Starting phenix.real_space_refine on Thu Feb 15 19:03:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj5_25916/02_2024/7tj5_25916_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj5_25916/02_2024/7tj5_25916.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj5_25916/02_2024/7tj5_25916_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj5_25916/02_2024/7tj5_25916_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj5_25916/02_2024/7tj5_25916_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj5_25916/02_2024/7tj5_25916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj5_25916/02_2024/7tj5_25916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj5_25916/02_2024/7tj5_25916_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tj5_25916/02_2024/7tj5_25916_updated.pdb" } resolution = 2.41 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= 0.001 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8732 2.51 5 N 2088 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 274": "OE1" <-> "OE2" Residue "A GLU 347": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B GLU 347": "OE1" <-> "OE2" Residue "C GLU 274": "OE1" <-> "OE2" Residue "C GLU 347": "OE1" <-> "OE2" Residue "D GLU 274": "OE1" <-> "OE2" Residue "D GLU 347": "OE1" <-> "OE2" 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: 13152 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "B" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "C" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "D" Number of atoms: 3121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3121 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 23, 'TRANS': 368} Chain breaks: 1 Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-3': 2, 'D21:plan-2': 4, 'D21:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-3': 2, 'D21:plan-2': 4, 'D21:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-3': 2, 'D21:plan-2': 4, 'D21:plan-1': 4} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 167 Unusual residues: {'D21': 7} Classifications: {'RNA': 1, 'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 207 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'D21:plan-3': 2, 'D21:plan-2': 4, 'D21:plan-1': 4} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 7.81, per 1000 atoms: 0.59 Number of scatterers: 13152 At special positions: 0 Unit cell: (103.5, 103.5, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2296 8.00 N 2088 7.00 C 8732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 5.47 Conformation dependent library (CDL) restraints added in 2.5 seconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 8 sheets defined 58.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 11 through 35 removed outlier: 3.622A pdb=" N TRP A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 44 through 62 removed outlier: 4.216A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 109 through 122 removed outlier: 3.784A pdb=" N LYS A 114 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 115 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 119 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 157 Processing helix chain 'A' and resid 166 through 181 Processing helix chain 'A' and resid 194 through 223 Processing helix chain 'A' and resid 227 through 245 Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.145A pdb=" N GLU A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 297 removed outlier: 6.557A pdb=" N ASP A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.527A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 414 Processing helix chain 'B' and resid 11 through 35 removed outlier: 3.622A pdb=" N TRP B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 44 through 62 removed outlier: 4.216A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 109 through 122 removed outlier: 3.784A pdb=" N LYS B 114 " --> pdb=" O ARG B 111 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 115 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 119 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 157 Processing helix chain 'B' and resid 166 through 181 Processing helix chain 'B' and resid 194 through 223 Processing helix chain 'B' and resid 227 through 245 Processing helix chain 'B' and resid 250 through 267 Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.145A pdb=" N GLU B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 297 removed outlier: 6.557A pdb=" N ASP B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 394 through 403 removed outlier: 3.527A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 414 Processing helix chain 'C' and resid 11 through 35 removed outlier: 3.623A pdb=" N TRP C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 44 through 62 removed