb=" O TYR P 55 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL P 43 " --> pdb=" O PHE P 39 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N PHE P 39 " --> pdb=" O VAL P 43 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU P 45 " --> pdb=" O GLU P 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 36 through 39 removed outlier: 3.647A pdb=" N SER R 38 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER T 60 " --> pdb=" O TYR R 55 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THR T 61 " --> pdb=" O TYR T 25 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR T 25 " --> pdb=" O THR T 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'T' and resid 35 through 40 removed outlier: 6.517A pdb=" N LEU T 45 " --> pdb=" O GLU T 37 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE T 39 " --> pdb=" O VAL T 43 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL T 43 " --> pdb=" O PHE T 39 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR J 61 " --> pdb=" O TYR J 25 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL J 63 " --> pdb=" O SER J 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 35 through 39 removed outlier: 7.245A pdb=" N LEU J 45 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE J 39 " --> pdb=" O VAL J 43 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL J 43 " --> pdb=" O PHE J 39 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER J 51 " --> pdb=" O PRO L 64 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER L 60 " --> pdb=" O TYR J 55 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR L 61 " --> pdb=" O TYR L 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN L 35 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU L 45 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE L 39 " --> pdb=" O VAL L 43 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL L 43 " --> pdb=" O PHE L 39 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN L 52 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER L 51 " --> pdb=" O PRO N 64 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET L 53 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N SER N 60 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL N 63 " --> pdb=" O SER N 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 35 through 39 removed outlier: 7.147A pdb=" N LEU N 45 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE N 39 " --> pdb=" O VAL N 43 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL N 43 " --> pdb=" O PHE N 39 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER P 60 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR P 25 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL P 62 " --> pdb=" O SER P 23 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER P 23 " --> pdb=" O VAL P 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 31 through 34 removed outlier: 3.616A pdb=" N VAL X 22 " --> pdb=" O GLY X 34 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR X 61 " --> pdb=" O TYR X 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 36 through 39 removed outlier: 6.894A pdb=" N SER Y 60 " --> pdb=" O TYR X 55 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR Y 25 " --> pdb=" O THR Y 61 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL Y 63 " --> pdb=" O SER Y 23 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU Y 45 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE Y 39 " --> pdb=" O VAL Y 43 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL Y 43 " --> pdb=" O PHE Y 39 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR S 61 " --> pdb=" O TYR S 25 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N SER S 51 " --> pdb=" O PRO U 64 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER U 60 " --> pdb=" O TYR S 55 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE U 36 " --> pdb=" O LYS U 47 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS U 47 " --> pdb=" O ILE U 36 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER U 38 " --> pdb=" O LEU U 45 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL U 43 " --> pdb=" O ASP U 40 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER U 51 " --> pdb=" O PRO V 64 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET U 53 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU V 45 " --> pdb=" O GLU V 37 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE V 39 " --> pdb=" O VAL V 43 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL V 43 " --> pdb=" O PHE V 39 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER W 60 " --> pdb=" O TYR V 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'W' and resid 36 through 39 removed outlier: 6.551A pdb=" N LEU W 45 " --> pdb=" O GLU W 37 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE W 39 " --> pdb=" O VAL W 43 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL W 43 " --> pdb=" O PHE W 39 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL W 54 " --> pdb=" O ILE W 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 22 through 26 removed outlier: 3.523A pdb=" N THR M 61 " --> pdb=" O TYR M 25 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER M 60 " --> pdb=" O TYR K 55 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER K 38 " --> pdb=" O LEU K 45 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL K 22 " --> pdb=" O GLY K 34 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER K 23 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL K 62 " --> pdb=" O SER K 23 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR K 25 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N SER K 60 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER