Starting phenix.real_space_refine on Tue Nov 19 03:19:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/11_2024/7zyv_15027_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/11_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_15027/11_2024/7zyv_15027.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/11_2024/7zyv_15027.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/11_2024/7zyv_15027_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zyv_15027/11_2024/7zyv_15027_trim.cif" } 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. Time to flip 78 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 11.20, per 1000 atoms: 0.68 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 - 3.00 Amino acid : True - 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: 5.26 Conformation dependent library (CDL) restraints added in 2.1 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... Secondary structure from input PDB file: 72 helices and 14 sheets defined 52.6% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.811A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 removed outlier: 3.619A pdb=" N ALA A 18 " --> pdb=" O ILE A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 34 Processing helix chain 'A' and resid 35 through 55 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 107 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 114 through 137 removed outlier: 3.769A pdb=" N TRP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.583A pdb=" N ALA A 157 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.654A pdb=" N LEU A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 189 through 210 removed outlier: 3.729A pdb=" N LEU A 193 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 19 Processing helix chain 'B' and resid 39 through 58 removed outlier: 3.548A pdb=" N VAL B 43 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 93 through 110 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) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 126 through 147 Processing helix chain 'B' and resid 148 through 149 No H-bonds generated for 'chain 'B' and resid 148 through 149' Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.702A pdb=" N ILE C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.774A pdb=" N GLY C 98 " --> pdb=" O LYS C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 138 removed outlier: 3.557A pdb=" N LYS C 138 " --> pdb=" O PRO C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 283 removed outlier: 3.626A pdb=" N ILE C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) 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 11 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 64 through 72 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) removed outlier: 3.579A pdb=" N HIS D 72 " --> pdb=" O TRP D 68 " (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 28 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 3 through 32 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 2 through 26 removed outlier: 3.675A pdb=" N LEU H 6 " --> pdb=" O ASP H 2 " (cutoff:3.500A) 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 13 removed outlier: 3.811A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 22 removed outlier: 3.619A pdb=" N ALA I 18 " --> pdb=" O ILE I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 34 Processing helix chain 'I' and resid 35 through 55 Processing helix chain 'I' and resid 64 through 75 Processing helix chain 'I' and resid 78 through 107 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 114 through 137 removed outlier: 3.769A pdb=" N TRP I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 Processing helix chain 'I' and resid 153 through 158 removed outlier: 3.582A pdb=" N ALA I 157 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.653A pdb=" N LEU I 165 " --> pdb=" O ILE I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 189 Processing helix chain 'I' and resid 189 through 210 removed outlier: 3.730A pdb=" N LEU I 193 " --> pdb=" O PHE I 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 19 Processing helix chain 'J' and resid 39 through 58 removed outlier: 3.550A pdb=" N VAL J 43 " --> pdb=" O ILE J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 81 through 89 Processing helix chain 'J' and resid 93 through 110 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) Processing helix chain 'J' and resid 110 through 115 Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'J' and resid 148 through 149 No H-bonds generated for 'chain 'J' and resid 148 through 149' Processing helix chain 'J' and resid 150 through 154 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.702A pdb=" N ILE K 89 " --> pdb=" O PRO K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 98 removed outlier: 3.774A pdb=" N GLY K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.557A pdb=" N LYS K 138 " --> pdb=" O PRO K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 283 removed outlier: 3.625A pdb=" N ILE K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) 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 11 through 40 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 Processing helix chain 'L' and resid 64 through 72 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 28 Processing helix chain 'N' and resid 2 through 34 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) Processing helix chain 'O' and resid 3 through 32 