outlier: 4.216A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 109 through 122 removed outlier: 3.784A pdb=" N LYS C 114 " --> pdb=" O ARG C 111 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C 115 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 119 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 157 Processing helix chain 'C' and resid 166 through 181 Processing helix chain 'C' and resid 194 through 223 Processing helix chain 'C' and resid 227 through 245 Processing helix chain 'C' and resid 250 through 267 Processing helix chain 'C' and resid 272 through 278 removed outlier: 4.145A pdb=" N GLU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 297 removed outlier: 6.557A pdb=" N ASP C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 394 through 403 removed outlier: 3.527A pdb=" N SER C 402 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 414 Processing helix chain 'D' and resid 11 through 35 removed outlier: 3.622A pdb=" N TRP D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 44 through 62 removed outlier: 4.216A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 109 through 122 removed outlier: 3.785A pdb=" N LYS D 114 " --> pdb=" O ARG D 111 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU D 115 " --> pdb=" O LEU D 112 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN D 119 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 157 Processing helix chain 'D' and resid 166 through 181 Processing helix chain 'D' and resid 194 through 223 Processing helix chain 'D' and resid 227 through 245 Processing helix chain 'D' and resid 250 through 267 Processing helix chain 'D' and resid 272 through 278 removed outlier: 4.145A pdb=" N GLU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 297 removed outlier: 6.557A pdb=" N ASP D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL D 295 " --> pdb=" O ILE D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 394 through 403 removed outlier: 3.527A pdb=" N SER D 402 " --> pdb=" O ASP D 398 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 414 Processing sheet with id= A, first strand: chain 'A' and resid 318 through 320 Processing sheet with id= B, first strand: chain 'A' and resid 380 through 383 removed outlier: 3.698A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 318 through 320 Processing sheet with id= D, first strand: chain 'B' and resid 380 through 383 removed outlier: 3.699A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 318 through 320 Processing sheet with id= F, first strand: chain 'C' and resid 380 through 383 removed outlier: 3.699A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 318 through 320 Processing sheet with id= H, first strand: chain 'D' and resid 380 through 383 removed outlier: 3.699A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1980 1.31 - 1.44: 3468 1.44 - 1.56: 7852 1.56 - 1.69: 72 1.69 - 1.81: 48 Bond restraints: 13420 Sorted by residual: bond pdb=" C LYS A 303 " pdb=" N GLY A 304 " ideal model delta sigma weight residual 1.331 1.244 0.087 1.40e-02 5.10e+03 3.88e+01 bond pdb=" C LYS D 303 " pdb=" N GLY D 304 " ideal model delta sigma weight residual 1.331 1.244 0.087 1.40e-02 5.10e+03 3.87e+01 bond pdb=" C LYS B 303 " pdb=" N GLY B 304 " ideal model delta sigma weight residual 1.331 1.244 0.087 1.40e-02 5.10e+03 3.87e+01 bond pdb=" C LYS C 303 " pdb=" N GLY C 304 " ideal model delta sigma weight residual 1.331 1.245 0.087 1.40e-02 5.10e+03 3.84e+01 bond pdb=" C PHE B 302 " pdb=" N LYS B 303 " ideal model delta sigma weight residual 1.331 1.251 0.079 1.31e-02 5.83e+03 3.65e+01 ... (remaining 13415 not shown) Histogram of bond angle deviations from ideal: 100.30 - 111.21: 5646 111.21 - 122.12: 10357 122.12 - 133.03: 2049 133.03 - 143.95: 28 143.95 - 154.86: 44 Bond angle restraints: 18124 Sorted by residual: angle pdb=" C40 D21 A 508 " pdb=" C41 D21 A 508 " pdb=" C42 D21 A 508 " ideal model delta sigma weight residual 120.01 154.86 -34.85 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C40 D21 C 602 " pdb=" C41 D21 C 602 " pdb=" C42 D21 C 602 " ideal model delta sigma weight residual 120.01 154.83 -34.82 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C40 D21 B 602 " pdb=" C41 D21 B 602 " pdb=" C42 D21 B 602 " ideal model delta sigma weight residual 120.01 154.83 -34.82 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C40 D21 D 602 " pdb=" C41 D21 D 602 " pdb=" C42 D21 D 602 " ideal model delta sigma weight residual 120.01 154.80 -34.79 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C39 D21 C 606 " pdb=" C40 D21 C 606 " pdb=" C41 D21 C 606 " ideal model delta sigma weight residual 120.02 154.66 -34.64 3.00e+00 1.11e-01 1.33e+02 ... (remaining 18119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.30: 