I 51 " --> pdb=" O PRO K 64 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN I 52 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER I 38 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LYS I 47 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE I 36 " --> pdb=" O LYS I 47 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER I 23 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL I 62 " --> pdb=" O SER I 23 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR I 25 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER I 60 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL F 43 " --> pdb=" O PHE F 39 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE F 39 " --> pdb=" O VAL F 43 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU F 45 " --> pdb=" O GLU F 37 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 35 through 39 removed outlier: 6.666A pdb=" N LEU M 45 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE M 39 " --> pdb=" O VAL M 43 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N VAL M 43 " --> pdb=" O PHE M 39 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR M 55 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N SER D 60 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR D 25 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL D 62 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N SER D 23 " --> pdb=" O VAL D 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 35 through 39 removed outlier: 6.755A pdb=" N LEU D 45 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N PHE D 39 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 43 " --> pdb=" O PHE D 39 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N SER D 51 " --> pdb=" O PRO E 64 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N SER E 60 " --> pdb=" O TYR D 55 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR E 25 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL E 62 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER E 23 " --> pdb=" O VAL E 62 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU E 45 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE E 39 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL E 43 " --> pdb=" O PHE E 39 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N SER E 51 " --> pdb=" O PRO F 64 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N SER F 60 " --> pdb=" O TYR E 55 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR F 25 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL F 62 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER F 23 " --> pdb=" O VAL F 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 56 through 58 removed outlier: 3.716A pdb=" N VAL Q 68 " --> pdb=" O CYS Q 58 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA Q 69 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU Q 33 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE Q 31 " --> pdb=" O TYR Q 71 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG Q 2 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N CYS Q 32 " --> pdb=" O ARG Q 2 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE Q 4 " --> pdb=" O CYS Q 32 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N GLN Q 34 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N VAL Q 6 " --> pdb=" O GLN Q 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE Q 250 " --> pdb=" O LYS Q 236 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 78 through 80 removed outlier: 3.801A pdb=" N ALA Q 78 " --> pdb=" O ASP Q 98 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE Q 104 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 56 through 58 removed outlier: 3.605A pdb=" N LEU G 33 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG G 2 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N CYS G 32 " --> pdb=" O ARG G 2 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE G 4 " --> pdb=" O CYS G 32 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE G 250 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA G 235 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP G 252 " --> pdb=" O ARG G 233 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 78 through 81 removed outlier: 3.540A pdb=" N ILE G 144 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU G 224 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 188 " --> pdb=" O LEU G 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 56 through 58 removed outlier: 3.577A pdb=" N TYR C 56 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 78 through 81 removed outlier: 6.558A pdb=" N SER C 103 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N CYS C 146 " --> pdb=" O SER C 103 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALA C 105 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER C 148 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU C 107 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL C 223 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY C 147 " --> pdb=" O TYR C 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 54 through 58 removed outlier: 3.601A pdb=" N TYR A 56 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG A 2 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS A 32 " --> pdb=" O ARG A 2 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE A 4 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N GLN A 34 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 6 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 250 " --> pdb=" O LYS A 236 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 234 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.651A pdb=" N VAL A 223 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY A 147 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 221 " --> pdb=" O GLY A 147 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 14.49 Time building geometry restraints manager: 31.