Starting phenix.real_space_refine on Sun Mar 17 06:07:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/03_2024/7zyv_15027_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/03_2024/7zyv_15027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/03_2024/7zyv_15027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/03_2024/7zyv_15027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/03_2024/7zyv_15027_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/03_2024/7zyv_15027_trim_updated.pdb" } resolution = 2.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.042 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 Fe 12 7.16 5 Mg 2 5.21 5 S 72 5.16 5 C 11008 2.51 5 N 2500 2.21 5 O 2858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A ASP 19": "OD1" <-> "OD2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C ASP 240": "OD1" <-> "OD2" Residue "C ARG 250": "NH1" <-> "NH2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 29": "NH1" <-> "NH2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "I TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 13": "OE1" <-> "OE2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I ASP 64": "OD1" <-> "OD2" Residue "I GLU 75": "OE1" <-> "OE2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J ASP 35": "OD1" <-> "OD2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J ASP 152": "OD1" <-> "OD2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K ASP 42": "OD1" <-> "OD2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K ASP 87": "OD1" <-> "OD2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K ARG 209": "NH1" <-> "NH2" Residue "K ASP 224": "OD1" <-> "OD2" Residue "K ASP 240": "OD1" <-> "OD2" Residue "K ARG 250": "NH1" <-> "NH2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L ASP 62": "OD1" <-> "OD2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L GLU 120": "OE1" <-> "OE2" Residue "L ARG 137": "NH1" <-> "NH2" Residue "L ARG 170": "NH1" <-> "NH2" Residue "L GLU 173": "OE1" <-> "OE2" Residue "N GLU 5": "OE1" <-> "OE2" Residue "N ARG 29": "NH1" <-> "NH2" Residue "N GLU 36": "OE1" <-> "OE2" Residue "O GLU 3": "OE1" <-> "OE2" Residue "O ARG 31": "NH1" <-> "NH2" Residue "O ASP 33": "OD1" <-> "OD2" Residue "R PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R ASP 52": "OD1" <-> "OD2" Residue "Q PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q ASP 52": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16452 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "B" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1225 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "C" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2158 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 23, 'TRANS': 254} Chain breaks: 1 Chain: "D" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1259 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 13, 'TRANS': 152} Chain breaks: 1 Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "G" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 266 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 32} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 222 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "J" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2167 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 23, 'TRANS': 255} Chain breaks: 1 Chain: "L" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1254 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 13, 'TRANS': 151} Chain breaks: 1 Chain: "M" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "N" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 264 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "O" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 261 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "P" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 223 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "Q" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "A" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 317 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'PL9': 1, 'UMQ': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 178 Unusual residues: {'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'BCR': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'UMQ': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 262 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'UMQ': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 