Starting phenix.real_space_refine on Fri Feb 16 07:13:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asj_15617/02_2024/8asj_15617_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asj_15617/02_2024/8asj_15617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asj_15617/02_2024/8asj_15617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asj_15617/02_2024/8asj_15617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asj_15617/02_2024/8asj_15617_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asj_15617/02_2024/8asj_15617_updated.pdb" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 12 5.49 5 S 74 5.16 5 C 9715 2.51 5 N 2338 2.21 5 O 2571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14720 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1342 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain: "B" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3477 Classifications: {'peptide': 433} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 404} Chain: "C" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1944 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 233} Chain: "D" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 222 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1357 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "F" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3471 Classifications: {'peptide': 432} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 403} Chain: "G" Number of atoms: 1944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1944 Classifications: {'peptide': 254} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 233} Chain: "H" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 203 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'FES': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 316 Unusual residues: {'HEM': 2, 'PEE': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 76 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'FES': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "F" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 265 Unusual residues: {'HEM': 2, 'PEE': 4, 'U10': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 913 SG CYS A 129 34.288 79.492 51.048 1.00 88.05 S ATOM 1053 SG CYS A 149 37.103 81.000 52.863 1.00 83.58 S ATOM 7913 SG CYS E 129 63.956 35.852 87.115 1.00178.24 S ATOM 8053 SG CYS E 149 59.607 34.141 86.774 1.00191.63 S Time building chain proxies: 7.84, per 1000 atoms: 0.53 Number of scatterers: 14720 At special positions: 0 Unit cell: (119.524, 114.836, 119.524, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 74 16.00 P 12 15.00 O 2571 8.00 N 2338 7.00 C 9715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 151 " 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.43 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE2 FES A 201 " - pdb=" ND1 HIS A 152 " pdb="FE2 FES A 201 " - pdb=" ND1 HIS A 131 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 149 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 129 " pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" NE2 HIS E 131 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 149 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 129 " pdb="FE2 FES E 201 " - pdb=" ND1 HIS E 152 " Number of angles added : 6 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3254 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 9 sheets defined 51.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 10 through 38 removed outlier: 3.588A pdb=" N THR A 19 " --> pdb=" O TYR A 16 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 25 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 27 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 29 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP A 32 " --> pdb=" O ALA A 29 " (cutoff:3.500A) Proline residue: A 33 - end of helix removed outlier: 4.551A pdb=" N GLN A 37 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 48 removed outlier: 3.829A pdb=" N ALA A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 removed outlier: 7.078A pdb=" N GLY A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'B' and resid 14 through 20 Processing helix chain 'B' and resid 25 through 33 Processing helix chain 'B' and resid 43 through 67 removed outlier: 3.988A pdb=" N TRP B 47 " --> pdb=" O MET B 44 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 48 " --> pdb=" O TRP B 45 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 58 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 61 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 90 through 118 removed outlier: 3.693A pdb=" N SER B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 149 Processing helix chain 'B' and resid 153 through 168 removed outlier: 4.139A pdb=" N PHE B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY B 167 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 181 Processing helix chain 'B' and resid 188 through 219 Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 244 through 269 removed outlier: 6.675A pdb=" N ILE B 249 " --> pdb=" O TRP B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 280 Processing helix chain 'B' and resid 296 through 307 Proline residue: B 300 - end of helix Processing helix chain 'B' and resid 313 through 321 Processing helix chain 'B' and resid 328 through 349 removed outlier: 4.015A pdb=" N ILE B 340 " --> pdb=" O MET B 336 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 359 No H-bonds generated for 'chain 'B' and resid 357 through 359' Processing helix chain 'B' and resid 363 through 382 removed outlier: 4.009A pdb=" N ALA B 382 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 405 removed outlier: 3.686A pdb=" N PHE B 404 " --> pdb=" O TRP B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.556A pdb=" N