Starting phenix.real_space_refine on Sat Feb 17 01:10:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qrm_14123/02_2024/7qrm_14123_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qrm_14123/02_2024/7qrm_14123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qrm_14123/02_2024/7qrm_14123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qrm_14123/02_2024/7qrm_14123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qrm_14123/02_2024/7qrm_14123_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qrm_14123/02_2024/7qrm_14123_trim_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 4 5.49 5 Mg 2 5.21 5 S 72 5.16 5 C 10966 2.51 5 N 2446 2.21 5 O 2834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C ARG 250": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "F GLU 5": "OE1" <-> "OE2" Residue "F ARG 29": "NH1" <-> "NH2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K ARG 209": "NH1" <-> "NH2" Residue "K ARG 250": "NH1" <-> "NH2" Residue "L GLU 16": "OE1" <-> "OE2" Residue "L ARG 77": "NH1" <-> "NH2" Residue "L PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 170": "NH1" <-> "NH2" Residue "L GLU 173": "OE1" <-> "OE2" Residue "N ARG 29": "NH1" <-> "NH2" Residue "O GLU 3": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16336 Number of models: 1 Model: "" Number of chains: 27 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: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2209 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 23, 'TRANS': 261} Chain: "D" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1263 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 13, 'TRANS': 153} 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: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 264 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} 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: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2209 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 23, 'TRANS': 261} 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: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 249 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} 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: "A" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 368 Unusual residues: {'CLA': 1, 'HEC': 1, 'HEM': 2, 'PGT': 1, 'PL9': 1, 'UMQ': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 123 Unusual residues: {'PL9': 1, 'UMQ': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 164 Unusual residues: {'FES': 1, 'PGT': 1, 'PL9': 1, 'SQD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 358 Unusual residues: {'HEC': 1, 'HEM': 2, 'PGT': 1, 'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 243 Unusual residues: {'CLA': 1, 'PL9': 2, 'UMQ': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 97 Unusual residues: {'HEC': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'FES': 1, 'PGT': 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 5839 SG CYS D 107 73.756 42.153 44.406 1.00 48.10 S ATOM 5975 SG CYS D 125 70.332 41.349 42.903 1.00 48.21 S ATOM 13208 SG CYS L 107 30.877 42.976 95.378 1.00 50.53 S ATOM 13344 SG CYS L 125 34.211 42.063 96.898 1.00 48.29 S Time building chain proxies: 9.47, per 1000 atoms: 0.58 Number of scatterers: 16336 At special positions: 0 Unit cell: (102.34, 121.26, 140.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 72 16.00 P 4 15.00 Mg 2 11.99 O 2834 8.00 N 2446 7.00 C 10966 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=2.04 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.24 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 203 " pdb="FE1 FES D 203 " - pdb=" SG CYS D 107 " pdb="FE1 FES D 203 " - pdb=" SG CYS D 125 " pdb="FE2 FES D 203 " - pdb=" ND1 HIS D 128 " pdb="FE2 FES D 203 " - pdb=" ND1 HIS D 109 " pdb=" FES L 802 " pdb="FE1 FES L 802 " - pdb=" SG CYS L 107 " pdb="FE1 FES L 802 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 802 " - pdb=" ND1 HIS L 128 " pdb="FE2 FES L 802 " - pdb=" ND1 HIS L 109 " Number of angles added : 6 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3478 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 13 sheets defined 46.4% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.755A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 23 removed outlier: 3.770A pdb=" N SER A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 56 removed outlier: 4.445A pdb=" N GLY A 37 " --> pdb=" O TYR A 34 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR A 50 " --> pdb=" O GLN A 47 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA A 53 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 79 through 107 removed outlier: 3.655A pdb=" N ALA A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 removed outlier: 