178 Unusual residues: {'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'HEC': 1, 'PL9': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'BCR': 1, 'UMQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5784 SG CYS D 107 42.317 69.391 44.000 1.00 96.15 S ATOM 5920 SG CYS D 125 40.722 65.931 43.166 1.00 95.70 S ATOM 13133 SG CYS L 107 93.565 26.930 43.993 1.00 96.40 S ATOM 13269 SG CYS L 125 95.166 30.393 43.162 1.00 96.16 S Time building chain proxies: 9.52, per 1000 atoms: 0.58 Number of scatterers: 16452 At special positions: 0 Unit cell: (136.74, 97.18, 122.12, 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) Fe 12 26.01 S 72 16.00 Mg 2 11.99 O 2858 8.00 N 2500 7.00 C 11008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 127 " distance=2.03 Simple disulfide: pdb=" SG CYS L 112 " - pdb=" SG CYS L 127 " 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.77 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 202 " pdb="FE1 FES D 202 " - pdb=" SG CYS D 107 " pdb="FE1 FES D 202 " - pdb=" SG CYS D 125 " pdb="FE2 FES D 202 " - pdb=" ND1 HIS D 128 " pdb="FE2 FES D 202 " - pdb=" ND1 HIS D 109 " pdb=" FES L 402 " pdb="FE1 FES L 402 " - pdb=" SG CYS L 107 " pdb="FE1 FES L 402 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 402 " - pdb=" ND1 HIS L 128 " pdb="FE2 FES L 402 " - pdb=" ND1 HIS L 109 " Number of angles added : 6 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3560 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 11 sheets defined 47.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 removed outlier: 3.811A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.537A pdb=" N SER A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 56 removed outlier: 4.546A pdb=" N GLY A 37 " --> pdb=" O TYR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 79 through 106 removed outlier: 3.671A pdb=" N ALA A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 removed outlier: 4.388A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.857A pdb=" N GLY A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 162 through 170 Processing helix chain 'A' and resid 177 through 188 Processing helix chain 'A' and resid 190 through 209 Processing helix chain 'B' and resid 12 through 20 removed outlier: 3.641A pdb=" N LYS B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 57 Processing helix chain 'B' and resid 79 through 88 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 94 through 114 removed outlier: 4.031A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix removed outlier: 3.753A pdb=" N THR B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 127 through 148 removed outlier: 4.498A pdb=" N THR B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 20 through 23 Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 248 through 282 removed outlier: 3.654A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 41 removed outlier: 3.650A pdb=" N SER D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix Proline residue: D 36 - end of helix removed outlier: 4.134A pdb=" N PHE D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 71 removed outlier: 3.985A pdb=" N LYS D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'E' and resid 2 through 27 Processing helix chain 'F' and resid 2 through 35 removed outlier: 3.836A pdb=" N THR F 17 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 31 removed outlier: 3.876A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 3 through 25 removed outlier: 3.752A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 12 removed outlier: 3.811A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 23 removed outlier: 3.537A pdb=" N SER I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 56 removed outlier: 4.546A pdb=" N GLY I 37 " --> pdb=" O TYR I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 74 Processing helix chain 'I' and resid 79 through 106 removed outlier: 3.671A pdb=" N ALA I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 137 removed outlier: 4.388A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 157 removed outlier: 3.856A pdb=" N GLY I 153 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL I 154 " --> pdb=" O ILE I 150 " (cutoff:3.500A) Proline residue: I 155 - end of helix Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'I' and resid 177 through 188 