Starting phenix.real_space_refine (version: dev) on Tue Feb 21 20:03:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2023/7zxy_15017_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2023/7zxy_15017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2023/7zxy_15017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2023/7zxy_15017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2023/7zxy_15017_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2023/7zxy_15017_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 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 Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 17": "OD1" <-> "OD2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 135": "OD1" <-> "OD2" Residue "C PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 148": "OD1" <-> "OD2" Residue "I GLU 180": "OE1" <-> "OE2" Residue "J ASP 35": "OD1" <-> "OD2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "K GLU 35": "OE1" <-> "OE2" Residue "K GLU 282": "OE1" <-> "OE2" Residue "L GLU 148": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 15606 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1750 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "B" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1211 Classifications: {'peptide': 158} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 140} Chain: "C" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2116 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "D" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1248 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain breaks: 1 Chain: "E" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 267 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'TRANS': 35} Chain: "G" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "H" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 235 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1750 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 210} Chain: "J" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1223 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2116 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1248 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 157} Chain breaks: 1 Chain: "M" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 239 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'TRANS': 31} Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 248 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "O" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 2, 'TRANS': 32} Chain: "P" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 235 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 170 Unusual residues: {'ECH': 1, 'HEC': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 154 Unusual residues: {'CLA': 1, 'PGV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'HEC': 1, 'LFA': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 221 Unusual residues: {'ECH': 1, 'HEC': 1, 'HEM': 2, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 211 Unusual residues: {'CLA': 1, 'PGV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5796 SG CYS D 120 78.989 77.612 95.772 1.00 30.79 S ATOM 5936 SG CYS D 138 76.370 80.248 96.868 1.00 33.12 S ATOM 13144 SG CYS L 120 34.375 76.130 50.594 1.00 30.90 S ATOM 13284 SG CYS L 138 37.537 74.579 48.855 1.00 31.82 S Time building chain proxies: 9.78, per 1000 atoms: 0.63 Number of scatterers: 15606 At special positions: 0 Unit cell: (114.48, 128.26, 139.92, 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 76 16.00 P 7 15.00 Mg 2 11.99 O 2731 8.00 N 2417 7.00 C 10361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 140 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.21 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 201 " pdb="FE1 FES D 201 " - pdb=" ND1 HIS D 122 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 138 " pdb="FE2 FES D 201 " - pdb=" SG CYS D 120 " pdb="FE1 FES D 201 " - pdb=" ND1 HIS D 141 " pdb=" FES L 201 " pdb="FE1 FES L 201 " - pdb=" ND1 HIS L 141 " pdb="FE1 FES L 201 " - pdb=" ND1 HIS L 122 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 138 " pdb="FE2 FES L 201 " - pdb=" SG CYS L 120 " Number of angles added : 6 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3446 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 13 sheets defined 45.3% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 11 through 19 removed outlier: 3.868A pdb=" N TRP A 14 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A 16 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 29 Processing helix chain 'A' and resid 39 through 63 removed outlier: 4.403A pdb=" N GLY A 44 " --> pdb=" O TYR A 41 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR A 57 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLY A 58 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 122 through 144 removed outlier: 4.399A pdb=" N SER A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 169 through 177 Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 40 through 57 Processing helix chain 'B' and resid 79 through 90 Proline residue: B 83 - end of helix Processing helix chain 'B' and resid 94 through 108 removed outlier: 3.993A pdb=" N ILE B 104 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix Processing helix chain 'B' and