Starting phenix.real_space_refine on Fri Feb 16 14:30:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2024/7zxy_15017_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2024/7zxy_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_2024/7zxy_15017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2024/7zxy_15017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2024/7zxy_15017_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zxy_15017/02_2024/7zxy_15017_updated.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 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. 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 9.20, per 1000 atoms: 0.59 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: 6.61 Conformation dependent library (CDL) restraints added in 2.8 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: 2.77 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: 3.94 Time building geometry restraints manager: 7.06 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: 8981 32.91 - 65.82: 225 65.82 - 98.74: 44 98.74 - 131.65: 2 131.65 - 164.56: 7 Dihedral angle restraints: 9259 sinusoidal: 3858 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 9256 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 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: 0.900 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: 3.110 Check model and map are aligned: 0.260 Set scattering table: 0.140 Process input model: 46.260 Find NCS groups from input model: 0.880 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: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 16.227 164.559 5810 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP L 190 HIS 0.009 0.001 HIS I 209 PHE 0.044 0.002 PHE A 138 TYR 0.012 0.001 TYR B 80 ARG 0.007 0.000 ARG A 18 *********************** 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 : 1.576 Fit side-chains REVERT: A 103 MET cc_start: 0.8118 (mmp) cc_final: 0.7320 (mmt) REVERT: B 153 LYS cc_start: 0.8350 (ptpp) cc_final: 0.7941 (pttt) REVERT: K 138 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6841 (pttm) REVERT: P 14 LEU cc_start: 0.8789 (tp) cc_final: 0.8447 (tt) REVERT: P 21 MET cc_start: 0.8176 (mmp) cc_final: 0.7906 (mmp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.2930 time to fit residues: 99.0367 Evaluate side-chains 209 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.4354 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16032 Z= 0.171 Angle : 0.684 25.249 21888 Z= 0.257 Chirality : 0.041 0.161 2385 Planarity : 0.004 0.053 2705 Dihedral : 14.990 157.822 2498 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.32 % Allowed : 5.47 % Favored : 94.20 % 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: -0.18 (0.19), residues: 1873 helix: 1.24 (0.17), residues: 922 sheet: -1.71 (0.37), residues: 182 loop : -1.39 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP L 190 HIS 0.005 0.001 HIS I 209 PHE 0.021 0.001 PHE A 12 TYR 0.012 0.001 TYR C 102 ARG 0.005 0.000 ARG A 18 *********************** 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 224 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 219 time to evaluate : 1.818 Fit side-chains REVERT: A 103 MET cc_start: 0.8217 (mmp) cc_final: 0.7433 (mmt) REVERT: B 153 LYS cc_start: 0.8376 (ptpp) cc_final: 0.7991 (pttt) REVERT: K 138 LYS cc_start: 0.7107 (mtmt) cc_final: 0.6868 (pttm) REVERT: P 14 LEU cc_start: 0.8850 (tp) cc_final: 0.8484 (tt) REVERT: P 21 MET cc_start: 0.8090 (mmp) cc_final: 0.7839 (mmp) outliers start: 5 outliers final: 1 residues processed: 221 average time/residue: 0.2888 time to fit residues: 94.6491 Evaluate side-chains 208 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 207 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 161 VAL 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: 0.1980 chunk 137 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 165 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7828 moved from start: 0.0824 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= 0.198 Angle : 0.693 27.557 21888 Z= 0.253 Chirality : 0.041 0.160 2385 Planarity : 0.004 0.048 2705 Dihedral : 14.139 168.975 2498 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.58 % Allowed : 6.95 % Favored : 92.47 % 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: 1.33 (0.17), residues: 922 sheet: -1.72 (0.37), residues: 182 loop : -1.27 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 153 HIS 0.006 0.001 HIS I 209 PHE 0.021 0.001 PHE A 12 TYR 0.008 0.001 TYR A 78 ARG 0.002 0.000 ARG K 155 *********************** 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: 9 poor density : 213 time to evaluate : 1.615 Fit side-chains REVERT: A 103 MET cc_start: 0.8259 (mmp) cc_final: 0.7464 (mmt) REVERT: A 138 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7749 (t80) REVERT: B 153 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8026 (pttt) REVERT: C 262 MET cc_start: 0.8339 (mtp) cc_final: 0.8137 (mtp) REVERT: I 103 MET cc_start: 0.8251 (mmt) cc_final: 0.7662 (mmp) REVERT: P 21 MET cc_start: 0.8085 (mmp) cc_final: 0.7857 (mmp) outliers start: 9 outliers final: 5 residues processed: 217 average time/residue: 0.2780 time to fit residues: 89.0803 Evaluate side-chains 211 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 205 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 157 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16032 Z= 0.186 Angle : 0.670 26.815 21888 Z= 0.247 Chirality : 0.041 0.155 2385 Planarity : 0.004 0.047 2705 Dihedral : 13.356 148.748 2498 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.52 % Allowed : 8.63 % Favored : 90.86 % 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: 0.03 (0.19), residues: 1873 helix: 1.33 (0.17), residues: 936 sheet: -1.82 (0.36), residues: 190 loop : -1.14 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 153 HIS 0.005 0.001 HIS I 209 PHE 0.017 0.001 PHE A 12 TYR 0.013 0.001 TYR D 114 ARG 0.006 0.000 ARG B 15 *********************** 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 225 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 217 time to evaluate : 1.536 Fit side-chains REVERT: A 103 MET cc_start: 0.8220 (mmp) cc_final: 0.7364 (mmt) REVERT: A 138 PHE cc_start: 0.8765 (OUTLIER) cc_final: 0.7768 (t80) REVERT: B 153 LYS cc_start: 0.8415 (ptpp) cc_final: 0.8028 (pttt) REVERT: C 262 MET cc_start: 0.8311 (mtp) cc_final: 0.8038 (mtp) REVERT: G 31 ARG cc_start: 0.6809 (mtt180) cc_final: 0.6567 (mtt180) REVERT: P 21 MET cc_start: 0.8068 (mmp) cc_final: 0.7846 (mmp) outliers start: 8 outliers final: 4 residues processed: 219 average time/residue: 0.2869 time to fit residues: 91.8421 Evaluate side-chains 211 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 0.0470 chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- 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** ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1060 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= 0.273 Angle : 0.736 29.072 21888 Z= 0.267 Chirality : 0.043 0.157 2385 Planarity : 0.004 0.048 2705 Dihedral : 13.095 120.344 2498 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.71 % Allowed : 9.79 % Favored : 89.50 % 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: 0.01 (0.19), residues: 1873 helix: 1.31 (0.17), residues: 917 sheet: -1.87 (0.37), residues: 180 loop : -1.08 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 153 HIS 0.007 0.001 HIS I 209 PHE 0.020 0.002 PHE A 12 TYR 0.010 0.001 TYR B 80 ARG 0.003 0.000 ARG K 155 *********************** 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 225 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 214 time to evaluate : 1.690 Fit side-chains REVERT: A 103 MET cc_start: 0.8243 (mmp) cc_final: 0.7354 (mmt) REVERT: A 138 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.8088 (t80) REVERT: A 222 LEU cc_start: 0.7930 (mp) cc_final: 0.7711 (mp) REVERT: C 262 MET cc_start: 0.8375 (mtp) cc_final: 0.8049 (mtp) REVERT: G 3 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: J 20 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8241 (mtpt) REVERT: P 21 MET cc_start: 0.8074 (mmp) cc_final: 0.7873 (mmp) outliers start: 11 outliers final: 6 residues processed: 218 average time/residue: 0.2895 time to fit residues: 92.8497 Evaluate side-chains 214 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 206 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 