4.290A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 151 removed outlier: 3.669A pdb=" N ILE A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 removed outlier: 3.621A pdb=" N LEU A 165 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) 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: 3.549A pdb=" N LYS B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 3.786A 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 110 removed outlier: 4.182A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix removed outlier: 3.898A pdb=" N THR B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) 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: 3.572A pdb=" N ALA B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 154 Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 248 through 282 removed outlier: 3.760A pdb=" N PHE C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 25 Processing helix chain 'D' and resid 27 through 41 Proline residue: D 36 - end of helix removed outlier: 4.105A pdb=" N PHE D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 71 removed outlier: 3.544A pdb=" N THR D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 157 No H-bonds generated for 'chain 'D' and resid 155 through 157' Processing helix chain 'E' and resid 2 through 25 Processing helix chain 'F' and resid 2 through 35 removed outlier: 3.514A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE F 9 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 11 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL F 12 " --> pdb=" O ARG F 8 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 17 " --> pdb=" O MET F 13 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL F 34 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 30 removed outlier: 3.868A 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: 3.806A pdb=" N ALA H 7 " --> pdb=" O ILE H 3 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N TRP H 8 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 12 removed outlier: 3.808A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 23 removed outlier: 3.700A pdb=" N SER I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 56 removed outlier: 3.602A pdb=" N CYS I 35 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU I 36 " --> pdb=" O PHE I 33 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY I 37 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE I 56 " --> pdb=" O ALA I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 74 Processing helix chain 'I' and resid 79 through 106 removed outlier: 3.701A pdb=" N ALA I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 115 through 137 removed outlier: 3.863A pdb=" N VAL I 119 " --> pdb=" O GLU I 115 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 156 removed outlier: 3.820A pdb=" N ILE I 150 " --> pdb=" O TRP I 146 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR I 152 " --> pdb=" O VAL I 148 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY I 153 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Proline residue: I 155 - end of helix Processing helix chain 'I' and resid 163 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: 3.994A 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 113 removed outlier: 4.217A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix removed outlier: 3.799A pdb=" N THR J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 3.945A 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: 4.579A 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 removed outlier: 3.705A pdb=" N ASN K 23 " --> pdb=" O VAL K 20 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 3.691A pdb=" N LYS K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) 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: 3.713A pdb=" N PHE K 256 " --> pdb=" O GLN K 252 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE K 257 " --> pdb=" O GLY K 253 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS K 272 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS K 273 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 41 removed outlier: 3.772A pdb=" N LEU L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN L 19 " --> pdb=" O ARG L 15 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix removed outlier: 3.604A pdb=" N LEU L 35 " --> pdb=" O GLY L 31 " (cutoff:3.500A) Proline residue: L 36 - end of helix removed outlier: 4.162A 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 34 removed outlier: 3.866A pdb=" N PHE N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR N 17 " --> pdb=" O MET N 13 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 29 removed outlier: 3.855A 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 removed outlier: 3.565A pdb=" N ALA P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP P 8 " --> pdb=" O VAL P 4 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL P 22 " --> pdb=" O SER P 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL P 23 " --> pdb=" O LEU P 19 " (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 73 through 76 Processing sheet with id= C, first strand: chain 'C' and resid 145 through 150 Processing sheet with id= D, first strand: chain 'C' and resid 202 through 206 removed outlier: 3.921A pdb=" N LYS C 181 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA C 195 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL C 179 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 77 through 81 Processing sheet with id= F, first strand: chain 'D' and resid 101 through 103 Processing sheet with id= G, first strand: chain 'D' and resid 115 through 117 Processing sheet with id= H, first strand: chain 'K' and resid 32 through 34 Processing sheet with id= I, first strand: chain 'K' and resid 38 through 40 removed outlier: 8.454A pdb=" N VAL K 39 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL K 244 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 73 through 76 Processing sheet with id= K, first strand: chain 'K' and resid 202 through 207 removed outlier: 5.126A pdb=" N ALA K 195 " --> pdb=" O VAL K 179 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL K 179 " --> pdb=" O ALA K 195 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 77 through 81 removed outlier: 3.844A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE L 103 " --> pdb=" O TYR L 89 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL L 91 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE L 101 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA L 150 " --> pdb=" O GLY L 102 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 122 through 124 637 hydrogen bonds defined for protein. 1746 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: 4.35 Time building geometry restraints manager: 7.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 6272 1.39 - 1.59: 10340 1.59 - 1.80: 57 1.80 - 2.00: 65 2.00 - 2.20: 48 Bond restraints: 16782 Sorted by residual: bond pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " ideal model delta sigma weight residual 1.334 1.466 -0.132 2.00e-02 2.50e+03 4.38e+01 bond pdb=" C2A HEC A 303 " pdb=" C3A HEC A 303 " ideal model delta sigma weight residual 1.334 1.464 -0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C2B HEC A 303 " pdb=" C3B HEC A 303 " ideal model delta sigma weight residual 1.334 1.462 -0.128 2.00e-02 2.50e+03 4.13e+01 bond pdb=" C1 SQD D 201 " pdb=" O5 SQD D 201 " ideal model delta sigma weight residual 1.500 1.397 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C1 SQD K 302 " pdb=" O5 SQD K 302 " ideal model delta sigma weight residual 1.500 1.399 0.101 2.00e-02 2.50e+03 2.55e+01 ... (remaining 16777 not shown) Histogram of bond angle deviations from ideal: 75.42 - 96.25: 44 96.25 - 117.07: 12075 117.07 - 137.90: 10738 137.90 - 158.72: 2 158.72 - 179.54: 20 Bond angle restraints: 22879 Sorted by residual: angle pdb=" N LEU A 12 " pdb=" CA LEU A 12 " pdb=" C LEU A 12 " ideal model delta sigma weight residual 112.88 121.45 -8.57 1.29e+00 6.01e-01 4.41e+01 angle pdb=" N ASN B 34 " pdb=" CA ASN B 34 " pdb=" C ASN B 34 " ideal model delta sigma weight residual 111.02 118.15 -7.13 1.22e+00 6.72e-01 3.41e+01 angle pdb=" O3P PGT D 204 " pdb=" P PGT D 204 " pdb=" O4P PGT D 204 " ideal model delta sigma weight residual 92.82 109.75 -16.93 3.00e+00 1.11e-01 3.18e+01 angle pdb=" O3P PGT L 801 " pdb=" P PGT L 801 " pdb=" O4P PGT L 801 " ideal model delta sigma weight residual 92.82 109.48 -16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" O3P PGT A 308 " pdb=" P PGT A 308 " pdb=" O4P PGT A 308 " ideal model delta sigma weight residual 92.82 109.36 -16.54 3.00e+00 1.11e-01 3.04e+01 ... (remaining 22874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.19: 9577 33.19 - 66.38: 469 66.38 - 99.58: 77 99.58 - 132.77: 26 132.77 - 165.96: 2 Dihedral angle restraints: 10151 sinusoidal: 4727 harmonic: 5424 Sorted by residual: dihedral pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sinusoidal sigma weight residual 60.00 0.13 59.87 2 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" C2B HEC A 303 " pdb=" C3B HEC A 303 " pdb=" CAB HEC A 303 " pdb=" CBB HEC A 303 " ideal model delta sinusoidal sigma weight residual 60.00 0.17 59.83 2 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA PRO A 159 " pdb=" C PRO A 159 " pdb=" N VAL A 160 " pdb=" CA VAL A 160 " ideal model delta harmonic sigma weight residual 180.00 -154.48 -25.52 0 5.00e+00 4.00e-02 2.60e+01 ... (remaining 10148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2144 0.069 - 0.138: 332 0.138 - 0.207: 35 0.207 - 0.276: 8 