resid 111 through 114 No H-bonds generated for 'chain 'B' and resid 111 through 114' 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: 3.994A pdb=" N THR B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 8 Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 92 through 98 Processing helix chain 'C' and resid 248 through 282 Processing helix chain 'D' and resid 25 through 54 Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 78 through 81 No H-bonds generated for 'chain 'D' and resid 78 through 81' Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'E' and resid 3 through 28 Processing helix chain 'F' and resid 8 through 31 Processing helix chain 'G' and resid 4 through 29 Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 4 through 25 Processing helix chain 'I' and resid 11 through 19 removed outlier: 3.949A pdb=" N ASP I 17 " --> pdb=" O TRP I 14 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU I 19 " --> pdb=" O ASN I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 30 Processing helix chain 'I' and resid 39 through 63 removed outlier: 4.440A pdb=" N GLY I 44 " --> pdb=" O TYR I 41 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY I 45 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR I 57 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY I 58 " --> pdb=" O PHE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 81 Processing helix chain 'I' and resid 86 through 114 Processing helix chain 'I' and resid 122 through 143 Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 161 through 164 Processing helix chain 'I' and resid 169 through 177 Processing helix chain 'I' and resid 184 through 195 Processing helix chain 'I' and resid 197 through 216 Processing helix chain 'J' and resid 12 through 20 Processing helix chain 'J' and resid 40 through 57 Processing helix chain 'J' and resid 79 through 90 Proline residue: J 83 - end of helix removed outlier: 4.121A pdb=" N ILE J 90 " --> pdb=" O ILE J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 109 removed outlier: 3.971A pdb=" N ILE J 104 " --> pdb=" O GLY J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix Processing helix chain 'J' and resid 111 through 114 No H-bonds generated for 'chain 'J' and resid 111 through 114' 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: 3.952A pdb=" N THR J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 8 Processing helix chain 'K' and resid 21 through 24 Processing helix chain 'K' and resid 92 through 98 Processing helix chain 'K' and resid 248 through 283 Processing helix chain 'L' and resid 25 through 54 Proline residue: L 49 - end of helix Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'M' and resid 3 through 28 Processing helix chain 'N' and resid 8 through 32 Processing helix chain 'O' and resid 4 through 29 Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 3 through 25 Processing sheet with id= A, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.635A pdb=" N VAL C 49 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 39 through 41 removed outlier: 8.359A pdb=" N VAL C 40 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL C 244 " --> pdb=" O VAL C 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.548A pdb=" N HIS C 150 " --> pdb=" O MET C 77 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 183 through 185 Processing sheet with id= E, first strand: chain 'D' and resid 89 through 94 removed outlier: 3.709A pdb=" N VAL D 91 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 116 " --> pdb=" O TYR D 102 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 128 through 130 Processing sheet with id= G, first strand: chain 'D' and resid 163 through 166 Processing sheet with id= H, first strand: chain 'K' and resid 33 through 35 Processing sheet with id= I, first strand: chain 'K' and resid 39 through 41 removed outlier: 8.014A pdb=" N VAL K 40 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL K 244 " --> pdb=" O VAL K 40 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 191 through 193 Processing sheet with id= K, first strand: chain 'L' and resid 90 through 94 Processing sheet with id= L, first strand: chain 'L' and resid 128 through 130 Processing sheet with id= M, first strand: chain 'L' and resid 163 through 165 696 hydrogen bonds defined for protein. 1869 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: 4.31 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 6385 1.41 - 1.61: 9459 1.61 - 1.81: 132 1.81 - 2.01: 8 2.01 - 2.20: 48 Bond restraints: 16032 Sorted by residual: bond pdb=" CAC HEC I 305 " pdb=" CBC HEC I 305 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC I 305 " pdb=" C3D HEC I 305 " ideal model delta sigma weight residual 1.544 1.332 0.212 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C2D HEC A 304 " pdb=" C3D HEC A 304 " ideal model delta sigma weight residual 1.544 1.333 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" CAB HEC I 305 " pdb=" CBB HEC I 305 " ideal model delta sigma weight residual 1.544 1.336 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" CAC HEC A 304 " pdb=" CBC HEC A 304 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 16027 not shown) Histogram of bond angle deviations from ideal: 75.26 - 96.13: 44 96.13 - 116.99: 11340 116.99 - 137.86: 10482 137.86 - 158.72: 2 158.72 - 