GLY B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B 413 " --> pdb=" O PRO B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 431 removed outlier: 3.554A pdb=" N HIS B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 56 Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 69 through 73 Processing helix chain 'C' and resid 82 through 91 removed outlier: 3.870A pdb=" N GLN C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 149 through 157 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 226 through 241 Processing helix chain 'C' and resid 245 through 277 removed outlier: 3.705A pdb=" N GLY C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 103 removed outlier: 3.635A pdb=" N ARG D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 38 removed outlier: 3.772A pdb=" N ALA E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Proline residue: E 33 - end of helix removed outlier: 4.812A pdb=" N MET E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 46 Processing helix chain 'E' and resid 58 through 61 No H-bonds generated for 'chain 'E' and resid 58 through 61' Processing helix chain 'E' and resid 81 through 87 Processing helix chain 'F' and resid 14 through 20 Processing helix chain 'F' and resid 25 through 33 Processing helix chain 'F' and resid 43 through 67 removed outlier: 3.935A pdb=" N TRP F 47 " --> pdb=" O MET F 44 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY F 48 " --> pdb=" O TRP F 45 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR F 61 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 90 through 118 removed outlier: 3.732A pdb=" N SER F 102 " --> pdb=" O ALA F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 148 Processing helix chain 'F' and resid 153 through 168 removed outlier: 3.777A pdb=" N PHE F 166 " --> pdb=" O ILE F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 3.657A pdb=" N LEU F 181 " --> pdb=" O THR F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 219 Proline residue: F 202 - end of helix Processing helix chain 'F' and resid 234 through 240 removed outlier: 3.505A pdb=" N LYS F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 269 removed outlier: 6.741A pdb=" N ILE F 249 " --> pdb=" O TRP F 245 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 280 Processing helix chain 'F' and resid 296 through 307 Proline residue: F 300 - end of helix Processing helix chain 'F' and resid 313 through 321 Processing helix chain 'F' and resid 328 through 349 removed outlier: 4.350A pdb=" N ILE F 340 " --> pdb=" O MET F 336 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Proline residue: F 347 - end of helix Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 363 through 382 removed outlier: 3.858A pdb=" N ALA F 382 " --> pdb=" O THR F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 405 removed outlier: 3.777A pdb=" N PHE F 404 " --> pdb=" O TRP F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 414 removed outlier: 3.704A pdb=" N ALA F 413 " --> pdb=" O PRO F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 431 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 58 through 60 No H-bonds generated for 'chain 'G' and resid 58 through 60' Processing helix chain 'G' and resid 69 through 73 Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.738A pdb=" N GLN G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 149 through 157 Processing helix chain 'G' and resid 226 through 241 Processing helix chain 'G' and resid 245 through 277 removed outlier: 4.142A pdb=" N GLY G 276 " --> pdb=" O ARG G 272 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 104 removed outlier: 4.016A pdb=" N PHE H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER H 103 " --> pdb=" O ALA H 99 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 61 through 67 removed outlier: 3.678A pdb=" N VAL A 61 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 74 " --> pdb=" O LEU A 63 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 52 through 54 removed outlier: 3.558A pdb=" N GLY A 187 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL A 54 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN A 185 " --> pdb=" O VAL A 54 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= D, first strand: chain 'C' and resid 93 through 95 Processing sheet with id= E, first strand: chain 'C' and resid 177 through 179 Processing sheet with id= F, first strand: chain 'E' and resid 72 through 76 Processing sheet with id= G, first strand: chain 'F' and resid 36 through 38 Processing sheet with id= H, first strand: chain 'G' and resid 93 through 95 Processing sheet with id= I, first strand: chain 'G' and resid 177 through 179 628 hydrogen bonds defined for protein. 1629 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: 4.27 Time building geometry restraints manager: 6.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.39: 6218 1.39 - 1.60: 8804 1.60 - 1.80: 112 1.80 - 2.01: 34 2.01 - 2.21: 32 Bond restraints: 15200 Sorted by residual: bond pdb=" C18 PEE B 508 " pdb=" C19 PEE B 508 " ideal model delta sigma weight residual 1.523 1.328 0.195 2.00e-02 2.50e+03 9.48e+01 bond pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " ideal model delta sigma weight residual 1.523 1.334 0.189 2.00e-02 2.50e+03 8.88e+01 bond pdb=" C38 PEE E 202 " pdb=" C39 PEE E 202 " ideal model delta sigma weight residual 1.523 1.335 0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" C38 PEE B 507 " pdb=" C39 PEE B 507 " ideal model delta sigma weight residual 1.523 1.335 0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" C38 PEE B 508 " pdb=" C39 PEE B 508 " ideal model delta sigma weight residual 1.523 1.338 0.185 2.00e-02 2.50e+03 8.52e+01 ... (remaining 15195 not shown) Histogram of bond angle deviations from ideal: 69.25 - 91.19: 