7604 31.30 - 62.59: 448 62.59 - 93.89: 72 93.89 - 125.19: 8 125.19 - 156.49: 4 Dihedral angle restraints: 8136 sinusoidal: 3524 harmonic: 4612 Sorted by residual: dihedral pdb=" C5' CMP C 603 " pdb=" O5' CMP C 603 " pdb=" P CMP C 603 " pdb=" O1P CMP C 603 " ideal model delta sinusoidal sigma weight residual 60.00 173.99 -113.99 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 173.99 -113.99 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" C5' CMP B 603 " pdb=" O5' CMP B 603 " pdb=" P CMP B 603 " pdb=" O1P CMP B 603 " ideal model delta sinusoidal sigma weight residual 60.00 173.99 -113.99 1 2.00e+01 2.50e-03 3.38e+01 ... (remaining 8133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1915 0.089 - 0.177: 172 0.177 - 0.266: 5 0.266 - 0.354: 4 0.354 - 0.443: 4 Chirality restraints: 2100 Sorted by residual: chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CB ILE D 58 " pdb=" CA ILE D 58 " pdb=" CG1 ILE D 58 " pdb=" CG2 ILE D 58 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.89e+00 chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 2097 not shown) Planarity restraints: 2204 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 116 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C ILE D 116 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE D 116 " -0.019 2.00e-02 2.50e+03 pdb=" N SER D 117 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 116 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.97e+00 pdb=" C ILE A 116 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE A 116 " 0.019 2.00e-02 2.50e+03 pdb=" N SER A 117 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 116 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" C ILE C 116 " 0.052 2.00e-02 2.50e+03 pdb=" O ILE C 116 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 117 " -0.017 2.00e-02 2.50e+03 ... (remaining 2201 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3235 2.81 - 3.33: 12025 3.33 - 3.85: 21505 3.85 - 4.38: 24745 4.38 - 4.90: 42897 Nonbonded interactions: 104407 Sorted by model distance: nonbonded pdb=" CD2 TYR B 327 " pdb=" NE ARG B 330 " model vdw 2.285 3.420 nonbonded pdb=" CD2 TYR C 327 " pdb=" NE ARG C 330 " model vdw 2.286 3.420 nonbonded pdb=" CD2 TYR D 327 " pdb=" NE ARG D 330 " model vdw 2.286 3.420 nonbonded pdb=" CD2 TYR A 327 " pdb=" NE ARG A 330 " model vdw 2.286 3.420 nonbonded pdb=" O TYR D 262 " pdb=" OG1 THR D 266 " model vdw 2.299 2.440 ... (remaining 104402 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 10 through 415 or (resid 505 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 506 and (name C34 or name C35 or name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C \ 44)) or (resid 507 and (name C15 or name C16 or name C19 or name C20 or name C21 \ or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name O17 or name O18 or name O22 or \ name O30 or name O32)) or (resid 508 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 o \ r name C44)))) selection = (chain 'B' and (resid 10 through 415 or (resid 605 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 606 and (name C34 or name C35 or name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C \ 44)) or (resid 607 and (name C15 or name C16 or name C19 or name C20 or name C21 \ or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name O17 or name O18 or name O22 or \ name O30 or name O32)) or (resid 608 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 o \ r name C44)))) selection = (chain 'C' and (resid 10 through 415 or (resid 605 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 606 and (name C34 or name C35 or name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C \ 44)) or (resid 607 and (name C15 or name C16 or name C19 or name C20 or name C21 \ or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name O17 or name O18 or name O22 or \ name O30 or name O32)) or (resid 608 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 o \ r name C44)))) selection = (chain 'D' and (resid 10 through 415 or (resid 605 and (name C31 or name C33 or \ name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or name C40 \ or name C41)) or (resid 606 and (name C34 or name C35 or name C36 or name C37 o \ r name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or name C \ 44)) or (resid 607 and (name C15 or name C16 or name C19 or name C20 or name C21 \ or name C31 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ C38 or name C39 or name C40 or name C41 or name O17 or name O18 or name O22 or \ name O30 or name O32)) or (resid 608 and (name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 o \ r name C44)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.340 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 