Processing helix chain 'I' and resid 190 through 209 Processing helix chain 'J' and resid 12 through 20 removed outlier: 3.642A pdb=" N LYS J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 57 Processing helix chain 'J' and resid 79 through 88 Proline residue: J 83 - end of helix Processing helix chain 'J' and resid 94 through 114 removed outlier: 4.031A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix removed outlier: 3.753A pdb=" N THR J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL J 111 " --> pdb=" O GLY J 107 " (cutoff:3.500A) Proline residue: J 112 - end of helix Processing helix chain 'J' and resid 123 through 125 No H-bonds generated for 'chain 'J' and resid 123 through 125' Processing helix chain 'J' and resid 127 through 148 removed outlier: 4.498A pdb=" N THR J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 153 No H-bonds generated for 'chain 'J' and resid 151 through 153' Processing helix chain 'K' and resid 2 through 8 Processing helix chain 'K' and resid 20 through 23 Processing helix chain 'K' and resid 86 through 88 No H-bonds generated for 'chain 'K' and resid 86 through 88' Processing helix chain 'K' and resid 91 through 97 Processing helix chain 'K' and resid 135 through 137 No H-bonds generated for 'chain 'K' and resid 135 through 137' Processing helix chain 'K' and resid 248 through 282 removed outlier: 3.654A pdb=" N LYS K 272 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 41 removed outlier: 3.556A pdb=" N GLU L 16 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR L 17 " --> pdb=" O GLN L 13 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN L 19 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix removed outlier: 3.678A pdb=" N LEU L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Proline residue: L 36 - end of helix removed outlier: 4.133A pdb=" N PHE L 41 " --> pdb=" O TYR L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 71 Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'M' and resid 2 through 27 Processing helix chain 'N' and resid 2 through 35 removed outlier: 3.872A pdb=" N THR N 17 " --> pdb=" O MET N 13 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU N 35 " --> pdb=" O GLU N 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 31 removed outlier: 3.876A pdb=" N ILE O 14 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 3 through 25 Processing helix chain 'R' and resid 36 through 42 removed outlier: 3.550A pdb=" N LYS R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 42 removed outlier: 3.550A pdb=" N LYS Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 32 through 34 Processing sheet with id= B, first strand: chain 'C' and resid 38 through 40 removed outlier: 8.493A pdb=" N VAL C 39 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL C 244 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 204 through 207 removed outlier: 7.016A pdb=" N ALA C 195 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 179 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 77 through 81 removed outlier: 3.592A pdb=" N THR D 78 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 101 through 103 Processing sheet with id= F, first strand: chain 'D' and resid 115 through 117 Processing sheet with id= G, first strand: chain 'K' and resid 32 through 34 Processing sheet with id= H, first strand: chain 'K' and resid 38 through 40 removed outlier: 8.494A pdb=" N VAL K 39 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL K 244 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 203 through 207 removed outlier: 7.017A pdb=" N ALA K 195 " --> pdb=" O VAL K 179 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL K 179 " --> pdb=" O ALA K 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 77 through 81 removed outlier: 3.576A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 101 through 103 701 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.18 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.41: 6621 1.41 - 1.61: 10127 1.61 - 1.81: 110 1.81 - 2.01: 4 2.01 - 2.20: 48 Bond restraints: 16910 Sorted by residual: bond pdb=" C1 SQD L 401 " pdb=" O5 SQD L 401 " ideal model delta sigma weight residual 1.500 1.397 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 SQD D 201 " pdb=" O5 SQD D 201 " ideal model delta sigma weight residual 1.500 1.398 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C5' UMQ B 403 " pdb=" O5' UMQ B 403 " ideal model delta sigma weight residual 1.413 1.504 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C5' UMQ J 404 " pdb=" O5' UMQ J 404 " ideal model delta sigma weight residual 1.413 1.504 -0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" C5 SQD L 401 " pdb=" O5 SQD L 401 " ideal model delta sigma weight residual 1.483 1.402 0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 16905 not shown) Histogram of bond angle deviations from ideal: 75.57 - 96.38: 44 96.38 - 117.20: 12322 117.20 - 138.02: 10711 138.02 - 158.84: 2 158.84 - 179.65: 20 Bond angle restraints: 23099 Sorted by residual: angle pdb=" N ARG E 29 " pdb=" CA ARG E 29 " pdb=" C ARG E 29 " ideal model delta sigma weight residual 112.86 117.39 -4.53 1.22e+00 6.72e-01 1.38e+01 angle pdb=" CG LYS C 222 " pdb=" CD LYS C 222 " pdb=" CE LYS C 222 " ideal model delta sigma weight residual 111.30 119.56 -8.26 2.30e+00 1.89e-01 1.29e+01 angle pdb=" CG LYS K 222 " pdb=" CD LYS K 222 " pdb=" CE LYS K 222 " ideal model delta sigma weight residual 111.30 119.55 -8.25 2.30e+00 1.89e-01 1.29e+01 angle pdb=" N LYS B 119 " pdb=" CA LYS B 119 " pdb=" C LYS B 119 " ideal model delta sigma weight residual 112.59 116.63 -4.04 1.22e+00 6.72e-01 1.10e+01 angle pdb=" CD LYS C 222 " pdb=" CE LYS C 222 " pdb=" NZ LYS C 222 " ideal model delta sigma weight residual 111.90 122.45 -10.55 3.20e+00 9.77e-02 1.09e+01 ... (remaining 23094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.05: 9221 27.05 - 54.11: 743 54.11 - 81.16: 112 81.16 - 108.21: 54 108.21 - 135.27: 13 Dihedral angle restraints: 10143 sinusoidal: 4595 harmonic: 5548 Sorted by residual: dihedral pdb=" CA LYS D 96 " pdb=" C LYS D 96 " pdb=" N THR D 97 " pdb=" CA THR D 97 " ideal model delta harmonic sigma weight residual -180.00 -157.69 -22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" O2 UMQ B 404 " pdb=" C1 UMQ B 404 " pdb=" C2 UMQ B 404 " pdb=" O5 UMQ B 404 " ideal model delta sinusoidal sigma weight residual 177.88 -46.85 -135.27 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" O1 UMQ B 404 " pdb=" C1 UMQ B 404 " pdb=" C2 UMQ B 404 " pdb=" O2 UMQ B 404 " ideal model delta sinusoidal sigma weight residual 59.79 -74.43 134.22 1 3.00e+01 1.11e-03 1.81e+01 ... (remaining 10140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2531 0.121 - 0.243: 34 0.243 - 0.364: 4 0.364 - 0.486: 1 0.486 - 0.607: 2 Chirality restraints: 2572 Sorted by residual: chirality pdb=" C1 UMQ B 403 " pdb=" C2 UMQ B 403 " pdb=" O1 UMQ B 403 " pdb=" O5 UMQ B 403 " both_signs ideal model delta sigma weight residual False -2.24 -1.64 -0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" C1 UMQ J 404 " pdb=" C2 UMQ J 404 " pdb=" O1 UMQ J 404 " pdb=" O5 UMQ J 404 " both_signs ideal model delta sigma weight residual False -2.24 -1.64 -0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" C1 SQD D 201 " pdb=" C2 SQD D 201 " pdb=" O5 SQD D 201 " pdb=" O6 SQD D 201 " both_signs ideal model delta sigma weight residual False -2.39 -2.02 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 2569 not shown) Planarity restraints: 2761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 SQD L 401 " 0.101 2.00e-02 2.50e+03 5.82e-02 3.39e+01 pdb=" C8 SQD L 401 " -0.030 2.00e-02 2.50e+03 pdb=" O47 SQD L 401 " -0.033 2.00e-02 2.50e+03 pdb=" O49 SQD L 401 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR F 101 " 0.038 2.00e-02 2.50e+03 3.89e-02 1.89e+01 pdb=" C21 BCR F 101 " -0.066 2.00e-02 2.50e+03 pdb=" C22 BCR F 101 " 0.033 2.00e-02 2.50e+03 pdb=" C23 BCR F 101 " 0.015 2.00e-02 2.50e+03 pdb=" C37 BCR F 101 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 BCR P 101 " 0.031 2.00e-02 2.50e+03 3.77e-02 1.78e+01 pdb=" C21 BCR P 101 " -0.060 2.00e-02 2.50e+03 pdb=" C22 BCR P 101 " 0.045 2.00e-02 2.50e+03 pdb=" C23 BCR P 101 " 0.006 2.00e-02 2.50e+03 pdb=" C37 BCR P 101 " -0.022 2.00e-02 2.50e+03 ... (remaining 2758 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 65 2.52 - 3.12: 11721 3.12 - 3.71: 23031 3.71 - 4.31: 33361 4.31 - 4.90: 57230 Nonbonded interactions: 125408 Sorted by model distance: nonbonded pdb=" O2 UMQ J 404 " pdb=" O3' UMQ J 404 " model vdw 1.927 2.440 nonbonded pdb=" O2 UMQ B 403 " pdb=" O3' UMQ B 403 " model vdw 1.928 2.440 nonbonded pdb=" O2 UMQ A 305 " pdb=" O3' UMQ A 305 " model vdw 1.985 2.440 nonbonded pdb=" O GLY K 177 " pdb=" OG SER K 220 " model vdw 2.003 2.440 