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 2 through 26 removed outlier: 3.684A pdb=" N LEU P 6 " --> pdb=" O ASP P 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 43 removed outlier: 3.550A pdb=" N LYS R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 35 through 43 removed outlier: 3.550A pdb=" N LYS Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.747A pdb=" N GLU C 82 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.320A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE C 112 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 103 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'C' and resid 204 through 207 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.896A pdb=" N PHE D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL D 91 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 103 " --> pdb=" O TYR D 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 78 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 117 removed outlier: 6.348A pdb=" N GLN D 131 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.747A pdb=" N GLU K 82 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 38 through 39 removed outlier: 6.319A pdb=" N VAL K 71 " --> pdb=" O PRO K 117 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE K 112 " --> pdb=" O TYR K 105 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN K 103 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AB3, first strand: chain 'K' and resid 203 through 207 Processing sheet with id=AB4, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.881A pdb=" N PHE L 101 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL L 91 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE L 103 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 123 through 124 removed outlier: 6.347A pdb=" N GLN L 131 " --> pdb=" O VAL L 139 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2277 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: 4.80 Time building geometry restraints manager: 5.72 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: 0.00 - 2.11: 22577 2.11 - 4.22: 437 4.22 - 6.33: 66 6.33 - 8.44: 13 8.44 - 10.55: 6 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: 11705 3.12 - 3.71: 22971 3.71 - 4.31: 33120 4.31 - 4.90: 57151 Nonbonded interactions: 125012 Sorted by model distance: nonbonded pdb=" O2 UMQ J 404 " pdb=" O3' UMQ J 404 " model vdw 1.927 3.040 nonbonded pdb=" O2 UMQ B 403 " pdb=" O3' UMQ B 403 " model vdw 1.928 3.040 nonbonded pdb=" O2 UMQ A 305 " pdb=" O3' UMQ A 305 " model vdw 1.985 3.040 nonbonded pdb=" O GLY K 177 " pdb=" OG SER K 220 " model vdw 2.003 3.040 nonbonded pdb=" O GLY C 177 " pdb=" OG SER C 220 " model vdw 2.004 3.040 ... (remaining 125007 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 3.170 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 42.340 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.510 ------------------------------------------------------------------------------- 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= 0.420 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 to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 2.030 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: 1.6354 time to fit residues: 383.0190 Evaluate side-chains 192 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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: 0.6980 chunk 139 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 144 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8841 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16910 Z= 0.233 Angle : 0.718 11.888 23099 Z= 0.330 Chirality : 0.047 0.205 2572 Planarity : 0.005 0.047 2761 Dihedral : 17.440 112.368 3117 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.42 % Allowed : 16.98 % Favored : 79.60 % 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: 1.17 (0.19), residues: 1902 helix: 2.46 (0.17), residues: 966 sheet: -0.01 (0.35), residues: 198 loop : -1.38 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.004 0.001 HIS L 72 PHE 0.020 0.001 PHE A 52 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 235 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 1.830 Fit side-chains revert: symmetry clash REVERT: C 184 ARG cc_start: 0.8071 (ttp80) cc_final: 0.7543 (tmm160) REVERT: D 166 GLU cc_start: 0.8052 (mp0) cc_final: 0.7828 (OUTLIER) REVERT: F 36 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: K 184 ARG cc_start: 0.8284 (ttp80) cc_final: 0.8024 (ttp80) outliers start: 56 outliers final: 22 residues processed: 216 average time/residue: 1.6854 time to fit residues: 397.6311 Evaluate side-chains 194 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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 C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 206 ILE Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 36 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 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 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: 0.8980 chunk 51 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 0.0670 chunk 167 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 overall best weight: 1.3920 ------------------------------------------------------------------------------- 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: 0.8837 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16910 Z= 0.227 Angle : 0.675 11.786 23099 Z= 0.312 Chirality : 0.046 