179.59: 20 Bond angle restraints: 21888 Sorted by residual: angle pdb=" C3C HEC I 305 " pdb=" CAC HEC I 305 " pdb=" CBC HEC I 305 " ideal model delta sigma weight residual 109.00 125.33 -16.33 3.00e+00 1.11e-01 2.96e+01 angle pdb=" C3B HEC I 305 " pdb=" CAB HEC I 305 " pdb=" CBB HEC I 305 " ideal model delta sigma weight residual 109.00 124.21 -15.21 3.00e+00 1.11e-01 2.57e+01 angle pdb=" O11 PGV B 202 " pdb=" P PGV B 202 " pdb=" O12 PGV B 202 " ideal model delta sigma weight residual 92.97 107.50 -14.53 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C3B HEC A 304 " pdb=" CAB HEC A 304 " pdb=" CBB HEC A 304 " ideal model delta sigma weight residual 109.00 123.45 -14.45 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C3C HEC A 304 " pdb=" CAC HEC A 304 " pdb=" CBC HEC A 304 " ideal model delta sigma weight residual 109.00 123.38 -14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 21883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.91: 8945 32.91 - 65.82: 201 65.82 - 98.74: 34 98.74 - 131.65: 2 131.65 - 164.56: 3 Dihedral angle restraints: 9185 sinusoidal: 3784 harmonic: 5401 Sorted by residual: dihedral pdb=" C2B HEC A 304 " pdb=" C3B HEC A 304 " pdb=" CAB HEC A 304 " pdb=" CBB HEC A 304 " ideal model delta sinusoidal sigma weight residual 60.00 -29.50 89.50 2 1.00e+01 1.00e-02 4.80e+01 dihedral pdb=" C2B HEC I 305 " pdb=" C3B HEC I 305 " pdb=" CAB HEC I 305 " pdb=" CBB HEC I 305 " ideal model delta sinusoidal sigma weight residual 60.00 -21.71 81.71 2 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" C2C HEC I 305 " pdb=" C3C HEC I 305 " pdb=" CAC HEC I 305 " pdb=" CBC HEC I 305 " ideal model delta sinusoidal sigma weight residual 60.00 0.17 59.83 2 1.00e+01 1.00e-02 3.59e+01 ... (remaining 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1786 0.047 - 0.095: 477 0.095 - 0.142: 107 0.142 - 0.189: 8 0.189 - 0.237: 7 Chirality restraints: 2385 Sorted by residual: chirality pdb=" C05 PGV C 303 " pdb=" C04 PGV C 303 " pdb=" C06 PGV C 303 " pdb=" O05 PGV C 303 " both_signs ideal model delta sigma weight residual False 2.29 2.53 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C05 PGV B 203 " pdb=" C04 PGV B 203 " pdb=" C06 PGV B 203 " pdb=" O05 PGV B 203 " both_signs ideal model delta sigma weight residual False 2.29 2.53 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" C05 PGV J 204 " pdb=" C04 PGV J 204 " pdb=" C06 PGV J 204 " pdb=" O05 PGV J 204 " both_signs ideal model delta sigma weight residual False 2.29 2.53 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2382 not shown) Planarity restraints: 2705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " -0.014 2.00e-02 2.50e+03 3.31e-02 2.47e+01 pdb=" C2C HEC C 301 " 0.090 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " -0.006 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " -0.003 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " -0.020 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " -0.015 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " 0.001 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 301 " -0.011 2.00e-02 2.50e+03 3.04e-02 2.08e+01 pdb=" C2C HEC K 301 " 0.083 2.00e-02 2.50e+03 pdb=" C3C HEC K 301 " -0.003 2.00e-02 2.50e+03 pdb=" C4C HEC K 301 " -0.001 2.00e-02 2.50e+03 pdb=" CAC HEC K 301 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEC K 301 " -0.016 2.00e-02 2.50e+03 pdb=" CHD HEC K 301 " 0.001 2.00e-02 2.50e+03 pdb=" CMC HEC K 301 " -0.025 2.00e-02 2.50e+03 pdb=" NC HEC K 301 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 86 " -0.052 5.00e-02 4.00e+02 7.93e-02 1.00e+01 pdb=" N PRO C 87 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 87 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 87 " -0.043 5.00e-02 4.00e+02 ... (remaining 2702 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 287 2.66 - 3.22: 14805 3.22 - 3.78: 25405 3.78 - 4.34: 35580 4.34 - 4.90: 58163 Nonbonded interactions: 134240 Sorted by model distance: nonbonded pdb=" NE2 HIS I 93 " pdb="FE HEM I 303 " model vdw 2.106 3.080 nonbonded pdb=" NE2 HIS I 209 " pdb="FE HEM I 304 " model vdw 2.170 3.080 nonbonded pdb=" OH TYR I 65 " pdb=" O LEU I 145 " model vdw 2.201 2.440 nonbonded pdb=" NE2 HIS A 209 " pdb="FE HEM A 303 " model vdw 2.210 3.080 nonbonded pdb=" O PHE I 59 " pdb=" OG1 THR I 62 " model vdw 2.211 2.440 ... (remaining 134235 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 3 through 222 or resid 301 or resid 303)) selection = (chain 'I' and (resid 3 through 222 or resid 301 or resid 303)) } ncs_group { reference = (chain 'B' and (resid 2 through 159 or (resid 202 and (name C01 or name C02 or n \ ame C03 or name C04 or name C05 or name C06 or name C1 or name C10 or name C11 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O \ 03 or name O04 or name O05 or name O06 or name O11 or name O12 or name O13 or na \ me O14 or name P )) or resid 203)) selection = (chain 'J' and (resid 2 through 159 or (resid 203 and (name C01 or name C02 or n \ ame C03 or name C04 or name C05 or name C06 or name C1 or name C10 or name C11 o \ r name C19 or name C2 or name C20 or name C21 or name C22 or name C23 or name C2 \ 4 or name C25 or name C26 or name C27 or name C28 or name C3 or name C4 or name \ C5 or name C6 or name C7 or name C8 or name C9 or name O01 or name O02 or name O \ 03 or name O04 or