10.0000 chunk 158 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 176 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 58 optimal weight: 0.0770 chunk 92 optimal weight: 1.9990 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16032 Z= 0.171 Angle : 0.658 26.171 21888 Z= 0.246 Chirality : 0.041 0.157 2385 Planarity : 0.004 0.045 2705 Dihedral : 12.629 114.585 2498 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.90 % Allowed : 10.37 % Favored : 88.73 % 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: 0.11 (0.19), residues: 1873 helix: 1.42 (0.17), residues: 927 sheet: -1.64 (0.33), residues: 218 loop : -1.09 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 153 HIS 0.003 0.001 HIS I 209 PHE 0.015 0.001 PHE A 12 TYR 0.012 0.001 TYR D 114 ARG 0.004 0.000 ARG L 90 *********************** 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 234 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 1.733 Fit side-chains REVERT: A 103 MET cc_start: 0.8233 (mmp) cc_final: 0.7870 (mmp) REVERT: A 138 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.7876 (t80) REVERT: A 222 LEU cc_start: 0.7924 (mp) cc_final: 0.7673 (mp) REVERT: I 103 MET cc_start: 0.8325 (mmt) cc_final: 0.7746 (mmp) REVERT: P 21 MET cc_start: 0.8063 (mmp) cc_final: 0.7857 (mmp) outliers start: 14 outliers final: 9 residues processed: 227 average time/residue: 0.2787 time to fit residues: 93.0747 Evaluate side-chains 223 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 213 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 148 optimal weight: 0.0570 chunk 98 optimal weight: 0.5980 chunk 175 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16032 Z= 0.184 Angle : 0.664 26.308 21888 Z= 0.247 Chirality : 0.041 0.151 2385 Planarity : 0.004 0.044 2705 Dihedral : 12.405 114.421 2498 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.84 % Allowed : 10.82 % Favored : 88.35 % 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: 0.17 (0.19), residues: 1873 helix: 1.45 (0.17), residues: 927 sheet: -1.59 (0.33), residues: 218 loop : -1.05 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 153 HIS 0.004 0.001 HIS I 209 PHE 0.017 0.001 PHE M 15 TYR 0.010 0.001 TYR B 80 ARG 0.004 0.000 ARG L 90 *********************** 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 229 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 216 time to evaluate : 1.660 Fit side-chains REVERT: A 103 MET cc_start: 0.8269 (mmp) cc_final: 0.7372 (mmt) REVERT: A 138 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.7764 (t80) REVERT: A 222 LEU cc_start: 0.7931 (mp) cc_final: 0.7677 (mp) REVERT: D 92 LEU cc_start: 0.8565 (pp) cc_final: 0.8196 (pp) REVERT: G 3 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: P 21 MET cc_start: 0.8064 (mmp) cc_final: 0.7845 (mmp) outliers start: 13 outliers final: 9 residues processed: 222 average time/residue: 0.2792 time to fit residues: 91.5919 Evaluate side-chains 219 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 104 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 119 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 137 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** I 171 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16032 Z= 0.162 Angle : 0.639 25.171 21888 Z= 0.241 Chirality : 0.041 0.150 2385 Planarity : 0.004 0.043 2705 Dihedral : 12.078 113.439 2498 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.71 % Allowed : 11.20 % Favored : 88.09 % 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: 1.58 (0.17), residues: 917 sheet: -1.51 (0.34), residues: 218 loop : -0.96 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 153 HIS 0.003 0.001 HIS I 209 PHE 0.017 0.001 PHE M 15 TYR 0.010 0.001 TYR B 80 ARG 0.004 0.000 ARG L 90 *********************** 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 226 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 215 time to evaluate : 1.858 Fit side-chains REVERT: A 138 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.7766 (t80) REVERT: A 222 LEU cc_start: 0.7905 (mp) cc_final: 0.7643 (mp) REVERT: D 92 LEU cc_start: 0.8485 (pp) cc_final: 0.8124 (pp) outliers start: 11 outliers final: 10 residues processed: 220 average time/residue: 