0.181 2572 Planarity : 0.005 0.051 2761 Dihedral : 15.419 93.079 3098 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.93 % Allowed : 17.47 % Favored : 79.60 % 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: 1.28 (0.20), residues: 1902 helix: 2.51 (0.17), residues: 967 sheet: 0.10 (0.35), residues: 206 loop : -1.31 (0.21), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.003 0.001 HIS I 202 PHE 0.016 0.001 PHE I 52 TYR 0.011 0.001 TYR C 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 225 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 177 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 154 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7965 (pmm150) REVERT: D 168 ASP cc_start: 0.8753 (t0) cc_final: 0.8531 (t0) REVERT: F 36 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8295 (pm20) REVERT: G 3 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7841 (mm-30) REVERT: K 154 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.8008 (pmm150) REVERT: O 3 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7846 (mm-30) outliers start: 48 outliers final: 22 residues processed: 208 average time/residue: 1.6865 time to fit residues: 380.8239 Evaluate side-chains 208 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.984 ------------------------------------------------------------------------------- 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 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 E residue 26 ASN 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 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 K residue 154 ARG 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 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: 7.9990 chunk 125 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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: 0.8844 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16910 Z= 0.241 Angle : 0.676 12.291 23099 Z= 0.313 Chirality : 0.046 0.257 2572 Planarity : 0.005 0.050 2761 Dihedral : 14.647 89.066 3098 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.75 % Allowed : 17.90 % Favored : 79.35 % 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: 1.30 (0.20), residues: 1902 helix: 2.54 (0.17), residues: 961 sheet: 0.14 (0.35), residues: 202 loop : -1.29 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 146 HIS 0.004 0.001 HIS A 202 PHE 0.015 0.001 PHE I 52 TYR 0.010 0.001 TYR K 190 ARG 0.005 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 to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 154 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7914 (pmm150) REVERT: D 137 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7353 (mtm-85) REVERT: D 168 ASP cc_start: 0.8742 (t0) cc_final: 0.8523 (t0) REVERT: F 36 GLU cc_start: 0.8611 (pm20) cc_final: 0.8313 (pm20) REVERT: G 3 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: K 154 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7769 (pmm150) REVERT: O 3 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7831 (mm-30) outliers start: 45 outliers final: 24 residues processed: 216 average time/residue: 1.6643 time to fit residues: 391.3649 Evaluate side-chains 210 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.811 ------------------------------------------------------------------------------- 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 152 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 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 154 ARG 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 O residue 31 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 122 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8820 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16910 Z= 0.209 Angle : 0.650 10.907 23099 Z= 0.302 Chirality : 0.046 0.337 2572 Planarity : 0.005 0.052 2761 Dihedral : 13.759 89.737 3094 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.81 % Allowed : 18.02 % Favored : 79.17 % 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: 1.45 (0.20), residues: 1902 helix: 2.67 (0.17), residues: 957 sheet: 0.26 (0.35), residues: 206 loop : -1.24 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 146 HIS 0.006 0.001 HIS A 202 PHE 0.015 0.001 PHE A 52 TYR 0.010 0.001 TYR K 53 ARG 0.005 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 235 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 67 GLU cc_start: 0.9194 (mp0) cc_final: 0.8943 (pm20) REVERT: D 137 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7364 (mtm-85) REVERT: D 173 GLU cc_start: 0.8718 (pt0) cc_final: 0.8509 (pm20) REVERT: F 36 GLU cc_start: 0.8584 (pm20) cc_final: 0.8256 (pm20) REVERT: G 3 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: K 184 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7894 (tmm-80) REVERT: K 209 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7128 (mtp180) REVERT: K 222 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8540 (ptmm) REVERT: L 32 TYR cc_start: 0.8297 (m-80) cc_final: 0.7808 (t80) REVERT: O 3 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7792 (mm-30) REVERT: O 31 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.7231 (ttp-170) outliers start: 46 outliers final: 22 residues processed: 213 average time/residue: 1.7783 time to fit residues: 414.9780 Evaluate side-chains 203 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 133 VAL 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 