name O05 or name O06 or name O11 or name O12 or name O13 or na \ me O14 or name P )) or (resid 204 and (name C01 or name C02 or name C03 or name \ C04 or name C05 or name C06 or name C1 or name C10 or name C11 or name C19 or na \ me C2 or name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or \ name C26 or name C27 or name C28 or name C29 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C4 or name C5 or name C6 or name C7 \ or name C8 or name C9 or name O01 or name O02 or name O03 or name O04 or name O \ 05 or name O06 or name O11 or name O12 or name O13 or name O14 or name P )))) } ncs_group { reference = (chain 'C' and (resid 1 through 285 or resid 301)) selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = (chain 'E' and resid 1 through 32) selection = chain 'M' } ncs_group { reference = (chain 'F' and resid 1 through 34) selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 7 5.49 5 Mg 2 5.21 5 S 76 5.16 5 C 10361 2.51 5 N 2417 2.21 5 O 2731 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.220 Process input model: 45.840 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.006 0.213 16032 Z= 0.366 Angle : 0.936 16.334 21888 Z= 0.402 Chirality : 0.046 0.237 2385 Planarity : 0.005 0.101 2705 Dihedral : 15.106 164.559 5736 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.44 (0.19), residues: 1873 helix: 0.96 (0.17), residues: 930 sheet: -1.75 (0.37), residues: 182 loop : -1.49 (0.20), residues: 761 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.711 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2974 time to fit residues: 100.7583 Evaluate side-chains 209 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.9980 chunk 137 optimal weight: 0.0370 chunk 76 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 142 optimal weight: 0.0570 chunk 55 optimal weight: 30.0000 chunk 86 optimal weight: 0.0170 chunk 106 optimal weight: 0.0670 chunk 165 optimal weight: 4.9990 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 16032 Z= 0.163 Angle : 0.676 25.453 21888 Z= 0.255 Chirality : 0.041 0.160 2385 Planarity : 0.004 0.053 2705 Dihedral : 12.931 143.565 2424 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.15 (0.19), residues: 1873 helix: 1.27 (0.17), residues: 922 sheet: -1.70 (0.37), residues: 182 loop : -1.39 (0.21), residues: 769 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 221 time to evaluate : 1.726 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 223 average time/residue: 0.2949 time to fit residues: 98.3433 Evaluate side-chains 212 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1808 time to fit residues: 3.1821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 165 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 16032 Z= 0.240 Angle : 0.727 28.518 21888 Z= 0.263 Chirality : 0.042 0.161 2385 Planarity : 0.004 0.050 2705 Dihedral : 12.358 116.312 2424 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.15 (0.19), residues: 1873 helix: 1.20 (0.17), residues: 934 sheet: -1.75 (0.37), residues: 190 loop : -1.30 (0.21), residues: 749 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 212 time to evaluate : 1.797 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 216 average time/residue: 0.2799 time to fit residues: 89.7484 Evaluate side-chains 213 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 208 time to evaluate : 1.687 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1466 time to fit residues: 3.5988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 10.0000 chunk 124 optimal weight: 0.0670 chunk 85 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 16032 Z= 0.222 Angle : 0.702 28.125 21888 Z= 0.257 Chirality : 0.042 0.159 2385 Planarity : 0.004 0.048 2705 Dihedral : 11.992 99.826 2424 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: -0.04 (0.19), residues: 1873 helix: 1.26 (0.17), residues: 934 sheet: -1.82 (0.37), residues: 180 loop : -1.18 (0.21), residues: 759 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 217 time to evaluate : 1.629 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 219 average time/residue: 0.3002 time to fit residues: 96.6866 Evaluate side-chains 210 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 1.722 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1686 time to fit residues: 3.2115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.0010 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 0.4980 chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 0.3980 chunk 150 optimal weight: 9.9990 chunk 121 optimal weight: 0.1980 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 16032 Z= 0.159 Angle : 0.648 25.684 21888 Z= 0.243 Chirality : 0.041 0.159 2385 Planarity : 0.004 0.046 2705 Dihedral : 11.496 92.630 2424 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.20 (0.19), residues: 1873 helix: 1.48 (0.17), residues: 927 sheet: -1.73 (0.36), residues: 190 loop : -1.04 (0.21), residues: 756 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 229 time to evaluate : 1.727 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 231 average time/residue: 0.2844 time to fit residues: 96.4878 Evaluate side-chains 215 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 1.774 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1541 time to fit residues: 