0.276 - 0.345: 4 Chirality restraints: 2523 Sorted by residual: 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 -2.04 -0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA LEU A 12 " pdb=" N LEU A 12 " pdb=" C LEU A 12 " pdb=" CB LEU A 12 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA ASN B 34 " pdb=" N ASN B 34 " pdb=" C ASN B 34 " pdb=" CB ASN B 34 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 2520 not shown) Planarity restraints: 2711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 BCR P 101 " 0.149 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" C21 BCR P 101 " -0.208 2.00e-02 2.50e+03 pdb=" C22 BCR P 101 " -0.026 2.00e-02 2.50e+03 pdb=" C23 BCR P 101 " 0.105 2.00e-02 2.50e+03 pdb=" C37 BCR P 101 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 BCR F 101 " -0.128 2.00e-02 2.50e+03 1.32e-01 1.74e+02 pdb=" C23 BCR F 101 " 0.116 2.00e-02 2.50e+03 pdb=" C24 BCR F 101 " 0.146 2.00e-02 2.50e+03 pdb=" C25 BCR F 101 " -0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 BCR P 101 " -0.103 2.00e-02 2.50e+03 1.05e-01 1.10e+02 pdb=" C23 BCR P 101 " 0.098 2.00e-02 2.50e+03 pdb=" C24 BCR P 101 " 0.111 2.00e-02 2.50e+03 pdb=" C25 BCR P 101 " -0.106 2.00e-02 2.50e+03 ... (remaining 2708 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 115 2.61 - 3.18: 13349 3.18 - 3.75: 22269 3.75 - 4.33: 33257 4.33 - 4.90: 55656 Nonbonded interactions: 124646 Sorted by model distance: nonbonded pdb=" O2 UMQ J 205 " pdb=" O3' UMQ J 205 " model vdw 2.033 2.440 nonbonded pdb=" O PHE A 52 " pdb=" OG1 THR A 55 " model vdw 2.128 2.440 nonbonded pdb=" O GLN C 37 " pdb=" O6 UMQ H 201 " model vdw 2.138 2.440 nonbonded pdb=" O ALA L 99 " pdb=" OG1 THR L 100 " model vdw 2.144 2.440 nonbonded pdb=" OE1 GLU L 173 " pdb=" N ALA L 174 " model vdw 2.194 2.520 ... (remaining 124641 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 302 or resid 306)) selection = (chain 'I' and (resid 2 through 215 or resid 2002 or resid 2006)) } ncs_group { reference = (chain 'B' and resid 2 through 160) 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 )))) } ncs_group { reference = chain 'C' selection = (chain 'K' and (resid 1 through 285 or resid 301)) } ncs_group { reference = (chain 'D' and (resid 8 through 51 or resid 53 through 178)) selection = (chain 'L' and resid 8 through 178) } 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' 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)))) } 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: 4.070 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: 14.230 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 49.260 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 : 0.009 0.132 16782 Z= 0.486 Angle : 0.910 16.931 22879 Z= 0.438 Chirality : 0.052 0.345 2523 Planarity : 0.008 0.132 2711 Dihedral : 20.049 165.960 6667 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.88 % Allowed : 1.19 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.52 (0.19), residues: 1866 helix: 1.10 (0.18), residues: 905 sheet: -1.02 (0.32), residues: 215 loop : -2.00 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 146 HIS 0.009 0.001 HIS I 202 PHE 0.031 0.002 PHE A 56 TYR 0.017 0.001 TYR A 136 ARG 0.007 0.000 ARG J 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 202 time to evaluate : 1.935 Fit side-chains REVERT: A 13 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8200 (mt-10) REVERT: B 5 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7648 (tttp) REVERT: B 15 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7163 (mtp85) REVERT: E 27 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8139 (tptt) REVERT: E 29 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.6625 (mmp-170) REVERT: J 119 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7795 (tttm) REVERT: K 103 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7495 (mm-40) outliers start: 30 outliers final: 7 residues processed: 217 average time/residue: 1.3724 time to fit residues: 327.8016 Evaluate side-chains 179 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 167 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 29 ARG Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 103 GLN Chi-restraints excluded: chain L residue 35 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 93 optimal weight: 0.0170 chunk 73 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 165 optimal weight: 0.0060 overall best weight: 0.4434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN C 103 GLN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16782 Z= 0.172 Angle : 0.647 15.523 22879 Z= 0.289 Chirality : 0.045 0.217 2523 Planarity : 0.005 0.057 2711 Dihedral : 18.808 176.509 3298 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.44 % Allowed : 7.08 