38.490 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.070 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 13420 Z= 0.382 Angle : 1.915 34.848 18124 Z= 0.750 Chirality : 0.053 0.443 2100 Planarity : 0.008 0.075 2204 Dihedral : 19.672 156.486 5160 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.22 % Allowed : 19.12 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.48 (0.22), residues: 1552 helix: 1.08 (0.16), residues: 1016 sheet: -1.15 (0.45), residues: 124 loop : -0.97 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 264 HIS 0.004 0.001 HIS D 292 PHE 0.016 0.001 PHE A 365 TYR 0.016 0.002 TYR A 404 ARG 0.006 0.001 ARG D 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 138 time to evaluate : 1.529 Fit side-chains outliers start: 3 outliers final: 4 residues processed: 141 average time/residue: 2.0599 time to fit residues: 307.3283 Evaluate side-chains 65 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain D residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 122 optimal weight: 0.0020 chunk 47 optimal weight: 0.0370 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 141 optimal weight: 0.5980 overall best weight: 0.5066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN B 364 GLN C 364 GLN D 364 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13420 Z= 0.182 Angle : 0.633 11.661 18124 Z= 0.301 Chirality : 0.042 0.317 2100 Planarity : 0.005 0.059 2204 Dihedral : 16.397 162.339 2208 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.46 % Allowed : 21.58 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1552 helix: 1.70 (0.17), residues: 1012 sheet: -0.72 (0.47), residues: 124 loop : -0.53 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 264 HIS 0.003 0.001 HIS D 292 PHE 0.005 0.001 PHE D 309 TYR 0.011 0.001 TYR D 11 ARG 0.005 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 77 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 8 residues processed: 98 average time/residue: 1.4735 time to fit residues: 156.9274 Evaluate side-chains 72 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN D 364 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13420 Z= 0.208 Angle : 0.597 7.275 18124 Z= 0.292 Chirality : 0.042 0.299 2100 Planarity : 0.005 0.055 2204 Dihedral : 14.115 130.159 2200 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.68 % Allowed : 22.62 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1552 helix: 1.87 (0.17), residues: 1012 sheet: -0.15 (0.50), residues: 112 loop : -0.22 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 264 HIS 0.005 0.001 HIS C 292 PHE 0.005 0.001 PHE B 366 TYR 0.009 0.001 TYR A 170 ARG 0.003 0.000 ARG C 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 83 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 7 residues processed: 114 average time/residue: 1.3577 time to fit residues: 168.3486 Evaluate side-chains 71 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13420 Z= 0.205 Angle : 0.619 9.564 18124 Z= 0.297 Chirality : 0.042 0.301 2100 Planarity : 0.004 0.045 2204 Dihedral : 13.351 132.883 2200 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.64 % Allowed : 23.36 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.22), residues: 1552 helix: 2.10 (0.17), residues: 980 sheet: -0.16 (0.49), residues: 112 loop : -0.12 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.004 0.001 HIS D 292 PHE 0.005 0.001 PHE A 242 TYR 0.012 0.001 TYR C 11 ARG 0.003 0.000 ARG C 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 94 average time/residue: 1.5526 time to fit residues: 157.9193 Evaluate side-chains 74 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.0170 chunk 85 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13420 Z= 0.188 Angle : 0.629 16.422 18124 Z= 0.297 Chirality : 0.042 0.303 2100 Planarity : 0.004 0.041 2204 Dihedral : 12.520 130.715 2200 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.79 % Allowed : 22.54 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.22), residues: 1552 helix: 2.16 (0.17), residues: 980 sheet: -0.19 (0.48), residues: 112 loop : 0.02 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.004 0.001 HIS B 292 PHE 0.005 0.001 PHE C 309 TYR 0.013 0.001 TYR B 11 ARG 0.001 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 100 average time/residue: 1.5603 time to fit residues: 168.7479 Evaluate side-chains 80 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 0.0970 chunk 37 optimal weight: 10.0000 chunk 150 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 49 optimal weight: 0.0170 chunk 79 optimal weight: 0.7980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13420 Z= 0.168 Angle : 0.600 11.388 18124 Z= 0.288 Chirality : 0.042 0.302 2100 Planarity : 0.004 0.040 2204 Dihedral : 11.460 130.891 2200 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.12 % Allowed : 23.59 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.03 (0.23), residues: 1552 helix: 2.15 (0.17), residues: 984 sheet: -0.62 (0.46), residues: 124 loop : 0.20 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 264 HIS 0.004 0.001 HIS C 292 PHE 0.005 0.001 PHE C 366 TYR 0.014 0.001 TYR D 11 ARG 0.001 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 92 average time/residue: 1.4864 time to fit residues: 148.4814 Evaluate side-chains 81 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 150 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13420 Z= 0.188 Angle : 0.639 18.786 18124 Z= 0.303 Chirality : 0.042 0.300 2100 Planarity : 0.004 0.039 2204 Dihedral : 11.067 130.571 2200 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.19 % Allowed : 23.44 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.22), residues: 1552 helix: 2.17 (0.17), residues: 988 sheet: -0.44 (0.53), residues: 100 loop : 0.20 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 264 HIS 0.004 0.001 HIS C 292 PHE 0.004 0.001 PHE B 309 TYR 0.013 0.001 TYR B 11 ARG 0.001 0.000 ARG B 254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 95 average time/residue: 1.6058 time to fit residues: 164.5838 Evaluate side-chains 77 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 0.0040 chunk 118 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 144 optimal weight: 0.3980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13420 Z= 0.187 Angle : 0.631 9.981 18124 Z= 0.305 Chirality : 0.042 0.301 2100 Planarity : 0.004 0.038 2204 Dihedral : 10.663 130.612 2200 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.97 % Allowed : 23.96 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.15 (0.23), residues: 1552 helix: 2.19 (0.17), residues: 988 sheet: -0.40 (0.53), residues: 100 loop : 0.27 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 264 HIS 0.004 0.001 HIS C 292 PHE 0.007 0.001 PHE B 365 TYR 0.014 0.001 TYR D 11 ARG 0.008 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 89 average time/residue: 1.5736 time to fit residues: 151.9103 Evaluate side-chains 80 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0970 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13420 Z= 0.196 Angle : 0.650 13.807 18124 Z= 0.312 Chirality : 0.042 0.304 2100 Planarity : 0.004 0.038 2204 Dihedral : 10.480 130.630 2200 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.74 % Allowed : 24.26 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.18 (0.23), residues: 1552 helix: 2.19 (0.17), residues: 988 sheet: -0.37 (0.53), residues: 100 loop : 0.34 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 264 HIS 0.004 0.001 HIS A 292 PHE 0.006 0.001 PHE A 365 TYR 0.014 0.001 TYR B 11 ARG 0.007 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 85 average time/residue: 1.5128 time to fit residues: 139.6358 Evaluate side-chains 81 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 143 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13420 Z= 0.194 Angle : 0.651 12.312 18124 Z= 0.313 Chirality : 0.042 0.305 2100 Planarity : 0.004 0.038 2204 Dihedral : 10.277 130.706 2200 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.67 % Allowed : 24.26 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.23), residues: 1552 helix: 2.18 (0.17), residues: 988 sheet: -0.34 (0.53), residues: 100 loop : 0.42 (0.32), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 264 HIS 0.003 0.001 HIS D 292 PHE 0.006 0.001 PHE A 365 TYR 0.015 0.001 TYR D 11 ARG 0.007 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 80 average time/residue: 1.6364 time to fit residues: 141.9430 Evaluate side-chains 81 residues out of total 1344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 410 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.110037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.072381 restraints weight = 28063.366| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.52 r_work: 0.3008 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13420 Z= 0.195 Angle : 0.652 13.055 18124 Z= 0.313 Chirality : 0.042 0.306 2100 Planarity : 0.004 0.038 2204 Dihedral : 10.185 130.527 2200 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.89 % Allowed : 24.18 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.23), residues: 1552 helix: 2.19 (0.17), residues: 988 sheet: -0.32 (0.54), residues: 100 loop : 0.45 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 264 HIS 0.004 0.001 HIS C 292 PHE 0.006 0.001 PHE A 365 TYR 0.016 0.001 TYR B 11 ARG 0.006 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4276.92 seconds wall clock time: 77 minutes 3.94 seconds (4623.94 seconds total)