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 56 PHE 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 152 ASP 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 52 ASP Chi-restraints excluded: chain Q residue 43 THR 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: 5.9990 chunk 160 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1579 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= 0.190 Angle : 0.625 10.114 23099 Z= 0.291 Chirality : 0.045 0.307 2572 Planarity : 0.005 0.049 2761 Dihedral : 13.149 89.912 3091 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.44 % Allowed : 18.51 % 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: 1.55 (0.20), residues: 1902 helix: 2.74 (0.17), residues: 957 sheet: 0.27 (0.34), residues: 211 loop : -1.17 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 146 HIS 0.005 0.001 HIS I 202 PHE 0.013 0.001 PHE A 52 TYR 0.010 0.001 TYR C 53 ARG 0.006 0.000 ARG O 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 216 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 1.871 Fit side-chains revert: symmetry clash REVERT: A 131 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8671 (m-80) REVERT: D 67 GLU cc_start: 0.9165 (mp0) cc_final: 0.8911 (pm20) REVERT: D 137 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7409 (mtm-85) REVERT: D 173 GLU cc_start: 0.8742 (pt0) cc_final: 0.8529 (pm20) REVERT: I 131 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8662 (m-80) REVERT: K 184 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7892 (tmm-80) REVERT: K 194 ILE cc_start: 0.9213 (pp) cc_final: 0.8665 (mp) REVERT: K 209 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7146 (mtp180) REVERT: L 32 TYR cc_start: 0.8277 (m-80) cc_final: 0.7824 (t80) outliers start: 40 outliers final: 24 residues processed: 201 average time/residue: 1.4124 time to fit residues: 307.9673 Evaluate side-chains 208 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 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 I residue 56 PHE Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 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 L residue 120 GLU Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 101 optimal weight: 0.0770 chunk 130 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- 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: 0.8809 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16910 Z= 0.202 Angle : 0.634 10.386 23099 Z= 0.296 Chirality : 0.045 0.254 2572 Planarity : 0.005 0.050 2761 Dihedral : 12.973 89.730 3090 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.32 % Allowed : 18.75 % 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: 1.53 (0.20), residues: 1902 helix: 2.72 (0.17), residues: 957 sheet: 0.23 (0.33), residues: 216 loop : -1.16 (0.21), residues: 729 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 0.015 0.001 PHE A 56 TYR 0.008 0.001 TYR C 53 ARG 0.007 0.000 ARG E 29 *********************** 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 219 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8719 (m-80) REVERT: D 67 GLU cc_start: 0.9170 (mp0) cc_final: 0.8939 (pm20) REVERT: D 137 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7420 (mtm-85) REVERT: D 173 GLU cc_start: 0.8735 (pt0) cc_final: 0.8530 (pm20) REVERT: G 3 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: I 131 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8712 (m-80) REVERT: K 194 ILE cc_start: 0.9143 (pp) cc_final: 0.8928 (mp) REVERT: L 32 TYR cc_start: 0.8260 (m-80) cc_final: 0.7808 (t80) REVERT: O 3 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7830 (mm-30) REVERT: O 31 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7241 (ttp-170) outliers start: 38 outliers final: 25 residues processed: 203 average time/residue: 1.4069 time to fit residues: 310.2110 Evaluate side-chains 208 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 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 G residue 3 GLU Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 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 L residue 120 GLU 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 52 ASP Chi-restraints excluded: chain Q residue 43 THR 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: 0.8980 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.8793 moved from start: 0.1677 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= 0.186 Angle : 0.618 10.084 23099 Z= 0.290 Chirality : 0.044 0.210 2572 Planarity : 0.005 0.052 2761 Dihedral : 12.676 89.964 3090 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.14 % Allowed : 18.81 % 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: 1.58 (0.20), residues: 1902 helix: 2.76 (0.17), residues: 954 sheet: 0.25 (0.33), residues: 216 loop : -1.12 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 PHE 0.013 0.001 PHE A 52 TYR 0.008 0.001 TYR C 53 ARG 0.007 0.000 ARG E 29 *********************** 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 216 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: D 67 GLU cc_start: 0.9182 (mp0) cc_final: 0.8962 (pm20) REVERT: D 137 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7412 (mtm-85) REVERT: D 173 GLU cc_start: 0.8742 (pt0) cc_final: 0.8533 (pm20) REVERT: G 3 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7788 (mm-30) REVERT: K 194 ILE cc_start: 0.9197 (pp) cc_final: 0.8837 (mp) REVERT: L 32 TYR cc_start: 0.8262 (m-80) cc_final: 