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.16 (0.19), residues: 1866 helix: 1.66 (0.18), residues: 909 sheet: -0.66 (0.33), residues: 215 loop : -1.68 (0.20), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 146 HIS 0.006 0.001 HIS I 202 PHE 0.018 0.001 PHE A 131 TYR 0.010 0.001 TYR C 53 ARG 0.006 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 1.975 Fit side-chains REVERT: A 64 ASP cc_start: 0.7775 (m-30) cc_final: 0.7465 (m-30) REVERT: B 5 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7482 (tttp) REVERT: B 15 ARG cc_start: 0.7304 (mtm-85) cc_final: 0.7002 (mtp85) REVERT: D 35 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7868 (mp) REVERT: E 25 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7840 (mp) REVERT: E 27 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8090 (tptt) REVERT: K 103 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7543 (mm-40) REVERT: O 3 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7692 (mt-10) outliers start: 23 outliers final: 9 residues processed: 193 average time/residue: 1.3624 time to fit residues: 289.9178 Evaluate side-chains 181 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 103 GLN Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 chunk 165 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 132 optimal weight: 0.0470 overall best weight: 0.5836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN C 103 GLN C 167 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16782 Z= 0.165 Angle : 0.619 15.800 22879 Z= 0.272 Chirality : 0.045 0.340 2523 Planarity : 0.005 0.059 2711 Dihedral : 16.621 176.618 3275 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.75 % Allowed : 8.58 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.51 (0.20), residues: 1866 helix: 1.92 (0.18), residues: 909 sheet: -0.45 (0.32), residues: 231 loop : -1.50 (0.20), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.007 0.001 HIS I 202 PHE 0.018 0.001 PHE A 131 TYR 0.009 0.001 TYR A 136 ARG 0.009 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 176 time to evaluate : 1.738 Fit side-chains REVERT: A 64 ASP cc_start: 0.7864 (m-30) cc_final: 0.7516 (m-30) REVERT: B 5 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7549 (tttm) REVERT: E 27 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8034 (tptt) REVERT: G 30 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6105 (mtt-85) REVERT: K 184 ARG cc_start: 0.6630 (mpt180) cc_final: 0.6273 (ttm-80) outliers start: 28 outliers final: 9 residues processed: 186 average time/residue: 1.4945 time to fit residues: 304.2519 Evaluate side-chains 181 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 170 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain N residue 33 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN K 6 GLN K 103 GLN ** K 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16782 Z= 0.308 Angle : 0.753 16.743 22879 Z= 0.332 Chirality : 0.049 0.372 2523 Planarity : 0.006 0.056 2711 Dihedral : 16.627 177.527 3269 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.19 % Allowed : 10.96 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.28 (0.19), residues: 1866 helix: 1.58 (0.18), residues: 913 sheet: -0.28 (0.34), residues: 201 loop : -1.47 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 142 HIS 0.012 0.002 HIS I 202 PHE 0.019 0.002 PHE I 56 TYR 0.017 0.002 TYR A 136 ARG 0.006 0.001 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 1.911 Fit side-chains REVERT: A 64 ASP cc_start: 0.7954 (m-30) cc_final: 0.7654 (m-30) REVERT: B 5 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7732 (tttm) REVERT: E 25 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7920 (mp) REVERT: H 1 MET cc_start: 0.5529 (OUTLIER) cc_final: 0.4506 (pmm) REVERT: J 119 LYS cc_start: 0.8429 (mptp) cc_final: 0.7646 (ttpm) REVERT: K 242 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: O 3 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7601 (mt-10) outliers start: 35 outliers final: 15 residues processed: 188 average time/residue: 1.4465 time to fit residues: 298.8812 Evaluate side-chains 181 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 24 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 130 optimal weight: 0.3980 chunk 72 optimal weight: 0.0670 chunk 150 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 157 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16782 Z= 0.155 Angle : 0.594 16.598 22879 Z= 0.262 Chirality : 0.044 0.355 2523 Planarity : 0.005 0.057 2711 Dihedral : 15.413 179.344 3265 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.94 % Allowed : 11.72 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.76 (0.20), residues: 1866 helix: 2.03 (0.18), residues: 911 sheet: -0.15 (0.33), residues: 230 loop : -1.31 (0.21), residues: 725 