29 91.19 - 113.13: 8414 113.13 - 135.07: 12278 135.07 - 157.00: 1 157.00 - 178.94: 12 Bond angle restraints: 20734 Sorted by residual: angle pdb=" C17 PEE B 508 " pdb=" C18 PEE B 508 " pdb=" C19 PEE B 508 " ideal model delta sigma weight residual 113.68 144.22 -30.54 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " pdb=" C40 PEE B 503 " ideal model delta sigma weight residual 112.47 85.91 26.56 3.00e+00 1.11e-01 7.84e+01 angle pdb=" C38 PEE B 507 " pdb=" C39 PEE B 507 " pdb=" C40 PEE B 507 " ideal model delta sigma weight residual 112.47 86.07 26.40 3.00e+00 1.11e-01 7.74e+01 angle pdb=" C38 PEE B 508 " pdb=" C39 PEE B 508 " pdb=" C40 PEE B 508 " ideal model delta sigma weight residual 112.47 91.41 21.06 3.00e+00 1.11e-01 4.93e+01 angle pdb=" O3P PEE F 503 " pdb=" P PEE F 503 " pdb=" O4P PEE F 503 " ideal model delta sigma weight residual 92.91 110.59 -17.68 3.00e+00 1.11e-01 3.47e+01 ... (remaining 20729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 8381 33.84 - 67.68: 215 67.68 - 101.52: 67 101.52 - 135.35: 28 135.35 - 169.19: 19 Dihedral angle restraints: 8710 sinusoidal: 3605 harmonic: 5105 Sorted by residual: dihedral pdb=" C6 U10 F 507 " pdb=" C7 U10 F 507 " pdb=" C8 U10 F 507 " pdb=" C9 U10 F 507 " ideal model delta sinusoidal sigma weight residual 101.51 -104.74 -153.75 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" C2B HEC G 301 " pdb=" C3B HEC G 301 " pdb=" CAB HEC G 301 " pdb=" CBB HEC G 301 " ideal model delta sinusoidal sigma weight residual 240.00 172.21 67.79 2 1.00e+01 1.00e-02 4.11e+01 dihedral pdb=" C2C HEC G 301 " pdb=" C3C HEC G 301 " pdb=" CAC HEC G 301 " pdb=" CBC HEC G 301 " ideal model delta sinusoidal sigma weight residual 240.00 179.16 60.84 2 1.00e+01 1.00e-02 3.66e+01 ... (remaining 8707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1542 0.043 - 0.087: 456 0.087 - 0.130: 127 0.130 - 0.173: 15 0.173 - 0.217: 7 Chirality restraints: 2147 Sorted by residual: chirality pdb=" C2 PEE A 202 " pdb=" C1 PEE A 202 " pdb=" C3 PEE A 202 " pdb=" O2 PEE A 202 " both_signs ideal model delta sigma weight residual False -2.33 -2.54 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB VAL F 242 " pdb=" CA VAL F 242 " pdb=" CG1 VAL F 242 " pdb=" CG2 VAL F 242 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2 PEE F 504 " pdb=" C1 PEE F 504 " pdb=" C3 PEE F 504 " pdb=" O2 PEE F 504 " both_signs ideal model delta sigma weight residual False -2.33 -2.53 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2144 not shown) Planarity restraints: 2582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " 0.024 2.00e-02 2.50e+03 8.25e-02 1.53e+02 pdb=" C2C HEC C 301 " -0.225 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " 0.052 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " 0.012 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " 0.032 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " 0.037 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " -0.008 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " 0.069 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC G 301 " 0.025 2.00e-02 2.50e+03 8.20e-02 1.51e+02 pdb=" C2C HEC G 301 " -0.225 2.00e-02 2.50e+03 pdb=" C3C HEC G 301 " 0.044 2.00e-02 2.50e+03 pdb=" C4C HEC G 301 " 0.012 2.00e-02 2.50e+03 pdb=" CAC HEC G 301 " 0.038 2.00e-02 2.50e+03 pdb=" CHC HEC G 301 " 0.040 2.00e-02 2.50e+03 pdb=" CHD HEC G 301 " -0.008 2.00e-02 2.50e+03 pdb=" CMC HEC G 301 " 0.064 2.00e-02 2.50e+03 pdb=" NC HEC G 301 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 230 " -0.203 9.50e-02 1.11e+02 9.16e-02 6.68e+00 pdb=" NE ARG B 230 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG B 230 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG B 230 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 230 " -0.000 2.00e-02 2.50e+03 ... (remaining 2579 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 407 2.71 - 3.26: 15539 3.26 - 3.81: 25177 3.81 - 4.35: 32042 4.35 - 4.90: 52027 Nonbonded interactions: 125192 Sorted by model distance: nonbonded pdb=" NE2 HIS F 97 " pdb="FE HEM F 502 " model vdw 2.165 3.080 nonbonded pdb=" CE MET C 207 " pdb="FE HEC C 301 " model vdw 2.200 3.420 nonbonded pdb=" SD MET G 207 " pdb="FE HEC G 301 " model vdw 2.210 3.360 nonbonded pdb=" NE2 HIS B 97 " pdb="FE HEM B 502 " model vdw 2.217 3.080 nonbonded pdb=" OD1 ASN B 272 " pdb=" OH TYR B 280 " model vdw 2.247 2.440 ... (remaining 125187 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 9 through 187 or resid 201 or (resid 202 and (name N or na \ me C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or \ name C16 or name C17 or name C18 or name C2 or name C3 or name C30 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C4 or name C5 or name O1P or name O2 or name O2P or name \ O3 or name O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'E' and (resid 9 through 187 or resid 201 through 202)) } ncs_group { reference = (chain 'B' and (resid 1 through 432 or resid 502 or resid 504 or (resid 505 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C4 or name C5 or name O1P or name O \ 2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P \ )) or resid 506 or (resid 507 and (name N or name C1 or name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name 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 C3 or name C30 or name C31 or n \ ame C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name C38 \ or name C39 or name C4 or name C40 or name C5 or name O1P or name O2 or name O2P \ or name O3 or name O3P or name O4 or name O4P or name O5 or name P )))) selection = (chain 'F' and (resid 1 through 432 or resid 501 or resid 503 or (resid 504 and \ (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name C14 o \ r name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C4 or name C5 or name