nonbonded pdb=" O GLY C 177 " pdb=" OG SER C 220 " model vdw 2.004 2.440 ... (remaining 125403 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 2 through 215 or resid 301 through 306)) selection = chain 'I' } ncs_group { reference = chain 'B' selection = (chain 'J' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 401 through 404)) } ncs_group { reference = chain 'C' selection = (chain 'K' and (resid 1 through 195 or resid 203 through 285 or resid 301)) } ncs_group { reference = (chain 'D' and (resid 8 through 178 or resid 201 through 202)) selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 36) selection = chain 'N' } ncs_group { reference = (chain 'G' and resid 1 through 33) selection = chain 'O' } ncs_group { reference = (chain 'H' and resid 1 through 29) selection = (chain 'P' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2)))) } ncs_group { reference = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 11.350 Check model and map are aligned: 0.190 Set scattering table: 0.150 Process input model: 47.570 Find NCS groups from input model: 0.940 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: 0.000 Load rotamer database and sin/cos tables:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 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 : 0.007 0.103 16910 Z= 0.418 Angle : 0.701 10.545 23099 Z= 0.326 Chirality : 0.051 0.607 2572 Planarity : 0.005 0.058 2761 Dihedral : 20.577 135.267 6577 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.20 % Allowed : 19.30 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.99 (0.20), residues: 1902 helix: 2.34 (0.17), residues: 946 sheet: 0.11 (0.37), residues: 188 loop : -1.45 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 146 HIS 0.003 0.001 HIS I 202 PHE 0.011 0.001 PHE I 131 TYR 0.011 0.001 TYR K 190 ARG 0.004 0.000 ARG L 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 184 time to evaluate : 1.768 Fit side-chains REVERT: C 184 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7246 (tmm160) REVERT: D 137 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8089 (ttp80) REVERT: J 152 ASP cc_start: 0.8793 (p0) cc_final: 0.8571 (p0) outliers start: 36 outliers final: 26 residues processed: 215 average time/residue: 1.5559 time to fit residues: 365.0555 Evaluate side-chains 192 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 165 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain K residue 124 SER Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 165 THR Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 33 SER Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 0.0010 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16910 Z= 0.282 Angle : 0.731 13.347 23099 Z= 0.334 Chirality : 0.048 0.212 2572 Planarity : 0.006 0.049 2761 Dihedral : 17.026 111.533 3117 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.30 % Allowed : 17.41 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.88 (0.19), residues: 1902 helix: 2.15 (0.17), residues: 963 sheet: -0.11 (0.35), residues: 202 loop : -1.39 (0.20), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 146 HIS 0.003 0.001 HIS K 25 PHE 0.015 0.002 PHE C 267 TYR 0.013 0.001 TYR K 190 ARG 0.005 0.000 ARG L 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 173 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 137 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7920 (ttt-90) REVERT: D 140 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.8402 (tmm-80) REVERT: F 36 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8314 (pm20) REVERT: G 3 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: L 140 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8382 (tmm-80) REVERT: O 3 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8012 (mm-30) outliers start: 54 outliers final: 25 residues processed: 204 average time/residue: 1.6473 time to fit residues: 365.7046 Evaluate side-chains 201 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 140 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 140 ARG Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 165 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16910 Z= 0.342 Angle : 0.751 14.784 23099 Z= 0.345 Chirality : 0.049 0.278 2572 Planarity : 0.006 0.053 2761 Dihedral : 15.443 94.603 3102 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.48 % Allowed : 16.86 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.78 (0.19), residues: 1902 helix: 2.05 (0.17), residues: 959 sheet: -0.01 (0.35), residues: 202 loop : -1.46 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 146 HIS 0.004 0.001 HIS I 202 PHE 0.017 0.002 PHE J 160 TYR 0.012 0.002 TYR K 190 ARG 0.006 0.000 ARG L 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 170 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 137 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.8025 (ttt-90) REVERT: D 168 ASP cc_start: 0.8615 (t0) cc_final: 0.8413 (t0) REVERT: F 36 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: G 3 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: K 184 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7645 (tpt90) REVERT: K 209 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7307 (mtp180) REVERT: O 3 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8021 (mm-30) outliers start: 57 outliers final: 35 residues processed: 206 average time/residue: 1.5886 time to fit residues: 356.2395 Evaluate side-chains 212 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 172 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 140 ASP Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 209 ARG Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 41 LYS Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 10.0000 chunk 125 optimal weight: 0.3980 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16910 Z= 0.174 Angle : 0.614 10.057 23099 Z= 0.281 Chirality : 0.044 0.310 2572 Planarity : 0.005 0.052 2761 Dihedral : 13.932 89.846 3102 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.75 % Allowed : 17.96 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.10 (0.20), residues: 1902 helix: 2.34 (0.17), residues: 951 sheet: 0.22 (0.35), residues: 206 loop : -1.35 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.004 0.001 HIS A 202 PHE 0.011 0.001 PHE J 160 TYR 0.010 0.001 TYR C 53 ARG 0.006 0.000 ARG L 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 188 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 137 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7962 (ttt-90) REVERT: D 168 ASP cc_start: 0.8628 (t0) cc_final: 0.8371 (t0) REVERT: F 36 GLU cc_start: 0.8631 (pm20) cc_final: 0.8312 (pm20) REVERT: G 3 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: J 152 ASP cc_start: 0.8837 (OUTLIER) cc_final: 0.8590 (p0) REVERT: K 184 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7865 (tmt170) REVERT: L 32 TYR cc_start: 0.8319 (m-10) cc_final: 0.7899 (t80) REVERT: L 140 ARG cc_start: 0.8280 (tmm-80) cc_final: 0.8067 (tpt-90) REVERT: O 3 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7931 (mm-30) outliers start: 45 outliers final: 17 residues processed: 220 average time/residue: 1.6102 time to fit residues: 386.5209 Evaluate side-chains 206 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 8.9990 chunk 100 optimal weight: 0.1980 chunk 2 optimal weight: 0.4980 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 44 optimal weight: 0.0030 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN L 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16910 Z= 0.161 Angle : 0.571 9.073 23099 Z= 0.264 Chirality : 0.043 0.306 2572 Planarity : 0.005 0.055 2761 Dihedral : 12.936 89.652 3097 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.02 % Allowed : 19.06 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.32 (0.20), residues: 1902 helix: 2.49 (0.17), residues: 945 sheet: 0.35 (0.33), residues: 221 loop : -1.19 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.003 0.001 HIS I 202 PHE 0.013 0.001 PHE I 131 TYR 0.010 0.001 TYR K 53 ARG 0.007 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 137 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7878 (ttt-90) REVERT: D 168 ASP cc_start: 0.8661 (t0) cc_final: 0.8418 (t0) REVERT: F 36 GLU cc_start: 0.8641 (pm20) cc_final: 0.8347 (pm20) REVERT: G 3 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7892 (mm-30) REVERT: J 152 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8570 (p0) REVERT: L 32 TYR cc_start: 0.8265 (m-10) cc_final: 0.7928 (t80) REVERT: O 3 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7928 (mm-30) outliers start: 33 outliers final: 16 residues processed: 214 average time/residue: 1.5194 time to fit residues: 355.3874 Evaluate side-chains 199 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 