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 0.011 0.001 PHE A 131 TYR 0.009 0.001 TYR J 80 ARG 0.008 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.715 Fit side-chains REVERT: A 64 ASP cc_start: 0.7927 (m-30) cc_final: 0.7585 (m-30) REVERT: A 131 PHE cc_start: 0.8924 (OUTLIER) cc_final: 0.8351 (m-80) REVERT: B 5 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7686 (tttm) REVERT: E 25 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7816 (mp) REVERT: G 30 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6223 (mtt-85) REVERT: H 1 MET cc_start: 0.5505 (OUTLIER) cc_final: 0.4425 (pmm) REVERT: J 119 LYS cc_start: 0.8356 (mptp) cc_final: 0.7540 (tttm) REVERT: K 184 ARG cc_start: 0.6669 (mpt180) cc_final: 0.6249 (ttm-80) REVERT: O 3 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7530 (mt-10) outliers start: 31 outliers final: 13 residues processed: 188 average time/residue: 1.4129 time to fit residues: 291.3158 Evaluate side-chains 186 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 61 MET Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN K 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16782 Z= 0.310 Angle : 0.743 16.744 22879 Z= 0.329 Chirality : 0.049 0.358 2523 Planarity : 0.006 0.057 2711 Dihedral : 15.955 179.283 3265 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.82 % Allowed : 11.78 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.48 (0.19), residues: 1866 helix: 1.70 (0.17), residues: 913 sheet: -0.10 (0.35), residues: 201 loop : -1.33 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 146 HIS 0.010 0.001 HIS I 202 PHE 0.018 0.002 PHE K 128 TYR 0.016 0.002 TYR A 136 ARG 0.007 0.001 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 1.747 Fit side-chains REVERT: A 64 ASP cc_start: 0.7980 (m-30) cc_final: 0.7712 (m-30) REVERT: B 5 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7768 (tttm) REVERT: E 25 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7940 (mp) REVERT: H 1 MET cc_start: 0.5614 (OUTLIER) cc_final: 0.4633 (pmm) REVERT: I 208 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7215 (ttmt) REVERT: J 119 LYS cc_start: 0.8392 (mptp) cc_final: 0.7625 (tttm) REVERT: K 154 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.6983 (ptp-170) REVERT: K 184 ARG cc_start: 0.6630 (mpt180) cc_final: 0.6357 (ttm-80) REVERT: O 3 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7602 (mt-10) outliers start: 45 outliers final: 22 residues processed: 185 average time/residue: 1.4842 time to fit residues: 300.8274 Evaluate side-chains 188 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 208 LYS Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 122 LYS Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain O residue 3 GLU Chi-restraints excluded: chain O residue 24 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 175 optimal weight: 0.4980 chunk 109 optimal weight: 0.3980 chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN L 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16782 Z= 0.153 Angle : 0.587 16.521 22879 Z= 0.260 Chirality : 0.043 0.353 2523 Planarity : 0.005 0.058 2711 Dihedral : 14.882 178.181 3265 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.82 % Allowed : 13.41 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1866 helix: 2.13 (0.18), residues: 909 sheet: -0.09 (0.34), residues: 238 loop : -1.17 (0.21), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 146 HIS 0.004 0.001 HIS I 202 PHE 0.012 0.001 PHE A 131 TYR 0.009 0.001 TYR J 80 ARG 0.008 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.838 Fit side-chains REVERT: A 64 ASP cc_start: 0.7994 (m-30) cc_final: 0.7684 (m-30) REVERT: A 131 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8405 (m-80) REVERT: B 5 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7764 (tttm) REVERT: E 25 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7791 (mp) REVERT: F 29 ARG cc_start: 0.7453 (tpp-160) cc_final: 0.7106 (tpm170) REVERT: H 1 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.4533 (pmm) REVERT: I 131 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.7188 (t80) REVERT: O 3 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7567 (mt-10) outliers start: 29 outliers final: 20 residues processed: 180 average time/residue: 1.4783 time to fit residues: 293.0156 Evaluate side-chains 185 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16782 Z= 0.216 Angle : 0.653 16.591 22879 Z= 0.288 Chirality : 0.045 0.365 2523 Planarity : 0.005 0.057 2711 Dihedral : 15.014 178.103 3265 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.94 % Allowed : 13.22 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.80 (0.20), residues: 1866 helix: 1.94 (0.18), residues: 921 sheet: 0.19 (0.36), residues: 206 loop : -1.22 