O1P or name O \ 2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P \ )) or resid 505 through 506)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 78 through 104) selection = chain 'H' } 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 group one per residue 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: 0.510 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: 3.090 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 43.260 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.110 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 : 0.008 0.195 15200 Z= 0.518 Angle : 1.092 30.544 20734 Z= 0.464 Chirality : 0.045 0.217 2147 Planarity : 0.009 0.092 2582 Dihedral : 20.537 169.193 5450 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.38 % Favored : 96.50 % Rotamer: Outliers : 0.21 % Allowed : 3.63 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: -0.91 (0.18), residues: 1773 helix: -0.36 (0.15), residues: 933 sheet: -1.68 (0.58), residues: 61 loop : -0.64 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 147 HIS 0.007 0.001 HIS B 291 PHE 0.042 0.002 PHE D 87 TYR 0.019 0.004 TYR E 156 ARG 0.022 0.004 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 327 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 68 LEU cc_start: 0.6307 (tp) cc_final: 0.5986 (tt) REVERT: A 76 ARG cc_start: 0.6714 (ttt180) cc_final: 0.6386 (mtp85) REVERT: A 89 GLN cc_start: 0.7314 (mt0) cc_final: 0.7075 (tp40) REVERT: A 113 ASN cc_start: 0.7524 (m-40) cc_final: 0.7261 (m-40) REVERT: A 184 ILE cc_start: 0.6547 (mt) cc_final: 0.6302 (mt) REVERT: B 34 MET cc_start: 0.8460 (mmm) cc_final: 0.8236 (mmt) REVERT: B 84 MET cc_start: 0.8076 (mmm) cc_final: 0.7647 (mmt) REVERT: B 133 MET cc_start: 0.7778 (mmm) cc_final: 0.7341 (mmm) REVERT: B 137 LEU cc_start: 0.7340 (mt) cc_final: 0.7057 (mt) REVERT: B 180 LEU cc_start: 0.7848 (mt) cc_final: 0.7586 (tp) REVERT: B 306 ARG cc_start: 0.6934 (mtm180) cc_final: 0.6719 (mmt180) REVERT: B 317 ILE cc_start: 0.6793 (mp) cc_final: 0.6348 (mt) REVERT: B 342 VAL cc_start: 0.8098 (p) cc_final: 0.7794 (m) REVERT: B 393 SER cc_start: 0.8428 (t) cc_final: 0.8010 (p) REVERT: B 431 HIS cc_start: 0.6475 (m-70) cc_final: 0.6151 (m170) REVERT: C 64 MET cc_start: 0.7671 (mtt) cc_final: 0.7460 (mtm) REVERT: C 70 ARG cc_start: 0.7513 (ptt90) cc_final: 0.7180 (ptt90) REVERT: C 79 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7443 (mt-10) REVERT: C 86 ARG cc_start: 0.6599 (ttm110) cc_final: 0.6259 (mtm-85) REVERT: C 141 SER cc_start: 0.8327 (t) cc_final: 0.8101 (t) REVERT: F 137 LEU cc_start: 0.7106 (mt) cc_final: 0.6530 (mt) REVERT: F 270 MET cc_start: 0.8622 (ptm) cc_final: 0.8289 (ptp) REVERT: F 282 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7393 (mt-10) REVERT: F 325 ILE cc_start: 0.8047 (mm) cc_final: 0.7820 (tt) REVERT: F 352 SER cc_start: 0.7327 (t) cc_final: 0.7039 (m) REVERT: F 426 GLU cc_start: 0.7482 (tt0) cc_final: 0.6491 (tp30) REVERT: F 431 HIS cc_start: 0.6176 (m-70) cc_final: 0.5720 (m-70) REVERT: G 136 MET cc_start: 0.6402 (tpp) cc_final: 0.5616 (mtm) REVERT: G 164 PRO cc_start: 0.6686 (Cg_exo) cc_final: 0.6364 (Cg_endo) REVERT: G 223 ASP cc_start: 0.7174 (t0) cc_final: 0.6893 (t70) REVERT: G 257 MET cc_start: 0.6781 (mmp) cc_final: 0.6570 (mmt) REVERT: G 267 TYR cc_start: 0.8117 (t80) cc_final: 0.7883 (t80) outliers start: 3 outliers final: 1 residues processed: 330 average time/residue: 0.3013 time to fit residues: 147.4507 Evaluate side-chains 228 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 385 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.2980 chunk 132 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN B 217 HIS C 113 HIS C 171 HIS F 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15200 Z= 0.193 Angle : 0.641 15.116 20734 Z= 0.297 Chirality : 0.044 0.215 2147 Planarity : 0.005 0.045 2582 Dihedral : 22.401 179.735 2394 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.26 % Favored : 97.63 % Rotamer: Outliers : 1.32 % Allowed : 8.51 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1773 helix: 0.94 (0.17), residues: 935 sheet: -1.65 (0.56), residues: 72 loop : -0.02 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 157 HIS 0.005 0.001 HIS B 291 PHE 0.029 0.002 PHE D 87 TYR 0.014 0.001 TYR B 359 ARG 0.003 0.000 ARG G 272 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 224 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 63 LEU cc_start: 0.7618 (mt) cc_final: 0.7150 (mm) REVERT: A 68 LEU cc_start: 0.6526 (tp) cc_final: 0.6134 (tt) REVERT: A 161 ARG cc_start: 0.6996 (mtm110) cc_final: 0.6647 (mtm180) REVERT: B 7 ASP cc_start: 0.6946 (m-30) cc_final: 0.6481 (m-30) REVERT: B 34 MET cc_start: 0.8468 (mmm) cc_final: 0.8122 (mmm) REVERT: B 84 MET cc_start: 0.7970 (mmm) cc_final: 0.7661 (mmt) REVERT: B 137 LEU cc_start: 0.7333 (mt) cc_final: 0.7068 (mt) REVERT: B 154 MET cc_start: 0.8480 (mmm) cc_final: 0.8143 (mmm) REVERT: B 227 VAL cc_start: 0.7030 (t) cc_final: 0.6770 (m) REVERT: B 317 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6391 (mp) REVERT: B 427 ASP cc_start: 0.8069 (t70) cc_final: 0.7563 (t0) REVERT: B 431 HIS cc_start: 0.6600 (m-70) cc_final: 0.6217 (m170) REVERT: C 70 ARG cc_start: 0.7453 (ptt90) cc_final: 0.7246 (ptt90) REVERT: C 74 GLU cc_start: 0.7211 (tt0) cc_final: 0.6521 (mm-30) REVERT: C 86 ARG cc_start: 0.6568 (ttm110) cc_final: 0.6318 (mtm-85) REVERT: C 141 SER cc_start: 0.8342 (t) cc_final: 0.8131 (t) REVERT: C 212 MET cc_start: 0.6862 (mmt) cc_final: 0.6565 (mtm) REVERT: F 325 ILE cc_start: 0.8155 (mm) cc_final: 0.7802 (tt) REVERT: F 352 SER cc_start: 0.7467 (t) cc_final: 0.7070 (m) REVERT: F 426 GLU cc_start: 0.7809 (tt0) cc_final: 0.6693 (tp30) REVERT: F 431 HIS cc_start: 0.5603 (m-70) cc_final: 0.4872 (m-70) REVERT: G 74 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6301 (mt-10) REVERT: G 136 MET cc_start: 0.5927 (tpp) cc_final: 0.5200 (mtm) REVERT: G 223 ASP cc_start: 0.7123 (t0) cc_final: 0.6910 (t70) REVERT: G 246 MET cc_start: 0.8061 (mmt) cc_final: 0.7478 (mmt) REVERT: G 257 MET cc_start: 0.7092 (mmp) cc_final: 0.6836 (mmt) REVERT: G 258 PHE cc_start: 0.7689 (m-10) cc_final: 0.7455 (m-10) outliers start: 19 outliers final: 12 residues processed: 233 average time/residue: 0.2577 time to fit residues: 89.9021 Evaluate side-chains 223 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 210 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain B residue 287 SER Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 83 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 171 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 157 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 127 optimal weight: 0.0060 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15200 Z= 0.185 Angle : 0.577 10.602 20734 Z= 0.270 Chirality : 0.042 0.217 2147 Planarity : 0.005 0.044 2582 Dihedral : 20.440 170.757 2394 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.12 % Rotamer: Outliers : 2.02 % Allowed : 8.79 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.71 (0.20), residues: 1773 helix: 1.07 (0.17), residues: 934 sheet: -1.61 (0.53), residues: 77 loop : 0.09 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 147 HIS 0.005 0.001 HIS B 111 PHE 0.021 0.002 PHE D 87 TYR 0.013 0.001 TYR F 399 ARG 0.002 0.000 ARG E 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 1.508 Fit side-chains REVERT: A 68 LEU cc_start: 0.6497 (tp) cc_final: 0.6230 (tt) REVERT: A 113 ASN cc_start: 0.7469 (m-40) cc_final: 0.7139 (m-40) REVERT: A 140 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7195 (t) REVERT: B 12 ARG cc_start: 0.6619 (mmp-170) cc_final: 0.5974 (mtm110) REVERT: B 137 LEU cc_start: 0.7390 (mt) cc_final: 0.7043 (mt) REVERT: B 227 VAL cc_start: 0.6943 (t) cc_final: 0.6703 (m) REVERT: B 317 ILE cc_start: 0.6721 (OUTLIER) cc_final: 0.6411 (mp) REVERT: B 362 MET cc_start: 0.7578 (mtp) cc_final: 0.7182 (ttm) REVERT: B 383 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7754 (mm-40) REVERT: B 431 HIS cc_start: 0.6629 (m-70) cc_final: 0.6148 (m170) REVERT: C 27 HIS cc_start: 0.5316 (m-70) cc_final: 0.4911 (p90) REVERT: C 74 GLU cc_start: 0.7168 (tt0) cc_final: 0.6507 (mm-30) REVERT: C 86 ARG cc_start: 0.6603 (ttm110) cc_final: 0.6287 (mtm-85) REVERT: C 141 SER cc_start: 0.8232 (t) cc_final: 0.7983 (t) REVERT: C 207 MET cc_start: 0.8388 (ttt) cc_final: 0.8173 (ttp) REVERT: C 212 MET cc_start: 0.6890 (mmt) cc_final: 0.6680 (mtm) REVERT: C 242 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7035 (mm-30) REVERT: C 246 MET cc_start: 0.7264 (mmm) cc_final: 0.6552 (mmm) REVERT: E 52 VAL cc_start: 0.2444 (OUTLIER) cc_final: 0.2231 (t) REVERT: F 249 ILE cc_start: 0.7153 (mt) cc_final: 0.6945 (tp) REVERT: F 325 ILE cc_start: 0.8116 (mm) cc_final: 0.7790 (tt) REVERT: F 352 SER cc_start: 0.7578 (t) cc_final: 0.7061 (m) REVERT: G 96 ASP cc_start: 0.6096 (t70) cc_final: 0.5450 (p0) REVERT: G 101 GLU cc_start: 0.6852 (pt0) cc_final: 0.6615 (pt0) REVERT: G 125 MET cc_start: 0.8393 (tpp) cc_final: 0.7961 (tpp) REVERT: G 136 MET cc_start: 0.5920 (tpp) cc_final: 0.4997 (mtm) REVERT: G 163 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7446 (mm-30) REVERT: G 223 ASP cc_start: 0.7275 (t0) cc_final: 0.7060 (t70) REVERT: G 246 MET cc_start: 0.8049 (mmt) cc_final: 0.7560 (mmt) REVERT: G 262 LEU cc_start: 0.7136 (tp) cc_final: 0.6844 (tp) outliers start: 29 outliers final: 17 residues processed: 246 average time/residue: 0.2467 time to fit residues: 91.5861 Evaluate side-chains 239 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 219 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 83 ASP Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.0470 chunk 119 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15200 Z= 0.197 Angle : 0.571 11.362 20734 Z= 0.265 Chirality : 0.042 0.191 2147 Planarity : 0.004 0.039 2582 Dihedral : 19.411 169.478 2394 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.07 % Rotamer: Outliers : 2.09 % Allowed : 9.34 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.68 (0.20), residues: 1773 helix: 1.04 (0.17), residues: 940 sheet: -1.46 (0.54), residues: 78 loop : 0.07 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 PHE 0.024 0.002 PHE D 87 TYR 0.014 0.001 TYR F 399 ARG 0.005 0.000 ARG B 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 228 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.5320 (OUTLIER) cc_final: 0.5062 (mm) REVERT: A 68 LEU cc_start: 0.6667 (tp) cc_final: 0.6429 (tt) REVERT: A 140 VAL cc_start: 0.7367 (OUTLIER) cc_final: 0.7087 (t) REVERT: A 144 PHE cc_start: 0.6993 (m-80) cc_final: 0.6723 (m-10) REVERT: B 7 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.6901 (p0) REVERT: B 12 ARG cc_start: 0.6708 (mmp-170) cc_final: 0.6156 (mtm110) REVERT: B 227 VAL cc_start: 0.7012 (t) cc_final: 0.6719 (m) REVERT: B 317 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6455 (mp) REVERT: B 343 MET cc_start: 0.7861 (ttp) cc_final: 0.7603 (ttp) REVERT: B 362 MET cc_start: 0.7633 (mtp) cc_final: 0.7091 (ttm) REVERT: B 431 HIS cc_start: 0.6582 (m-70) cc_final: 0.6009 (m170) REVERT: C 27 HIS cc_start: 0.5053 (m-70) cc_final: 0.4699 (p90) REVERT: C 74 GLU cc_start: 0.7141 (tt0) cc_final: 0.6488 (mm-30) REVERT: C 141 SER cc_start: 0.8259 (t) cc_final: 0.8006 (t) REVERT: C 242 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6907 (mm-30) REVERT: C 246 MET cc_start: 0.7356 (mmm) cc_final: 0.6566 (mmm) REVERT: F 140 MET cc_start: 0.5914 (mtp) cc_final: 0.5710 (mtm) REVERT: F 325 ILE cc_start: 0.7979 (mm) cc_final: 0.7728 (tt) REVERT: F 352 SER cc_start: 0.7578 (t) cc_final: 0.7068 (m) REVERT: F 431 HIS cc_start: 0.5695 (m-70) cc_final: 0.4987 (m-70) REVERT: G 64 MET cc_start: 0.7690 (mtt) cc_final: 0.7477 (mtm) REVERT: G 125 MET cc_start: 0.8372 (tpp) cc_final: 0.7932 (tpp) REVERT: G 136 MET cc_start: 0.6228 (tpp) cc_final: 0.5225 (mtm) REVERT: G 163 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7414 (mm-30) REVERT: G 223 ASP cc_start: 0.7316 (t0) cc_final: 0.7093 (t70) outliers start: 30 outliers final: 20 residues processed: 247 average time/residue: 0.2422 time to fit residues: 90.3334 Evaluate side-chains 244 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 220 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 414 ILE Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 195 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 2.9990 chunk 96 optimal weight: 0.0670 chunk 2 optimal weight: 0.0670 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15200 Z= 0.170 Angle : 0.541 8.980 20734 Z= 0.250 Chirality : 0.041 0.195 2147 Planarity : 0.004 0.041 2582 Dihedral : 18.656 178.636 2394 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 1.88 % Allowed : 9.55 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1773 helix: 1.16 (0.17), residues: 929 sheet: -1.49 (0.54), residues: 78 loop : 0.10 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 147 HIS 0.005 0.001 HIS F 212 PHE 0.022 0.001 PHE D 87 TYR 0.017 0.001 TYR G 267 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 224 time to evaluate : 1.699 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.6280 (OUTLIER) cc_final: 0.5937 (m) REVERT: A 47 LEU cc_start: 0.5310 (OUTLIER) cc_final: 0.5054 (mm) REVERT: A 68 LEU cc_start: 0.6634 (tp) cc_final: 0.6366 (tt) REVERT: A 140 VAL cc_start: 0.7408 (OUTLIER) cc_final: 0.7106 (t) REVERT: A 144 PHE cc_start: 0.6951 (m-80) cc_final: 0.6718 (m-10) REVERT: A 170 ASN cc_start: 0.7601 (m-40) cc_final: 0.7369 (m-40) REVERT: B 7 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6603 (m-30) REVERT: B 227 VAL cc_start: 0.6984 (t) cc_final: 0.6694 (m) REVERT: B 317 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6423 (mp) REVERT: B 343 MET cc_start: 0.7851 (ttp) cc_final: 0.7626 (ttp) REVERT: B 362 MET cc_start: 0.7702 (mtp) cc_final: 0.7099 (ttm) REVERT: B 427 ASP cc_start: 0.8056 (t70) cc_final: 0.7565 (t0) REVERT: B 431 HIS cc_start: 0.6598 (m-70) cc_final: 0.5856 (m170) REVERT: C 27 HIS cc_start: 0.5140 (m-70) cc_final: 0.4877 (p90) REVERT: C 74 GLU cc_start: 0.7016 (tt0) cc_final: 0.6318 (mm-30) REVERT: C 141 SER cc_start: 0.8264 (t) cc_final: 0.8038 (t) REVERT: C 242 GLU cc_start: 0.7370 (mt-10) cc_final: 0.7001 (mm-30) REVERT: C 246 MET cc_start: 0.7355 (mmm) cc_final: 0.6546 (mmm) REVERT: F 325 ILE cc_start: 0.7949 (mm) cc_final: 0.7742 (tt) REVERT: F 352 SER cc_start: 0.7570 (t) cc_final: 0.7073 (m) REVERT: F 431 HIS cc_start: 0.5828 (m-70) cc_final: 0.5091 (m-70) REVERT: G 64 MET cc_start: 0.7689 (mtt) cc_final: 0.7485 (mtm) REVERT: G 125 MET cc_start: 0.8421 (tpp) cc_final: 0.8007 (tpp) REVERT: G 136 MET cc_start: 0.6257 (tpp) cc_final: 0.5252 (mtm) REVERT: G 163 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7389 (mm-30) REVERT: G 223 ASP cc_start: 0.7327 (t0) cc_final: 0.7094 (t70) REVERT: G 246 MET cc_start: 0.8032 (mmt) cc_final: 0.7613 (mmp) REVERT: G 262 LEU cc_start: 0.7096 (tp) cc_final: 0.6849 (tp) outliers start: 27 outliers final: 18 residues processed: 242 average time/residue: 0.2427 time to fit residues: 88.7791 Evaluate side-chains 235 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 140 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15200 Z= 0.211 Angle : 0.568 10.484 20734 Z= 0.262 Chirality : 0.042 0.183 2147 Planarity : 0.004 0.039 2582 Dihedral : 18.386 164.563 2393 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 1.88 % Allowed : 9.76 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.71 (0.20), residues: 1773 helix: 1.06 (0.17), residues: 929 sheet: -1.56 (0.54), residues: 78 loop : 0.12 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 157 HIS 0.007 0.001 HIS F 212 PHE 0.024 0.002 PHE D 87 TYR 0.015 0.001 TYR F 399 ARG 0.003 0.000 ARG C 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.426 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.6403 (OUTLIER) cc_final: 0.6058 (m) REVERT: A 47 LEU cc_start: 0.5188 (OUTLIER) cc_final: 0.4923 (mm) REVERT: A 140 VAL cc_start: 0.7280 (OUTLIER) cc_final: 0.6990 (t) REVERT: A 144 PHE cc_start: 0.6925 (m-80) cc_final: 0.6688 (m-10) REVERT: A 170 ASN cc_start: 0.7636 (m-40) cc_final: 0.7359 (m-40) REVERT: B 227 VAL cc_start: 0.7038 (t) cc_final: 0.6735 (m) REVERT: B 317 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6352 (mp) REVERT: B 362 MET cc_start: 0.7749 (mtp) cc_final: 0.7162 (ttm) REVERT: B 431 HIS cc_start: 0.6705 (m-70) cc_final: 0.6075 (m170) REVERT: C 74 GLU cc_start: 0.7011 (tt0) cc_final: 0.6343 (mm-30) REVERT: C 141 SER cc_start: 0.8317 (t) cc_final: 0.8081 (t) REVERT: C 242 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6971 (mm-30) REVERT: C 246 MET cc_start: 0.7366 (mmm) cc_final: 0.6537 (mmm) REVERT: E 45 GLN cc_start: 0.6431 (mp10) cc_final: 0.5930 (mp10) REVERT: F 325 ILE cc_start: 0.7974 (mm) cc_final: 0.7774 (tt) REVERT: F 352 SER cc_start: 0.7602 (t) cc_final: 0.7113 (m) REVERT: F 431 HIS cc_start: 0.5955 (m-70) cc_final: 0.5214 (m-70) REVERT: G 64 MET cc_start: 0.7817 (mtt) cc_final: 0.7594 (mtm) REVERT: G 74 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6069 (mt-10) REVERT: G 125 MET cc_start: 0.8414 (tpp) cc_final: 0.7994 (tpp) REVERT: G 136 MET cc_start: 0.6240 (tpp) cc_final: 0.5218 (mtm) REVERT: G 163 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7400 (mm-30) REVERT: G 223 ASP cc_start: 0.7359 (t0) cc_final: 0.7145 (t70) outliers start: 27 outliers final: 20 residues processed: 241 average