0.2950 time to fit residues: 95.4754 Evaluate side-chains 219 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 208 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 71 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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: 0.7837 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16032 Z= 0.210 Angle : 0.687 27.042 21888 Z= 0.253 Chirality : 0.041 0.156 2385 Planarity : 0.004 0.044 2705 Dihedral : 12.103 114.882 2498 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.71 % Allowed : 11.78 % Favored : 87.51 % 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: 0.24 (0.19), residues: 1873 helix: 1.47 (0.17), residues: 927 sheet: -1.50 (0.33), residues: 218 loop : -0.98 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 153 HIS 0.005 0.001 HIS I 209 PHE 0.016 0.001 PHE M 15 TYR 0.010 0.001 TYR B 80 ARG 0.004 0.000 ARG L 90 *********************** 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 223 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 212 time to evaluate : 1.719 Fit side-chains REVERT: A 138 PHE cc_start: 0.8918 (OUTLIER) cc_final: 0.7969 (t80) REVERT: A 222 LEU cc_start: 0.7940 (mp) cc_final: 0.7711 (mp) REVERT: J 20 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8317 (ttpp) outliers start: 11 outliers final: 10 residues processed: 216 average time/residue: 0.2905 time to fit residues: 91.8972 Evaluate side-chains 221 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 210 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.0980 chunk 172 optimal weight: 0.9980 chunk 105 optimal weight: 0.0050 chunk 82 optimal weight: 6.9990 chunk 120 optimal weight: 0.0010 chunk 181 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 0.3400 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16032 Z= 0.155 Angle : 0.635 24.918 21888 Z= 0.242 Chirality : 0.041 0.153 2385 Planarity : 0.004 0.043 2705 Dihedral : 11.806 121.911 2498 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.71 % Allowed : 11.98 % Favored : 87.31 % 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: 1.65 (0.17), residues: 918 sheet: -1.42 (0.34), residues: 218 loop : -0.87 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 153 HIS 0.003 0.001 HIS I 209 PHE 0.016 0.001 PHE M 15 TYR 0.011 0.001 TYR B 80 ARG 0.003 0.000 ARG L 90 ********************** 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 224 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 1.564 Fit side-chains REVERT: A 138 PHE cc_start: 0.8743 (OUTLIER) cc_final: 0.7745 (t80) REVERT: A 222 LEU cc_start: 0.7896 (mp) cc_final: 0.7645 (mp) REVERT: D 92 LEU cc_start: 0.8494 (pp) cc_final: 0.8169 (pp) REVERT: J 20 LYS cc_start: 0.8535 (mtpt) cc_final: 0.8319 (ttpp) REVERT: P 21 MET cc_start: 0.8199 (mmp) cc_final: 0.7972 (mmt) outliers start: 11 outliers final: 8 residues processed: 219 average time/residue: 0.2859 time to fit residues: 92.0617 Evaluate side-chains 215 residues out of total 1553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 206 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain E residue 11 TYR Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain N residue 14 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 148 optimal weight: 0.0010 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.158097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127962 restraints weight = 17640.356| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.24 r_work: 0.2980 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16032 Z= 0.168 Angle : 0.646 25.221 21888 Z= 0.244 Chirality : 0.041 0.152 2385 Planarity : 0.004 0.042 2705 Dihedral : 11.700 126.085 2498 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.64 % Allowed : 12.17 % Favored : 87.19 % 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: 0.47 (0.19), residues: 1873 helix: 1.67 (0.17), residues: 917 sheet: -1.42 (0.34), residues: 218 loop : -0.85 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 153 HIS 0.003 0.001 HIS I 209 PHE 0.015 0.001 PHE M 15 TYR 0.011 0.001 TYR B 80 ARG 0.004 0.000 ARG L 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3187.51 seconds wall clock time: 59 minutes 1.50 seconds (3541.50 seconds total)