2.9990 chunk 160 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 178 optimal weight: 0.0370 chunk 147 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16910 Z= 0.167 Angle : 0.581 9.673 23099 Z= 0.268 Chirality : 0.043 0.265 2572 Planarity : 0.005 0.053 2761 Dihedral : 12.654 89.437 3094 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.71 % Allowed : 19.24 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.37 (0.20), residues: 1902 helix: 2.47 (0.17), residues: 951 sheet: 0.44 (0.34), residues: 211 loop : -1.11 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 146 HIS 0.005 0.001 HIS I 202 PHE 0.010 0.001 PHE A 131 TYR 0.008 0.001 TYR C 53 ARG 0.005 0.000 ARG G 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.773 Fit side-chains revert: symmetry clash REVERT: D 137 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7861 (ttt-90) REVERT: D 168 ASP cc_start: 0.8666 (t0) cc_final: 0.8409 (t0) REVERT: G 3 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7942 (mm-30) REVERT: J 152 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8569 (p0) REVERT: K 194 ILE cc_start: 0.9132 (pp) cc_final: 0.8755 (mp) REVERT: L 32 TYR cc_start: 0.8282 (m-10) cc_final: 0.7929 (t80) REVERT: O 3 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7930 (mm-30) outliers start: 28 outliers final: 14 residues processed: 197 average time/residue: 1.5885 time to fit residues: 340.9124 Evaluate side-chains 196 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 149 optimal weight: 0.0020 chunk 99 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16910 Z= 0.168 Angle : 0.578 9.825 23099 Z= 0.268 Chirality : 0.043 0.201 2572 Planarity : 0.005 0.053 2761 Dihedral : 12.381 89.617 3092 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.53 % Allowed : 19.24 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.39 (0.20), residues: 1902 helix: 2.47 (0.17), residues: 955 sheet: 0.48 (0.34), residues: 211 loop : -1.11 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.005 0.001 HIS I 202 PHE 0.010 0.001 PHE I 131 TYR 0.008 0.001 TYR Q 49 ARG 0.004 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 1.933 Fit side-chains revert: symmetry clash REVERT: D 137 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7886 (ttt-90) REVERT: D 168 ASP cc_start: 0.8657 (t0) cc_final: 0.8412 (t0) REVERT: G 3 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: J 152 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8568 (p0) REVERT: L 32 TYR cc_start: 0.8296 (m-10) cc_final: 0.7936 (t80) REVERT: O 3 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7913 (mm-30) REVERT: O 31 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7461 (ttp-170) outliers start: 25 outliers final: 18 residues processed: 198 average time/residue: 1.5897 time to fit residues: 343.1721 Evaluate side-chains 200 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 105 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.0980 chunk 120 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16910 Z= 0.180 Angle : 0.591 10.039 23099 Z= 0.273 Chirality : 0.043 0.188 2572 Planarity : 0.005 0.051 2761 Dihedral : 12.228 89.599 3092 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.71 % Allowed : 19.24 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.20), residues: 1902 helix: 2.45 (0.17), residues: 955 sheet: 0.47 (0.34), residues: 206 loop : -1.09 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 146 HIS 0.005 0.001 HIS I 202 PHE 0.010 0.001 PHE A 131 TYR 0.008 0.001 TYR C 53 ARG 0.004 0.000 ARG G 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.829 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8660 (m-80) REVERT: D 137 ARG cc_start: 0.8328 (tmm-80) cc_final: 0.7892 (ttt-90) REVERT: D 168 ASP cc_start: 0.8716 (t0) cc_final: 0.8420 (t0) REVERT: G 3 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: I 131 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.8651 (m-80) REVERT: J 152 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8570 (p0) REVERT: L 32 TYR cc_start: 0.8317 (m-10) cc_final: 0.7950 (t80) REVERT: O 3 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7916 (mm-30) outliers start: 28 outliers final: 20 residues processed: 200 average time/residue: 1.6134 time to fit residues: 351.4726 Evaluate side-chains 202 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 36 GLU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 