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18887 1.03 - 1.23: 19 1.23 - 1.42: 8442 1.42 - 1.62: 11288 1.62 - 1.81: 92 Bond restraints: 38728 Sorted by residual: bond pdb=" N ALA G 0 " pdb=" CA ALA G 0 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" N ALA G 0 " pdb=" H ALA G 0 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C HIS X 57 " pdb=" N ALA X 58 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.17e-02 7.31e+03 9.63e-01 bond pdb=" CA LEU C 70 " pdb=" C LEU C 70 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.10e-02 8.26e+03 8.99e-01 bond pdb=" CA MET G 1 " pdb=" CB MET G 1 " ideal model delta sigma weight residual 1.530 1.516 0.015 1.69e-02 3.50e+03 7.53e-01 ... (remaining 38723 not shown) Histogram of bond angle deviations from ideal: 100.65 - 107.32: 1475 107.32 - 113.99: 45745 113.99 - 120.66: 12961 120.66 - 127.34: 9475 127.34 - 134.01: 351 Bond angle restraints: 70007 Sorted by residual: angle pdb=" N PHE A 99 " pdb=" CA PHE A 99 " pdb=" C PHE A 99 " ideal model delta sigma weight residual 110.80 105.84 4.96 2.13e+00 2.20e-01 5.42e+00 angle pdb=" N ARG A 196 " pdb=" CA ARG A 196 " pdb=" C ARG A 196 " ideal model delta sigma weight residual 112.57 110.01 2.56 1.13e+00 7.83e-01 5.15e+00 angle pdb=" N LEU P 7 " pdb=" CA LEU P 7 " pdb=" C LEU P 7 " ideal model delta sigma weight residual 114.56 111.69 2.87 1.27e+00 6.20e-01 5.10e+00 angle pdb=" C VAL G 8 " pdb=" CA VAL G 8 " pdb=" CB VAL G 8 " ideal model delta sigma weight residual 112.16 108.66 3.50 1.55e+00 4.16e-01 5.09e+00 angle pdb=" C PHE A 99 " pdb=" CA PHE A 99 " pdb=" CB PHE A 99 " ideal model delta sigma weight residual 110.42 114.87 -4.45 1.99e+00 2.53e-01 5.00e+00 ... (remaining 70002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 17697 34.30 - 68.59: 450 68.59 - 102.89: 46 102.89 - 137.19: 10 137.19 - 171.48: 8 Dihedral angle restraints: 18211 sinusoidal: 10456 harmonic: 7755 Sorted by residual: dihedral pdb=" O4' C B 57 " pdb=" C1' C B 57 " pdb=" N1 C B 57 " pdb=" C2 C B 57 " ideal model delta sinusoidal sigma weight residual -128.00 25.02 -153.02 1 1.70e+01 3.46e-03 6.28e+01 dihedral pdb=" CB CYS Q 32 " pdb=" SG CYS Q 32 " pdb=" SG CYS Q 146 " pdb=" CB CYS Q 146 " ideal model delta sinusoidal sigma weight residual 93.00 31.71 61.29 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" O4' A B 77 " pdb=" C1' A B 77 " pdb=" N9 A B 77 " pdb=" C4 A B 77 " ideal model delta sinusoidal sigma weight residual -106.00 -170.10 64.10 1 1.70e+01 3.46e-03 1.87e+01 ... (remaining 18208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2053 0.030 - 0.059: 624 0.059 - 0.089: 117 0.089 - 0.118: 224 0.118 - 0.148: 45 Chirality restraints: 3063 Sorted by residual: chirality pdb=" C3' A B 82 " pdb=" C4' A B 82 " pdb=" O3' A B 82 " pdb=" C2' A B 82 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA ILE G 144 " pdb=" N ILE G 144 " pdb=" C ILE G 144 " pdb=" CB ILE G 144 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA VAL P 20 " pdb=" N VAL P 20 " pdb=" C VAL P 20 " pdb=" CB VAL P 20 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 3060 not shown) Planarity restraints: 5428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP I 9 " 0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO I 10 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO I 10 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 10 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 172 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO A 173 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP P 9 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.35e+00 pdb=" N PRO P 10 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO P 10 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO P 10 " -0.016 5.00e-02 4.00e+02 ... (remaining 5425 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1374 2.16 - 2.77: 74204 2.77 - 3.38: 106777 3.38 - 3.99: 140006 3.99 - 4.60: 215726 Nonbonded interactions: 538087 Sorted by model distance: nonbonded pdb=" O HIS G 131 " pdb=" HG SER G 134 " model vdw 1.546 1.850 nonbonded pdb=" O GLY G 115 " pdb=" HG SER G 118 " model vdw 1.581 1.850 nonbonded pdb=" H LYS F 31 " pdb=" OP2 A B 58 " model vdw 1.636 1.850 nonbonded pdb=" OE1 GLU G 174 " pdb=" H GLU G 174 " model vdw 1.638 1.850 nonbonded pdb=" O GLY C 115 " pdb=" HG SER C 118 " model vdw 1.639 1.850 ... (remaining 538082 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 0 through 11 or resid 13 through 31 or (resid 32 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 33 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 147 through 258)) selection = (chain 'C' and (resid 0 through 11 or resid 13 through 31 or (resid 32 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 33 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 147 through 258)) selection = (chain 'G' and (resid 0 through 11 or resid 13 through 31 or (resid 32 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 33 through 145 or (resid 146 and (name N or name \ CA or name C or name O or name CB or name SG or name H or name HA or name HB2 o \ r name HB3)) or resid 147 through 245 or (resid 246 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 247 through 258)) selection = (chain 'Q' and (resid 0 through 11 or resid 13 through 258)) } ncs_group { reference = (chain 