3.2217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 16032 Z= 0.202 Angle : 0.681 26.719 21888 Z= 0.251 Chirality : 0.041 0.156 2385 Planarity : 0.004 0.045 2705 Dihedral : 11.452 90.380 2424 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.16 (0.19), residues: 1873 helix: 1.46 (0.17), residues: 925 sheet: -1.60 (0.33), residues: 218 loop : -1.08 (0.22), residues: 730 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 214 time to evaluate : 1.730 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 217 average time/residue: 0.2951 time to fit residues: 94.0077 Evaluate side-chains 218 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.643 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1467 time to fit residues: 3.1732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 98 optimal weight: 0.2980 chunk 175 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.003 0.056 16032 Z= 0.227 Angle : 0.698 27.665 21888 Z= 0.255 Chirality : 0.042 0.154 2385 Planarity : 0.004 0.044 2705 Dihedral : 11.375 90.070 2424 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.16 (0.19), residues: 1873 helix: 1.45 (0.17), residues: 919 sheet: -1.61 (0.33), residues: 218 loop : -1.03 (0.22), residues: 736 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 214 time to evaluate : 1.675 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 219 average time/residue: 0.2961 time to fit residues: 95.5774 Evaluate side-chains 213 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 210 time to evaluate : 1.721 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1385 time to fit residues: 3.0524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.9990 chunk 70 optimal weight: 0.0010 chunk 104 optimal weight: 0.6980 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 119 optimal weight: 0.0370 chunk 86 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 overall best weight: 0.4664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN I 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16032 Z= 0.163 Angle : 0.640 25.435 21888 Z= 0.242 Chirality : 0.041 0.151 2385 Planarity : 0.004 0.043 2705 Dihedral : 11.070 89.304 2424 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.32 (0.19), residues: 1873 helix: 1.59 (0.17), residues: 915 sheet: -1.51 (0.34), residues: 218 loop : -0.97 (0.21), residues: 740 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 221 time to evaluate : 1.679 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 221 average time/residue: 0.2899 time to fit residues: 93.8967 Evaluate side-chains 215 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 1.715 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1913 time to fit residues: 2.9483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 163 optimal weight: 0.3980 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 147 optimal weight: 0.1980 chunk 154 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 16032 Z= 0.167 Angle : 0.646 25.214 21888 Z= 0.245 Chirality : 0.041 0.150 2385 Planarity : 0.004 0.043 2705 Dihedral : 10.903 87.791 2424 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.38 (0.19), residues: 1873 helix: 1.61 (0.17), residues: 917 sheet: -1.44 (0.34), residues: 218 loop : -0.91 (0.22), residues: 738 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 1.675 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 214 average time/residue: 0.2948 time to fit residues: 92.6094 Evaluate side-chains 209 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 1.739 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1457 time to fit residues: 2.6417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.0170 chunk 172 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 166 optimal weight: 0.0270 chunk 144 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 111 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 16032 Z= 0.161 Angle : 0.644 25.193 21888 Z= 0.245 Chirality : 0.041 0.216 2385 Planarity : 0.004 0.042 2705 Dihedral : 10.737 86.783 2424 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.44 (0.19), residues: 1873 helix: 1.64 (0.17), residues: 918 sheet: -1.41 (0.33), residues: 218 loop : -0.86 (0.22), residues: 737 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3746 Ramachandran restraints generated. 1873 Oldfield, 0 Emsley, 1873 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 1.860 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.2967 time to fit residues: 93.1072 Evaluate side-chains 205 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.676 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114311 restraints weight = 17825.045| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.52 r_work: 0.2973 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16032 Z= 0.207 Angle : 0.682 26.760 21888 Z= 0.254 Chirality : 0.042 0.197 2385 Planarity : 0.004 0.043 2705 Dihedral : 10.800 88.492 2424 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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: 0.35 (0.19), residues: 1873 helix: 1.53 (0.17), residues: 927 sheet: -1.44 (0.33), residues: 218 loop : -0.89 (0.22), residues: 728 =============================================================================== Job complete usr+sys time: 2905.13 seconds wall clock time: 53 minutes 42.46 seconds (3222.46 seconds total)