time/residue: 0.2548 time to fit residues: 92.9225 Evaluate side-chains 241 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 217 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 ASN B 279 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15200 Z= 0.201 Angle : 0.567 14.424 20734 Z= 0.260 Chirality : 0.042 0.182 2147 Planarity : 0.004 0.040 2582 Dihedral : 18.194 163.447 2393 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 2.30 % Allowed : 9.83 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.71 (0.20), residues: 1773 helix: 1.06 (0.17), residues: 929 sheet: -1.59 (0.55), residues: 78 loop : 0.11 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 PHE 0.024 0.001 PHE D 87 TYR 0.015 0.001 TYR G 267 ARG 0.003 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 221 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.6505 (OUTLIER) cc_final: 0.6223 (m) REVERT: A 47 LEU cc_start: 0.5255 (OUTLIER) cc_final: 0.4843 (mm) REVERT: A 70 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6963 (mtmm) REVERT: A 140 VAL cc_start: 0.7223 (OUTLIER) cc_final: 0.6938 (t) REVERT: A 144 PHE cc_start: 0.6857 (m-80) cc_final: 0.6613 (m-10) REVERT: A 170 ASN cc_start: 0.7664 (m-40) cc_final: 0.7151 (m-40) REVERT: B 227 VAL cc_start: 0.7034 (t) cc_final: 0.6726 (m) REVERT: B 317 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6377 (mp) REVERT: B 362 MET cc_start: 0.7774 (mtp) cc_final: 0.7144 (ttm) REVERT: B 431 HIS cc_start: 0.6704 (m-70) cc_final: 0.5972 (m170) REVERT: C 74 GLU cc_start: 0.7003 (tt0) cc_final: 0.6327 (mm-30) REVERT: C 242 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6982 (mm-30) REVERT: C 246 MET cc_start: 0.7352 (mmm) cc_final: 0.6512 (mmm) REVERT: E 125 MET cc_start: 0.5519 (mpp) cc_final: 0.3914 (mtm) REVERT: F 140 MET cc_start: 0.6037 (mtp) cc_final: 0.5807 (mtm) REVERT: F 352 SER cc_start: 0.7623 (t) cc_final: 0.7155 (m) REVERT: F 431 HIS cc_start: 0.5902 (m-70) cc_final: 0.5157 (m-70) REVERT: G 64 MET cc_start: 0.7754 (mtt) cc_final: 0.7534 (mtm) REVERT: G 125 MET cc_start: 0.8437 (tpp) cc_final: 0.8028 (tpp) REVERT: G 136 MET cc_start: 0.6431 (tpp) cc_final: 0.5423 (mtm) REVERT: G 223 ASP cc_start: 0.7366 (t0) cc_final: 0.7158 (t70) outliers start: 33 outliers final: 24 residues processed: 244 average time/residue: 0.2498 time to fit residues: 91.8956 Evaluate side-chains 247 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 167 CYS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 138 THR Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 33 optimal weight: 0.0370 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 279 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 15200 Z= 0.165 Angle : 0.531 8.331 20734 Z= 0.247 Chirality : 0.041 0.174 2147 Planarity : 0.004 0.041 2582 Dihedral : 17.830 163.179 2393 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 1.88 % Allowed : 10.60 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.82 (0.20), residues: 1773 helix: 1.19 (0.17), residues: 930 sheet: -1.58 (0.55), residues: 78 loop : 0.12 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 157 HIS 0.004 0.001 HIS F 212 PHE 0.024 0.001 PHE D 87 TYR 0.012 0.001 TYR G 177 ARG 0.002 0.000 ARG G 70 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.743 Fit side-chains revert: symmetry clash REVERT: A 25 VAL cc_start: 0.6485 (OUTLIER) cc_final: 0.6251 (m) REVERT: A 47 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4488 (mm) REVERT: A 70 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6778 (mtmm) REVERT: A 140 VAL cc_start: 0.7125 (OUTLIER) cc_final: 0.6877 (t) REVERT: A 144 PHE cc_start: 0.6803 (m-80) cc_final: 0.6596 (m-10) REVERT: A 170 ASN cc_start: 0.7588 (m-40) cc_final: 0.7201 (m-40) REVERT: B 227 VAL cc_start: 0.6956 (t) cc_final: 0.6689 (m) REVERT: B 317 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6404 (mp) REVERT: B 362 MET cc_start: 0.7760 (mtp) cc_final: 0.7117 (ttm) REVERT: B 431 HIS cc_start: 0.6737 (m-70) cc_final: 0.6184 (m170) REVERT: C 64 MET cc_start: 0.7905 (mtt) cc_final: 0.7545 (mtm) REVERT: C 74 GLU cc_start: 0.7001 (tt0) cc_final: 0.6304 (mm-30) REVERT: C 242 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7026 (mm-30) REVERT: C 246 MET cc_start: 0.7333 (mmm) cc_final: 0.6548 (mmm) REVERT: E 125 MET cc_start: 0.5433 (mpp) cc_final: 0.4000 (mtm) REVERT: F 140 MET cc_start: 0.6055 (mtp) cc_final: 0.5823 (mtm) REVERT: F 352 SER cc_start: 0.7584 (t) cc_final: 0.7112 (m) REVERT: F 362 MET cc_start: 0.6689 (ttm) cc_final: 0.6410 (ttm) REVERT: F 431 HIS cc_start: 0.5875 (m-70) cc_final: 0.5118 (m-70) REVERT: G 125 MET cc_start: 0.8457 (tpp) cc_final: 0.8057 (tpp) REVERT: G 136 MET cc_start: 0.6412 (tpp) cc_final: 0.5385 (mtm) REVERT: G 223 ASP cc_start: 0.7397 (t0) cc_final: 0.7175 (t70) REVERT: G 246 MET cc_start: 0.7974 (mmm) cc_final: 0.7533 (mmp) outliers start: 27 outliers final: 19 residues processed: 241 average time/residue: 0.2694 time to fit residues: 98.3532 Evaluate side-chains 237 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 0.8980 chunk 147 optimal weight: 0.0050 chunk 157 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 142 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15200 Z= 0.167 Angle : 0.528 8.177 20734 Z= 0.246 Chirality : 0.041 0.167 2147 Planarity : 0.004 0.040 2582 Dihedral : 17.604 162.658 2393 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.21 % Favored : 96.73 % Rotamer: Outliers : 1.88 % Allowed : 10.81 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.86 (0.20), residues: 1773 helix: 1.22 (0.17), residues: 928 sheet: -1.58 (0.58), residues: 73 loop : 0.13 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 157 HIS 0.005 0.001 HIS F 212 PHE 0.023 0.001 PHE D 87 TYR 0.016 0.001 TYR G 267 ARG 0.001 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 