0.7812 (t80) REVERT: O 3 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7784 (mm-30) REVERT: O 31 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7194 (ttp-170) outliers start: 35 outliers final: 22 residues processed: 201 average time/residue: 2.1071 time to fit residues: 462.3851 Evaluate side-chains 199 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 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 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 33 ASP Chi-restraints excluded: chain I residue 56 PHE 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 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 52 ASP Chi-restraints excluded: chain Q residue 43 THR 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: 1.9990 chunk 155 optimal weight: 1.9990 chunk 165 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 50 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 overall best weight: 0.6480 ------------------------------------------------------------------------------- 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: 0.8769 moved from start: 0.1793 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= 0.173 Angle : 0.602 9.838 23099 Z= 0.284 Chirality : 0.043 0.162 2572 Planarity : 0.005 0.052 2761 Dihedral : 12.320 89.970 3088 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.83 % Allowed : 19.30 % Favored : 78.86 % 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: 1.64 (0.20), residues: 1902 helix: 2.81 (0.17), residues: 954 sheet: 0.25 (0.32), residues: 216 loop : -1.08 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 146 HIS 0.004 0.001 HIS A 202 PHE 0.013 0.001 PHE I 131 TYR 0.008 0.001 TYR K 53 ARG 0.007 0.000 ARG E 29 *********************** 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 212 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 2.008 Fit side-chains revert: symmetry clash REVERT: D 137 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7383 (mtm-85) REVERT: D 173 GLU cc_start: 0.8752 (pt0) cc_final: 0.8539 (pm20) REVERT: L 32 TYR cc_start: 0.8268 (m-80) cc_final: 0.7857 (t80) outliers start: 30 outliers final: 23 residues processed: 198 average time/residue: 1.7553 time to fit residues: 377.3218 Evaluate side-chains 205 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 PHE Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 154 ARG 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 33 ASP Chi-restraints excluded: chain I residue 56 PHE Chi-restraints excluded: chain I residue 167 GLU Chi-restraints excluded: chain J residue 152 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 L residue 120 GLU Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL 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: 1.9990 chunk 106 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 168 optimal weight: 0.5980 chunk 145 optimal weight: 0.0170 chunk 15 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- 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: 0.8780 moved from start: 0.1815 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= 0.185 Angle : 0.625 10.086 23099 Z= 0.295 Chirality : 0.043 0.166 2572 Planarity : 0.005 0.051 2761 Dihedral : 12.212 89.815 3088 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.47 % Allowed : 19.85 % Favored : 78.68 % 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: 1.64 (0.20), residues: 1902 helix: 2.79 (0.17), residues: 954 sheet: 0.31 (0.32), residues: 216 loop : -1.07 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 146 HIS 0.005 0.001 HIS A 202 PHE 0.013 0.001 PHE A 52 TYR 0.009 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 209 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: D 137 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7405 (mtm-85) REVERT: D 173 GLU cc_start: 0.8756 (pt0) cc_final: 0.8542 (pm20) REVERT: L 32 TYR cc_start: 0.8234 (m-80) cc_final: 0.7790 (t80) outliers start: 24 outliers final: 21 residues processed: 199 average time/residue: 1.6873 time to fit residues: 365.5029 Evaluate side-chains 201 residues out of total 1638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 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 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 G residue 33 ASP Chi-restraints excluded: chain I residue 56 PHE 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 M residue 26 ASN Chi-restraints excluded: chain N residue 34 VAL 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 155 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.092116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.055268 restraints weight = 25605.240| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 2.00 r_work: 0.2526 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16910 Z= 0.252 Angle : 0.680 11.852 23099 Z= 0.321 Chirality : 0.045 0.155 2572 Planarity : 0.005 0.050 2761 Dihedral : 12.509 89.148 3088 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.34 % Allowed : 19.91 % Favored : 78.74 % 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: 1.46 (0.19), residues: 1902 helix: 2.58 (0.17), residues: 958 sheet: 0.30 (0.32), residues: 216 loop : -1.11 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 146 HIS 0.006 0.001 HIS A 202 PHE 0.014 0.001 PHE C 128 TYR 0.008 0.001 TYR D 132 ARG 0.007 0.001 ARG G 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6892.71 seconds wall clock time: 143 minutes 27.49 seconds (8607.49 seconds total)