'D' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'E' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'I' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'J' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'L' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'M' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'N' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'P' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'R' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'S' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'T' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'U' and (resid 8 through 47 or (resid 48 and (name N or name CA or name C \ or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA or \ name HB2 or name HB3 or name HD22)) or resid 49 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB or name CG or name ND1 or name CD \ 2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name H \ D2 or name HE1)) or resid 58 through 66)) selection = (chain 'V' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'W' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'X' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD22)) or r \ esid 49 through 56 or (resid 57 and (name N or name CA or name C or name O or na \ me CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H or na \ me HA or name HB2 or name HB3 or name HD2 or name HE1)) or resid 58 through 66)) \ selection = (chain 'Y' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 9 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name \ HB3 or name HD2 or name HE1)) or resid 58 through 66)) } 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=0.49 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: 1.740 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: 0.620 Extract box with map and model: 7.740 Check model and map are aligned: 0.570 Set scattering table: 0.320 Process input model: 137.990 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.002 0.033 19827 Z= 0.127 Angle : 0.472 4.959 27140 Z= 0.272 Chirality : 0.041 0.148 3063 Planarity : 0.002 0.032 3283 Dihedral : 15.009 166.167 7781 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -2.56 (0.17), residues: 2198 helix: -0.52 (0.21), residues: 517 sheet: -2.80 (0.17), residues: 713 loop : -1.24 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 217 HIS 0.002 0.000 HIS R 57 PHE 0.012 0.001 PHE A 99 TYR 0.009 0.000 TYR X 11 ARG 0.002 0.000 ARG C 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 3.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4949 (tpp) cc_final: -0.5646 (ttm) REVERT: J 53 MET cc_start: -0.5369 (tpp) cc_final: -0.5810 (mtt) REVERT: N 53 MET cc_start: -0.6499 (tpp) cc_final: -0.7468 (ttt) REVERT: P 32 LEU cc_start: 0.9195 (mp) cc_final: 0.8947 (mm) REVERT: Y 55 TYR cc_start: 0.9097 (m-80) cc_final: 0.8885 (m-10) REVERT: S 55 TYR cc_start: 0.8225 (m-80) cc_final: 0.7980 (m-80) REVERT: U 59 ILE cc_start: 0.9177 (mt) cc_final: 0.8968 (mt) REVERT: V 23 SER cc_start: 0.8887 (p) cc_final: 0.7910 (p) REVERT: V 35 GLN cc_start: 0.9118 (mt0) cc_final: 0.8764 (pm20) REVERT: V 38 SER cc_start: 0.9209 (m) cc_final: 0.9003 (p) REVERT: V 53 MET cc_start: 0.7440 (ttp) cc_final: 0.6909 (tmm) REVERT: V 55 TYR cc_start: 0.8404 (m-80) cc_final: 0.8067 (m-10) REVERT: W 59 ILE cc_start: 0.9462 (mt) cc_final: 0.9158 (mt) REVERT: K 60 SER cc_start: 0.7782 (m) cc_final: 0.7363 (t) REVERT: E 25 TYR cc_start: 0.8906 (m-80) cc_final: 0.8694 (m-10) REVERT: I 53 MET cc_start: 0.6858 (ttm) cc_final: 0.6475 (tmm) REVERT: Q 80 ILE cc_start: 0.9269 (pt) cc_final: 0.8938 (pt) REVERT: Q 107 LEU cc_start: 0.9036 (tp) cc_final: 0.8699 (tt) REVERT: Q 177 TRP cc_start: 0.8595 (t60) cc_final: 0.8009 (t60) REVERT: Q 187 TYR cc_start: 0.9082 (m-80) cc_final: 0.8076 (m-80) REVERT: G 5 SER cc_start: 0.8810 (t) cc_final: 0.8535 (t) REVERT: G 180 GLU cc_start: 0.9266 (tm-30) cc_final: 0.9038 (tp30) REVERT: G 193 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8021 (tm-30) REVERT: G 220 ASP cc_start: 0.8330 (m-30) cc_final: 0.7886 (t0) REVERT: G 222 GLN cc_start: 0.8989 (mm110) cc_final: 0.8591 (mm-40) REVERT: C 56 TYR cc_start: 0.8739 (m-80) cc_final: 0.8531 (m-80) REVERT: C 106 THR cc_start: 0.7806 (p) cc_final: 0.7309 (p) REVERT: C 143 TYR cc_start: 0.7326 (m-80) cc_final: 0.6427 (m-80) REVERT: A 212 MET cc_start: 0.9361 (tpt) cc_final: 0.9125 (tpt) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.8847 time to fit residues: 781.0690 Evaluate side-chains 420 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 0.0980 chunk 56 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 197 optimal weight: 50.0000 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 GLN K 35 GLN D 8 GLN E 13 ASN F 48 ASN F 52 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN C 26 GLN C 75 GLN A 75 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19827 Z= 0.291 Angle : 0.627 9.216 27140 Z= 0.331 Chirality : 0.043 0.175 3063 Planarity : 0.004 0.073 3283 Dihedral : 14.254 167.081 3284 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.15 % Allowed : 1.39 % Favored : 98.46 % 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: -1.53 (0.18), residues: 2198 helix: 0.30 (0.23), residues: 533 sheet: -2.37 (0.18), residues: 677 loop : -0.51 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 203 HIS 0.008 0.001 HIS K 57 PHE 0.014 0.001 PHE A 129 TYR 0.021 0.002 TYR D 11 ARG 0.025 0.001 ARG J 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 438 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4876 (tpp) cc_final: -0.5147 (tpp) REVERT: N 53 MET cc_start: -0.5594 (tpp) cc_final: -0.6777 (ttt) REVERT: P 53 MET cc_start: -0.2303 (tpp) cc_final: -0.2863 (tpt) REVERT: Y 37 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8672 (tm-30) REVERT: V 9 ASP cc_start: 0.9248 (t70) cc_final: 