223 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 47 LEU cc_start: 0.4888 (OUTLIER) cc_final: 0.4565 (mm) REVERT: A 70 LYS cc_start: 0.7254 (mttm) cc_final: 0.6654 (mtmm) REVERT: A 140 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.6957 (t) REVERT: A 170 ASN cc_start: 0.7549 (m-40) cc_final: 0.7138 (m-40) REVERT: A 186 LEU cc_start: 0.6256 (mt) cc_final: 0.5753 (tp) REVERT: B 12 ARG cc_start: 0.7127 (mmp-170) cc_final: 0.6865 (mmp-170) REVERT: B 317 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6402 (mp) REVERT: B 362 MET cc_start: 0.7778 (mtp) cc_final: 0.7142 (ttm) REVERT: B 431 HIS cc_start: 0.6614 (m-70) cc_final: 0.6049 (m170) REVERT: C 64 MET cc_start: 0.7902 (mtt) cc_final: 0.7549 (mtm) REVERT: C 74 GLU cc_start: 0.7000 (tt0) cc_final: 0.6303 (mm-30) REVERT: C 242 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6958 (mm-30) REVERT: C 246 MET cc_start: 0.7333 (mmm) cc_final: 0.6547 (mmm) REVERT: E 125 MET cc_start: 0.5294 (mpp) cc_final: 0.4022 (mtm) REVERT: F 140 MET cc_start: 0.6091 (mtp) cc_final: 0.5864 (mtm) REVERT: F 352 SER cc_start: 0.7583 (t) cc_final: 0.7114 (m) REVERT: F 362 MET cc_start: 0.6688 (ttm) cc_final: 0.6403 (ttm) REVERT: F 431 HIS cc_start: 0.5917 (m-70) cc_final: 0.5137 (m-70) REVERT: G 64 MET cc_start: 0.8181 (mtm) cc_final: 0.7940 (mtp) REVERT: G 125 MET cc_start: 0.8432 (tpp) cc_final: 0.8026 (tpp) REVERT: G 136 MET cc_start: 0.6406 (tpp) cc_final: 0.5375 (mtm) REVERT: G 223 ASP cc_start: 0.7401 (t0) cc_final: 0.7180 (t70) outliers start: 27 outliers final: 21 residues processed: 242 average time/residue: 0.2680 time to fit residues: 97.6108 Evaluate side-chains 240 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 216 time to evaluate : 1.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 133 HIS Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 268 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.0570 chunk 101 optimal weight: 8.9990 chunk 78 optimal weight: 0.0570 chunk 115 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN C 227 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15200 Z= 0.156 Angle : 0.521 7.807 20734 Z= 0.243 Chirality : 0.040 0.162 2147 Planarity : 0.004 0.041 2582 Dihedral : 17.465 162.346 2393 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.01 % Rotamer: Outliers : 1.60 % Allowed : 11.44 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1773 helix: 1.25 (0.17), residues: 930 sheet: -1.57 (0.59), residues: 73 loop : 0.11 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 157 HIS 0.004 0.001 HIS F 212 PHE 0.037 0.001 PHE A 144 TYR 0.012 0.001 TYR G 177 ARG 0.002 0.000 ARG A 163 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.4783 (OUTLIER) cc_final: 0.4472 (mm) REVERT: A 70 LYS cc_start: 0.7242 (mttm) cc_final: 0.6616 (mtmm) REVERT: A 140 VAL cc_start: 0.7249 (OUTLIER) cc_final: 0.6981 (t) REVERT: A 170 ASN cc_start: 0.7489 (m-40) cc_final: 0.7052 (m-40) REVERT: B 7 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: B 12 ARG cc_start: 0.7186 (mmp-170) cc_final: 0.6806 (mmp-170) REVERT: B 317 ILE cc_start: 0.6726 (OUTLIER) cc_final: 0.6403 (mp) REVERT: B 362 MET cc_start: 0.7762 (mtp) cc_final: 0.7122 (ttm) REVERT: B 431 HIS cc_start: 0.6602 (m-70) cc_final: 0.6051 (m170) REVERT: C 64 MET cc_start: 0.7872 (mtt) cc_final: 0.7513 (mtm) REVERT: C 74 GLU cc_start: 0.6928 (tt0) cc_final: 0.6249 (mm-30) REVERT: C 242 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6812 (mm-30) REVERT: C 246 MET cc_start: 0.7332 (mmm) cc_final: 0.6548 (mmm) REVERT: F 140 MET cc_start: 0.6083 (mtp) cc_final: 0.5861 (mtm) REVERT: F 343 MET cc_start: 0.8366 (ttt) cc_final: 0.7827 (tmm) REVERT: F 352 SER cc_start: 0.7572 (t) cc_final: 0.7116 (m) REVERT: F 431 HIS cc_start: 0.5932 (m-70) cc_final: 0.5134 (m-70) REVERT: G 125 MET cc_start: 0.8422 (tpp) cc_final: 0.8011 (tpp) REVERT: G 136 MET cc_start: 0.6404 (tpp) cc_final: 0.5373 (mtm) REVERT: G 223 ASP cc_start: 0.7399 (t0) cc_final: 0.7186 (t70) REVERT: G 246 MET cc_start: 0.7972 (mmm) cc_final: 0.7534 (mmp) outliers start: 23 outliers final: 17 residues processed: 236 average time/residue: 0.2562 time to fit residues: 90.7486 Evaluate side-chains 238 residues out of total 1434 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 217 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 CYS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain F residue 216 PHE Chi-restraints excluded: chain F residue 242 VAL Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 195 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 0.0970 chunk 142 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN E 62 GLN ** E 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.143903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.128367 restraints weight = 15778.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.107781 restraints weight = 38339.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.104159 restraints weight = 38094.292| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15200 Z= 0.183 Angle : 0.544 10.178 20734 Z= 0.250 Chirality : 0.041 0.158 2147 Planarity : 0.004 0.041 2582 Dihedral : 17.377 161.544 2393 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.16 % Favored : 96.79 % Rotamer: Outliers : 1.74 % Allowed : 11.37 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % 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: 0.85 (0.20), residues: 1773 helix: 1.18 (0.17), residues: 927 sheet: -1.56 (0.59), residues: 73 loop : 0.16 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 157 HIS 0.006 0.001 HIS F 212 PHE 0.023 0.001 PHE D 87 TYR 0.018 0.001 TYR G 267 ARG 0.002 0.000 ARG F 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2811.27 seconds wall clock time: 52 minutes 1.91 seconds (3121.91 seconds total)