103 SER Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 3.9990 chunk 155 optimal weight: 0.2980 chunk 165 optimal weight: 0.1980 chunk 99 optimal weight: 4.9990 chunk 71 optimal weight: 0.3980 chunk 129 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN L 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16910 Z= 0.164 Angle : 0.579 9.567 23099 Z= 0.270 Chirality : 0.042 0.187 2572 Planarity : 0.005 0.052 2761 Dihedral : 11.927 89.877 3088 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.65 % Allowed : 19.24 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.44 (0.20), residues: 1902 helix: 2.51 (0.17), residues: 951 sheet: 0.47 (0.33), residues: 214 loop : -1.05 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 146 HIS 0.004 0.001 HIS I 202 PHE 0.010 0.001 PHE I 131 TYR 0.008 0.001 TYR C 53 ARG 0.007 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.827 Fit side-chains REVERT: D 137 ARG cc_start: 0.8308 (tmm-80) cc_final: 0.7870 (ttt-90) REVERT: D 168 ASP cc_start: 0.8718 (t0) cc_final: 0.8466 (t0) REVERT: G 3 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7955 (mm-30) REVERT: J 152 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8569 (p0) REVERT: L 32 TYR cc_start: 0.8302 (m-10) cc_final: 0.7943 (t80) REVERT: O 3 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: O 31 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7422 (ttp-170) outliers start: 27 outliers final: 16 residues processed: 191 average time/residue: 1.6088 time to fit residues: 334.4405 Evaluate side-chains 189 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 169 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 11 ASP Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 120 GLU Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 31 ARG Chi-restraints excluded: chain R residue 52 ASP Chi-restraints excluded: chain Q residue 52 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 0.8980 chunk 106 optimal weight: 0.2980 chunk 82 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 168 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 15 optimal weight: 0.0370 chunk 112 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16910 Z= 0.161 Angle : 0.572 9.223 23099 Z= 0.267 Chirality : 0.042 0.192 2572 Planarity : 0.005 0.051 2761 Dihedral : 11.544 89.482 3086 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.22 % Allowed : 19.49 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.20), residues: 1902 helix: 2.57 (0.17), residues: 947 sheet: 0.51 (0.33), residues: 223 loop : -1.00 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 146 HIS 0.004 0.001 HIS I 202 PHE 0.013 0.001 PHE A 131 TYR 0.007 0.001 TYR C 53 ARG 0.007 0.000 ARG O 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.718 Fit side-chains REVERT: B 152 ASP cc_start: 0.8871 (OUTLIER) cc_final: 0.8629 (p0) REVERT: D 137 ARG cc_start: 0.8270 (tmm-80) cc_final: 0.7830 (ttt-90) REVERT: D 168 ASP cc_start: 0.8714 (t0) cc_final: 0.8489 (t0) REVERT: G 3 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: J 152 ASP cc_start: 0.8772 (p0) cc_final: 0.8570 (p0) REVERT: L 32 TYR cc_start: 0.8277 (m-10) cc_final: 0.7934 (t80) REVERT: O 3 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7926 (mm-30) outliers start: 20 outliers final: 10 residues processed: 184 average time/residue: 1.6522 time to fit residues: 331.0064 Evaluate side-chains 183 residues out of total 1638 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain K residue 179 VAL Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.053655 restraints weight = 25597.433| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 2.01 r_work: 0.2489 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16910 Z= 0.366 Angle : 0.727 16.165 23099 Z= 0.340 Chirality : 0.048 0.189 2572 Planarity : 0.006 0.048 2761 Dihedral : 12.420 88.549 3080 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.53 % Allowed : 19.43 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.16 (0.19), residues: 1902 helix: 2.20 (0.17), residues: 960 sheet: 0.48 (0.34), residues: 204 loop : -1.15 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 146 HIS 0.007 0.001 HIS I 202 PHE 0.018 0.002 PHE C 128 TYR 0.015 0.002 TYR R 49 ARG 0.008 0.001 ARG K 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6803.27 seconds wall clock time: 120 minutes 27.62 seconds (7227.62 seconds total)