0.8822 (t0) REVERT: W 59 ILE cc_start: 0.9487 (mt) cc_final: 0.9277 (mt) REVERT: K 60 SER cc_start: 0.7609 (m) cc_final: 0.7341 (p) REVERT: E 45 LEU cc_start: 0.8882 (tp) cc_final: 0.8626 (tp) REVERT: I 51 SER cc_start: 0.8231 (t) cc_final: 0.7946 (p) REVERT: I 53 MET cc_start: 0.7679 (ttm) cc_final: 0.6709 (tmm) REVERT: Q 107 LEU cc_start: 0.9172 (tp) cc_final: 0.8774 (tt) REVERT: Q 167 MET cc_start: 0.9007 (mtp) cc_final: 0.8728 (mtp) REVERT: Q 187 TYR cc_start: 0.9076 (m-80) cc_final: 0.8188 (m-80) REVERT: Q 230 ARG cc_start: 0.8992 (ptm-80) cc_final: 0.8775 (ptm-80) REVERT: G 175 ARG cc_start: 0.9347 (mtm-85) cc_final: 0.9130 (ttp-110) REVERT: G 180 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8992 (tp30) REVERT: G 193 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8163 (tm-30) REVERT: G 224 LEU cc_start: 0.9250 (pt) cc_final: 0.9007 (pt) REVERT: G 232 VAL cc_start: 0.9313 (m) cc_final: 0.8779 (m) REVERT: C 143 TYR cc_start: 0.7530 (m-80) cc_final: 0.6644 (m-80) REVERT: C 146 CYS cc_start: 0.8846 (t) cc_final: 0.8583 (t) outliers start: 3 outliers final: 1 residues processed: 440 average time/residue: 0.8944 time to fit residues: 559.1474 Evaluate side-chains 365 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.0970 chunk 61 optimal weight: 0.9980 chunk 164 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 197 optimal weight: 20.0000 chunk 213 optimal weight: 50.0000 chunk 175 optimal weight: 6.9990 chunk 195 optimal weight: 40.0000 chunk 67 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 overall best weight: 2.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 57 HIS V 8 GLN ** V 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN F 8 GLN ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19827 Z= 0.190 Angle : 0.532 5.484 27140 Z= 0.279 Chirality : 0.043 0.165 3063 Planarity : 0.004 0.060 3283 Dihedral : 14.242 168.218 3284 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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 (0.18), residues: 2198 helix: 0.43 (0.23), residues: 531 sheet: -2.09 (0.20), residues: 634 loop : -0.35 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 177 HIS 0.012 0.001 HIS Q 153 PHE 0.046 0.001 PHE A 129 TYR 0.014 0.001 TYR U 55 ARG 0.009 0.000 ARG U 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4890 (tpp) cc_final: -0.5519 (ttm) REVERT: N 53 MET cc_start: -0.5463 (tpp) cc_final: -0.6647 (ttt) REVERT: N 66 ARG cc_start: 0.8974 (ttp80) cc_final: 0.8630 (ttt180) REVERT: P 53 MET cc_start: -0.2621 (tpp) cc_final: -0.3181 (tpt) REVERT: Y 36 ILE cc_start: 0.9068 (mp) cc_final: 0.8567 (tt) REVERT: Y 37 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8654 (tm-30) REVERT: U 52 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8251 (mp-120) REVERT: U 55 TYR cc_start: 0.8641 (m-80) cc_final: 0.7965 (m-80) REVERT: U 59 ILE cc_start: 0.9058 (mt) cc_final: 0.8797 (mt) REVERT: V 18 GLU cc_start: 0.8910 (tt0) cc_final: 0.8700 (tt0) REVERT: V 35 GLN cc_start: 0.8619 (pm20) cc_final: 0.8341 (pm20) REVERT: K 60 SER cc_start: 0.7533 (m) cc_final: 0.7279 (p) REVERT: E 45 LEU cc_start: 0.8897 (tp) cc_final: 0.8482 (tp) REVERT: I 53 MET cc_start: 0.7428 (ttm) cc_final: 0.6636 (tmm) REVERT: Q 167 MET cc_start: 0.9018 (mtp) cc_final: 0.8704 (mtp) REVERT: G 180 GLU cc_start: 0.9312 (tm-30) cc_final: 0.9011 (tp30) REVERT: G 193 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8119 (tm-30) REVERT: G 220 ASP cc_start: 0.8795 (m-30) cc_final: 0.8363 (m-30) REVERT: G 232 VAL cc_start: 0.9352 (m) cc_final: 0.9051 (m) REVERT: G 242 ARG cc_start: 0.5513 (mmp80) cc_final: 0.5246 (mmp80) REVERT: C 56 TYR cc_start: 0.8732 (m-80) cc_final: 0.8342 (m-80) REVERT: C 143 TYR cc_start: 0.7705 (m-80) cc_final: 0.7227 (m-80) REVERT: C 146 CYS cc_start: 0.8818 (t) cc_final: 0.8515 (t) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.8706 time to fit residues: 513.6857 Evaluate side-chains 359 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 50.0000 chunk 148 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 21 optimal weight: 50.0000 chunk 94 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 198 optimal weight: 50.0000 chunk 209 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 187 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 5 HIS ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 HIS P 5 HIS ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS V 8 GLN ** V 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 5 HIS D 52 GLN ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.5216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 19827 Z= 0.381 Angle : 0.712 7.550 27140 Z= 0.383 Chirality : 0.044 0.190 3063 Planarity : 0.005 0.055 3283 Dihedral : 14.780 170.380 3284 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 24.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 0.10 % Allowed : 1.79 % Favored : 98.11 % 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: -1.60 (0.18), residues: 2198 helix: -0.39 (0.22), residues: 538 sheet: -2.05 (0.20), residues: 584 loop : -0.65 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 177 HIS 0.010 0.002 HIS K 57 PHE 0.037 0.002 PHE A 129 TYR 0.025 0.003 TYR C 187 ARG 0.014 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 360 time to evaluate : 3.