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.008 0.001 HIS I 202 PHE 0.014 0.002 PHE A 131 TYR 0.012 0.001 TYR A 136 ARG 0.008 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 162 time to evaluate : 1.870 Fit side-chains REVERT: A 64 ASP cc_start: 0.7978 (m-30) cc_final: 0.7693 (m-30) REVERT: B 5 LYS cc_start: 0.8103 (ttpt) cc_final: 0.7774 (tttm) REVERT: H 1 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.4604 (pmm) REVERT: J 119 LYS cc_start: 0.8446 (mptp) cc_final: 0.7601 (tttm) REVERT: O 3 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7500 (mt-10) outliers start: 31 outliers final: 21 residues processed: 180 average time/residue: 1.4560 time to fit residues: 287.3169 Evaluate side-chains 185 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 162 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 0.0040 chunk 154 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN L 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16782 Z= 0.181 Angle : 0.618 16.526 22879 Z= 0.273 Chirality : 0.044 0.330 2523 Planarity : 0.005 0.058 2711 Dihedral : 14.751 176.486 3265 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.57 % Allowed : 13.78 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1866 helix: 2.03 (0.18), residues: 915 sheet: 0.40 (0.38), residues: 186 loop : -1.12 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.007 0.001 HIS I 202 PHE 0.013 0.001 PHE A 131 TYR 0.010 0.001 TYR A 136 ARG 0.008 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.794 Fit side-chains REVERT: A 64 ASP cc_start: 0.8001 (m-30) cc_final: 0.7694 (m-30) REVERT: B 5 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7822 (tttm) REVERT: H 1 MET cc_start: 0.5582 (OUTLIER) cc_final: 0.4587 (pmm) REVERT: I 131 PHE cc_start: 0.9152 (OUTLIER) cc_final: 0.7059 (t80) REVERT: J 119 LYS cc_start: 0.8428 (mptp) cc_final: 0.7598 (tttm) REVERT: O 3 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7536 (mt-10) outliers start: 25 outliers final: 19 residues processed: 176 average time/residue: 1.4885 time to fit residues: 286.7227 Evaluate side-chains 184 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN L 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16782 Z= 0.177 Angle : 0.610 16.431 22879 Z= 0.270 Chirality : 0.044 0.269 2523 Planarity : 0.005 0.057 2711 Dihedral : 14.498 174.296 3265 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.63 % Allowed : 13.78 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1866 helix: 2.11 (0.18), residues: 911 sheet: 0.36 (0.37), residues: 196 loop : -1.11 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.007 0.001 HIS I 202 PHE 0.013 0.001 PHE A 131 TYR 0.009 0.001 TYR A 136 ARG 0.009 0.000 ARG O 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7975 (m-30) cc_final: 0.7654 (m-30) REVERT: A 131 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: B 5 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7824 (tttm) REVERT: I 131 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.7006 (t80) REVERT: J 119 LYS cc_start: 0.8361 (mptp) cc_final: 0.7591 (tttm) REVERT: O 3 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7495 (mt-10) outliers start: 26 outliers final: 21 residues processed: 181 average time/residue: 1.5197 time to fit residues: 304.1778 Evaluate side-chains 188 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain C residue 122 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 91 VAL Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 165 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain J residue 9 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 32 ASP Chi-restraints excluded: chain K residue 140 ASP Chi-restraints excluded: chain K residue 154 ARG Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain O residue 3 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 148 optimal weight: 0.0050 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.138700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102160 restraints weight = 18978.414| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.28 r_work: 0.2917 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16782 Z= 0.192 Angle : 0.627 16.612 22879 Z= 0.278 Chirality : 0.044 0.244 2523 Planarity : 0.005 0.057 2711 Dihedral : 14.510 172.374 3265 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.01 % Allowed : 13.47 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.92 (0.20), residues: 1866 helix: 2.00 (0.18), residues: 921 sheet: 0.44 (0.38), residues: 186 loop : -1.14 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.007 0.001 HIS I 202 PHE 0.013 0.001 PHE A 131 TYR 0.010 0.001 TYR A 136 ARG 0.009 0.000 ARG O 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5748.15 seconds wall clock time: 102 minutes 45.89 seconds (6165.89 seconds total)