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4281 (tpp) cc_final: -0.4785 (ttm) REVERT: J 53 MET cc_start: -0.4616 (tpp) cc_final: -0.4885 (mtp) REVERT: N 53 MET cc_start: -0.4879 (tpp) cc_final: -0.6130 (ttt) REVERT: N 66 ARG cc_start: 0.9208 (ttp80) cc_final: 0.8870 (ttt180) REVERT: P 53 MET cc_start: -0.2718 (tpp) cc_final: -0.3191 (tpt) REVERT: Y 31 LYS cc_start: 0.9212 (mttt) cc_final: 0.8757 (ttmt) REVERT: Y 36 ILE cc_start: 0.9231 (mp) cc_final: 0.8854 (tt) REVERT: Y 37 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8791 (tm-30) REVERT: U 55 TYR cc_start: 0.8989 (m-80) cc_final: 0.8265 (m-80) REVERT: V 37 GLU cc_start: 0.9097 (tp30) cc_final: 0.8757 (tp30) REVERT: V 61 THR cc_start: 0.8012 (p) cc_final: 0.7780 (p) REVERT: E 45 LEU cc_start: 0.9091 (tp) cc_final: 0.8823 (tp) REVERT: E 53 MET cc_start: 0.8538 (ttp) cc_final: 0.7923 (tpp) REVERT: F 45 LEU cc_start: 0.8507 (mp) cc_final: 0.8255 (mp) REVERT: F 46 LEU cc_start: 0.9193 (tp) cc_final: 0.8954 (tp) REVERT: I 53 MET cc_start: 0.7549 (ttm) cc_final: 0.6688 (tmm) REVERT: Q 167 MET cc_start: 0.8956 (mtp) cc_final: 0.8565 (mtp) REVERT: Q 187 TYR cc_start: 0.9218 (m-80) cc_final: 0.8437 (m-80) REVERT: C 72 SER cc_start: 0.9134 (m) cc_final: 0.8719 (t) REVERT: C 144 ILE cc_start: 0.9413 (mm) cc_final: 0.9181 (mp) REVERT: C 146 CYS cc_start: 0.8811 (t) cc_final: 0.8452 (t) REVERT: C 167 MET cc_start: 0.7878 (mmm) cc_final: 0.7648 (mmm) outliers start: 2 outliers final: 1 residues processed: 362 average time/residue: 0.8897 time to fit residues: 459.2045 Evaluate side-chains 305 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 3 optimal weight: 50.0000 chunk 156 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 0 optimal weight: 50.0000 chunk 107 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 28 ASN Y 57 HIS W 5 HIS F 52 GLN ** I 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19827 Z= 0.176 Angle : 0.536 5.070 27140 Z= 0.279 Chirality : 0.043 0.155 3063 Planarity : 0.004 0.046 3283 Dihedral : 14.400 168.671 3284 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: -1.11 (0.18), residues: 2198 helix: 0.34 (0.23), residues: 531 sheet: -1.88 (0.20), residues: 600 loop : -0.41 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 177 HIS 0.006 0.001 HIS G 246 PHE 0.024 0.001 PHE A 129 TYR 0.016 0.001 TYR Q 143 ARG 0.003 0.000 ARG Q 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.4303 (tpp) cc_final: -0.4824 (ttm) REVERT: J 53 MET cc_start: -0.4786 (tpp) cc_final: -0.5119 (mtp) REVERT: N 53 MET cc_start: -0.4725 (tpp) cc_final: -0.6322 (ttt) REVERT: N 66 ARG cc_start: 0.9140 (ttp80) cc_final: 0.8790 (ttt180) REVERT: P 53 MET cc_start: -0.3011 (tpp) cc_final: -0.3388 (tpt) REVERT: Y 36 ILE cc_start: 0.9247 (mp) cc_final: 0.8889 (tt) REVERT: Y 37 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8718 (tm-30) REVERT: U 55 TYR cc_start: 0.8799 (m-80) cc_final: 0.8122 (m-80) REVERT: V 5 HIS cc_start: 0.8602 (p90) cc_final: 0.8393 (p90) REVERT: V 23 SER cc_start: 0.8952 (p) cc_final: 0.8595 (p) REVERT: I 53 MET cc_start: 0.7498 (ttm) cc_final: 0.6681 (tmm) REVERT: Q 56 TYR cc_start: 0.8492 (m-10) cc_final: 0.8169 (m-10) REVERT: Q 167 MET cc_start: 0.8900 (mtp) cc_final: 0.8538 (mtp) REVERT: G 1 MET cc_start: 0.8229 (tpp) cc_final: 0.7827 (tpp) REVERT: G 180 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9206 (tp30) REVERT: G 193 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8330 (tm-30) REVERT: G 236 LYS cc_start: 0.9435 (mtmm) cc_final: 0.9035 (mtmm) REVERT: C 72 SER cc_start: 0.9134 (m) cc_final: 0.8762 (t) REVERT: C 146 CYS cc_start: 0.8761 (t) cc_final: 0.8450 (t) REVERT: C 167 MET cc_start: 0.7825 (mmm) cc_final: 0.7570 (mmm) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.8744 time to fit residues: 455.1395 Evaluate side-chains 310 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 3.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 209 optimal weight: 40.0000 chunk 174 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 17 optimal weight: 40.0000 chunk 69 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS ** V 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19827 Z= 0.317 Angle : 0.634 7.754 27140 Z= 0.341 Chirality : 0.043 0.196 3063 Planarity : 0.004 0.048 3283 Dihedral : 14.579 169.427 3284 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -1.36 (0.18), residues: 2198 helix: -0.06 (0.23), residues: 534 sheet: -1.85 (0.21), residues: 571 loop : -0.64 (0.19), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 177 HIS 0.009 0.001 HIS K 57 PHE 0.022 0.002 PHE G 85 TYR 0.017 0.002 TYR C 187 ARG 0.011 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 331 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.3918 (tpp) cc_final: -0.4395 (ttm) REVERT: J 53 MET cc_start: -0.4100 (tpp) cc_final: -0.4380 (mtp) REVERT: N 53 MET cc_start: -0.3742 (tpp) cc_final: -0.5417 (ttp) REVERT: N 66 ARG cc_start: 0.9247 (ttp80) cc_final: 0.8808 (ttt180) REVERT: P 53 MET cc_start: -0.3186 (tpp) cc_final: -0.3631 (tpt) REVERT: Y 31 LYS cc_start: 0.9193 (mttt) cc_final: 0.8770 (ttmt) REVERT: Y 36 ILE cc_start: 0.9296 (mp) cc_final: 0.8983 (tt) REVERT: Y 37 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8794 (tm-30) REVERT: U 46 LEU cc_start: 0.9185 (tp) cc_final: 0.8904 (tp) REVERT: U 55 TYR cc_start: 0.8985 (m-80) cc_final: 0.8233 (m-80) REVERT: V 5 HIS cc_start: 0.8748 (p90) cc_final: 0.8507 (p90) REVERT: V 37 GLU cc_start: 0.9104 (tp30) cc_final: 0.8766 (tp30) REVERT: W 35 GLN cc_start: 0.8884 (pp30) cc_final: 0.8548 (pp30) REVERT: E 45 LEU cc_start: 0.9120 (tp) cc_final: 0.8902 (tp) REVERT: I 45 LEU cc_start: 0.9063 (tp) cc_final: 0.8846 (tp) REVERT: I 53 MET cc_start: 0.7667 (ttm) cc_final: 0.6776 (tmm) REVERT: Q 56 TYR cc_start: 0.8531 (m-10) cc_final: 0.8236 (m-10) REVERT: Q 167 MET cc_start: 0.8880 (mtp) cc_final: 0.8486 (mtp) REVERT: Q 187 TYR cc_start: 0.9268 (m-80) cc_final: 0.8547 (m-80) REVERT: G 1 MET cc_start: 0.8422 (tpp) cc_final: 0.7902 (tpp) REVERT: G 135 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8342 (tttm) REVERT: C 146 CYS cc_start: 0.8840 (t) cc_final: 0.8489 (t) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.8730 time to fit residues: 414.5222 Evaluate side-chains 286 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 40.0000 chunk 23 optimal weight: 40.0000 chunk 119 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 176 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS D 8 GLN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN B ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19827 Z= 0.233 Angle : 0.573 7.489 27140 Z= 0.302 Chirality : 0.043 0.169 3063 Planarity : 0.004 0.058 3283 Dihedral : 14.511 169.062 3284 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % 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: -1.23 (0.18), residues: 2198 helix: 0.09 (0.23), residues: 535 sheet: -1.80 (0.20), residues: 600 loop : -0.51 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 177 HIS 0.009 0.001 HIS Q 131 PHE 0.019 0.002 PHE G 85 TYR 0.041 0.002 TYR M 55 ARG 0.009 0.001 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 2.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.3825 (tpp) cc_final: -0.4474 (ttm) REVERT: J 53 MET cc_start: -0.4082 (tpp) cc_final: -0.4423 (mtp) REVERT: N 53 MET cc_start: -0.4203 (tpp) cc_final: -0.5822 (ttp) REVERT: N 66 ARG cc_start: 0.9199 (ttp80) cc_final: 0.8783 (ttt180) REVERT: P 53 MET cc_start: -0.3191 (tpp) cc_final: -0.3638 (tpt) REVERT: Y 36 ILE cc_start: 0.9308 (mp) cc_final: 0.8990 (tt) REVERT: Y 37 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8751 (tm-30) REVERT: U 55 TYR cc_start: 0.8924 (m-80) cc_final: 0.8145 (m-80) REVERT: V 37 GLU cc_start: 0.9092 (tp30) cc_final: 0.8599 (tp30) REVERT: W 28 ASN cc_start: 0.8603 (p0) cc_final: 0.8115 (p0) REVERT: E 45 LEU cc_start: 0.9101 (tp) cc_final: 0.8863 (tp) REVERT: E 52 GLN cc_start: 0.9014 (mt0) cc_final: 0.8458 (mt0) REVERT: F 46 LEU cc_start: 0.9248 (tp) cc_final: 0.9035 (tp) REVERT: I 53 MET cc_start: 0.7642 (ttm) cc_final: 0.7214 (tmm) REVERT: Q 56 TYR cc_start: 0.8471 (m-10) cc_final: 0.8259 (m-10) REVERT: Q 167 MET cc_start: 0.8871 (mtp) cc_final: 0.8519 (mtp) REVERT: Q 187 TYR cc_start: 0.9282 (m-80) cc_final: 0.8568 (m-80) REVERT: G 1 MET cc_start: 0.8307 (tpp) cc_final: 0.7911 (tpp) REVERT: G 135 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8360 (tttm) REVERT: G 236 LYS cc_start: 0.9434 (mtmm) cc_final: 0.9157 (mtmm) REVERT: C 146 CYS cc_start: 0.8884 (t) cc_final: 0.8545 (t) REVERT: C 167 MET cc_start: 0.7909 (mmm) cc_final: 0.7677 (mmm) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.8739 time to fit residues: 429.0172 Evaluate side-chains 295 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 40 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 103 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 164 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 ASN ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 HIS ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19827 Z= 0.205 Angle : 0.545 5.482 27140 Z= 0.286 Chirality : 0.043 0.172 3063 Planarity : 0.004 0.067 3283 Dihedral : 14.447 169.164 3284 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.05 % Allowed : 0.25 % Favored : 99.70 % 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: -1.08 (0.18), residues: 2198 helix: 0.31 (0.23), residues: 530 sheet: -1.83 (0.20), residues: 607 loop : -0.38 (0.20), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 177 HIS 0.006 0.001 HIS G 153 PHE 0.018 0.001 PHE G 85 TYR 0.028 0.001 TYR M 55 ARG 0.009 0.001 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 337 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.3837 (tpp) cc_final: -0.4447 (ttm) REVERT: J 53 MET cc_start: -0.4125 (tpp) cc_final: -0.4453 (mtp) REVERT: N 53 MET cc_start: -0.4166 (tpp) cc_final: -0.5718 (ttp) REVERT: N 66 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8741 (tpt-90) REVERT: P 53 MET cc_start: -0.3198 (tpp) cc_final: -0.3603 (tpt) REVERT: Y 36 ILE cc_start: 0.9282 (mp) cc_final: 0.8953 (tt) REVERT: Y 37 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8725 (tm-30) REVERT: V 37 GLU cc_start: 0.9082 (tp30) cc_final: 0.8872 (tp30) REVERT: W 28 ASN cc_start: 0.8572 (p0) cc_final: 0.8018 (p0) REVERT: E 45 LEU cc_start: 0.9076 (tp) cc_final: 0.8839 (tp) REVERT: E 52 GLN cc_start: 0.9006 (mt0) cc_final: 0.8471 (mt0) REVERT: F 46 LEU cc_start: 0.9255 (tp) cc_final: 0.9015 (tp) REVERT: I 53 MET cc_start: 0.7953 (ttm) cc_final: 0.7090 (tmm) REVERT: Q 167 MET cc_start: 0.8862 (mtp) cc_final: 0.8495 (mtp) REVERT: G 135 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8283 (tttm) REVERT: G 236 LYS cc_start: 0.9412 (mtmm) cc_final: 0.9074 (mtmm) REVERT: C 146 CYS cc_start: 0.8935 (t) cc_final: 0.8655 (t) REVERT: C 167 MET cc_start: 0.7926 (mmm) cc_final: 0.7702 (mmm) outliers start: 0 outliers final: 0 residues processed: 337 average time/residue: 0.8538 time to fit residues: 415.6534 Evaluate side-chains 296 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 3.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 9.9990 chunk 200 optimal weight: 50.0000 chunk 182 optimal weight: 0.6980 chunk 194 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 chunk 84 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 176 optimal weight: 1.9990 chunk 184 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.6568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19827 Z= 0.207 Angle : 0.544 6.378 27140 Z= 0.286 Chirality : 0.043 0.177 3063 Planarity : 0.004 0.047 3283 Dihedral : 14.417 169.282 3284 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % 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: -1.00 (0.18), residues: 2198 helix: 0.42 (0.23), residues: 529 sheet: -1.82 (0.21), residues: 591 loop : -0.36 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 177 HIS 0.006 0.001 HIS G 246 PHE 0.015 0.001 PHE A 129 TYR 0.023 0.001 TYR M 55 ARG 0.007 0.001 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.3802 (tpp) cc_final: -0.4394 (ttm) REVERT: J 53 MET cc_start: -0.4040 (tpp) cc_final: -0.4380 (mtp) REVERT: N 53 MET cc_start: -0.4304 (tpp) cc_final: -0.5799 (ttp) REVERT: N 66 ARG cc_start: 0.9230 (ttp80) cc_final: 0.8785 (ttt180) REVERT: P 53 MET cc_start: -0.3183 (tpp) cc_final: -0.3601 (tpt) REVERT: Y 36 ILE cc_start: 0.9267 (mp) cc_final: 0.8935 (tt) REVERT: Y 37 GLU cc_start: 0.9083 (tm-30) cc_final: 0.8720 (tm-30) REVERT: U 55 TYR cc_start: 0.8902 (m-80) cc_final: 0.8464 (m-80) REVERT: V 37 GLU cc_start: 0.9098 (tp30) cc_final: 0.8883 (tp30) REVERT: W 28 ASN cc_start: 0.8614 (p0) cc_final: 0.8100 (p0) REVERT: W 37 GLU cc_start: 0.9427 (pt0) cc_final: 0.9104 (pt0) REVERT: E 45 LEU cc_start: 0.9099 (tp) cc_final: 0.8862 (tp) REVERT: E 52 GLN cc_start: 0.9053 (mt0) cc_final: 0.8521 (mt0) REVERT: F 46 LEU cc_start: 0.9250 (tp) cc_final: 0.8999 (tp) REVERT: I 53 MET cc_start: 0.7917 (ttm) cc_final: 0.7017 (tmm) REVERT: Q 167 MET cc_start: 0.8851 (mtp) cc_final: 0.8484 (mtp) REVERT: G 135 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8379 (tttm) REVERT: G 236 LYS cc_start: 0.9415 (mtmm) cc_final: 0.9066 (mtmm) REVERT: C 146 CYS cc_start: 0.8908 (t) cc_final: 0.8635 (t) REVERT: C 167 MET cc_start: 0.7860 (mmm) cc_final: 0.7635 (mmm) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.8761 time to fit residues: 420.5645 Evaluate side-chains 294 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 40.0000 chunk 125 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 216 optimal weight: 8.9990 chunk 198 optimal weight: 50.0000 chunk 172 optimal weight: 9.9990 chunk 17 optimal weight: 30.0000 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19827 Z= 0.198 Angle : 0.532 5.797 27140 Z= 0.279 Chirality : 0.043 0.147 3063 Planarity : 0.004 0.053 3283 Dihedral : 14.363 169.335 3284 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.05 % Allowed : 0.15 % Favored : 99.80 % 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: -0.93 (0.18), residues: 2198 helix: 0.49 (0.23), residues: 535 sheet: -1.75 (0.21), residues: 588 loop : -0.35 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 177 HIS 0.005 0.001 HIS G 246 PHE 0.014 0.001 PHE A 129 TYR 0.024 0.001 TYR M 55 ARG 0.007 0.001 ARG G 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4396 Ramachandran restraints generated. 2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: T 53 MET cc_start: -0.3941 (tpp) cc_final: -0.4516 (ttm) REVERT: J 53 MET cc_start: -0.3964 (tpp) cc_final: -0.4345 (mtp) REVERT: N 53 MET cc_start: -0.4223 (tpp) cc_final: -0.5745 (ttp) REVERT: N 66 ARG cc_start: 0.9235 (ttp80) cc_final: 0.8778 (ttt180) REVERT: P 53 MET cc_start: -0.3215 (tpp) cc_final: -0.3662 (tpt) REVERT: Y 36 ILE cc_start: 0.9269 (mp) cc_final: 0.8944 (tt) REVERT: Y 37 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8716 (tm-30) REVERT: U 55 TYR cc_start: 0.8891 (m-80) cc_final: 0.8474 (m-80) REVERT: V 37 GLU cc_start: 0.9084 (tp30) cc_final: 0.8829 (tp30) REVERT: W 28 ASN cc_start: 0.8678 (p0) cc_final: 0.8071 (p0) REVERT: W 37 GLU cc_start: 0.9426 (pt0) cc_final: 0.9069 (pt0) REVERT: E 45 LEU cc_start: 0.9095 (tp) cc_final: 0.8853 (tp) REVERT: E 52 GLN cc_start: 0.9082 (mt0) cc_final: 0.8522 (mt0) REVERT: F 46 LEU cc_start: 0.9247 (tp) cc_final: 0.8975 (tp) REVERT: I 53 MET cc_start: 0.7873 (ttm) cc_final: 0.6984 (tmm) REVERT: Q 167 MET cc_start: 0.8809 (mtp) cc_final: 0.8442 (mtp) REVERT: Q 187 TYR cc_start: 0.9333 (m-80) cc_final: 0.8612 (m-80) REVERT: G 5 SER cc_start: 0.8838 (t) cc_final: 0.8573 (t) REVERT: G 135 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8307 (tppt) REVERT: G 236 LYS cc_start: 0.9420 (mtmm) cc_final: 0.9212 (mtmm) REVERT: C 146 CYS cc_start: 0.8914 (t) cc_final: 0.8688 (t) REVERT: C 167 MET cc_start: 0.7869 (mmm) cc_final: 0.7641 (mmm) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.8577 time to fit residues: 409.4810 Evaluate side-chains 291 residues out of total 2006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 chunk 158 optimal weight: 0.0170 chunk 25 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 21 optimal weight: 40.0000 chunk 31 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 overall best weight: 3.6824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 52 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 57 HIS ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 GLN ** G 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.085411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.055589 restraints weight = 443580.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058008 restraints weight = 185455.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.059734 restraints weight = 104732.627| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19827 Z= 0.203 Angle : 0.539 5.593 27140 Z= 0.283 Chirality : 0.043 0.150 3063 Planarity : 0.004 0.058 3283 Dihedral : 14.375 169.338 3284 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.05 % Allowed : 0.40 % Favored : 99.55 % 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: -0.93 (0.18), residues: 2198 helix: 0.50 (0.23), residues: 535 sheet: -1.71 (0.21), residues: 584 loop : -0.38 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 177 HIS 0.005 0.001 HIS G 246 PHE 0.013 0.001 PHE A 129 TYR 0.023 0.001 TYR M 55 ARG 0.009 0.001 ARG G 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10026.86 seconds wall clock time: 178 minutes 14.05 seconds (10694.05 seconds total)