Starting phenix.real_space_refine on Thu Jul 2 16:35:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gz3_34389/07_2026/8gz3_34389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz3_34389/07_2026/8gz3_34389.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gz3_34389/07_2026/8gz3_34389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz3_34389/07_2026/8gz3_34389.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gz3_34389/07_2026/8gz3_34389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz3_34389/07_2026/8gz3_34389.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gz3_34389/07_2026/8gz3_34389.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gz3_34389/07_2026/8gz3_34389.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.007 sd= 0.191 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 2 7.16 5 P 3 5.49 5 S 33 5.16 5 C 5476 2.51 5 N 1485 2.21 5 O 1543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8542 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1030 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4187 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 506} Chain breaks: 3 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 3, 'ASN:plan1': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "L" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1055 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'CIS': 1, 'TRANS': 209} Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 633 Unresolved non-hydrogen dihedrals: 211 Planarities with less than four sites: {'UNK:plan-1': 211} Unresolved non-hydrogen planarities: 211 Chain: "H" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1070 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 428 Unresolved non-hydrogen angles: 642 Unresolved non-hydrogen dihedrals: 214 Planarities with less than four sites: {'UNK:plan-1': 214} Unresolved non-hydrogen planarities: 214 Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 945 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 216 Unusual residues: {'FAD': 1, 'HEM': 2, 'LBN': 1, 'NAG': 2} Classifications: {'undetermined': 6, 'water': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.65, per 1000 atoms: 0.19 Number of scatterers: 8542 At special positions: 0 Unit cell: (72.8344, 80.2234, 184.725, 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 2 26.01 S 33 16.00 P 3 15.00 O 1543 8.00 N 1485 7.00 C 5476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 244 " - pdb=" SG CYS B 257 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 604 " - " ASN B 132 " " NAG B 605 " - " ASN B 240 " " NAG C 1 " - " ASN B 149 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 198.5 milliseconds 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 16 sheets defined 58.6% alpha, 40.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 5 through 31 removed outlier: 4.223A pdb=" N TRP A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 54 removed outlier: 4.212A pdb=" N GLY A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 4.329A pdb=" N MET A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 86 removed outlier: 3.652A pdb=" N ARG A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 100 through 103 removed outlier: 3.705A pdb=" N PHE A 103 " --> pdb=" O PRO A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 104 through 128 removed outlier: 4.130A pdb=" N LEU A 109 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 33 removed outlier: 3.519A pdb=" N TYR B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 40 removed outlier: 3.688A pdb=" N PHE B 39 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 69 Proline residue: B 56 - end of helix removed outlier: 3.562A pdb=" N MET B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 68 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 3.723A pdb=" N SER B 82 " --> pdb=" O PHE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 95 removed outlier: 3.895A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 131 removed outlier: 3.628A pdb=" N LYS B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 173 through 192 removed outlier: 3.848A pdb=" N ILE B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 201 Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.525A pdb=" N ILE B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 246 through 251 removed outlier: 5.159A pdb=" N SER B 249 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 293 removed outlier: 3.630A pdb=" N TRP B 272 " --> pdb=" O MET B 268 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLY B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 359 through 370 Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 413 through 430 removed outlier: 3.757A pdb=" N ALA B 417 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER B 418 " --> pdb=" O THR B 414 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 468 removed outlier: 3.634A pdb=" N ALA B 455 " --> pdb=" O PHE B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 527 removed outlier: 3.760A pdb=" N LYS B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 554 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.752A pdb=" N UNK L 83 " --> pdb=" O UNK L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 127 removed outlier: 3.594A pdb=" N UNK L 127 " --> pdb=" O UNK L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 4.033A pdb=" N UNK L 189 " --> pdb=" O UNK L 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'H' and resid 191 through 197 removed outlier: 4.492A pdb=" N UNK H 195 " --> pdb=" O UNK H 191 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N UNK H 196 " --> pdb=" O UNK H 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.623A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 111 Processing sheet with id=AA1, first strand: chain 'B' and resid 229 through 231 Processing sheet with id=AA2, first strand: chain 'B' and resid 296 through 303 removed outlier: 5.420A pdb=" N ILE B 297 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS B 313 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 307 " --> pdb=" O HIS B 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 338 through 341 Processing sheet with id=AA4, first strand: chain 'B' and resid 509 through 511 removed outlier: 6.176A pdb=" N ILE B 439 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASN B 477 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE B 441 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR B 479 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TRP B 443 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 403 " --> pdb=" O GLY B 533 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N PHE B 535 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 509 through 511 removed outlier: 6.176A pdb=" N ILE B 439 " --> pdb=" O SER B 475 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ASN B 477 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N PHE B 441 " --> pdb=" O ASN B 477 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR B 479 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TRP B 443 " --> pdb=" O TYR B 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.550A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N UNK L 37 " --> pdb=" O UNK L 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.185A pdb=" N UNK L 131 " --> pdb=" O UNK L 181 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N UNK L 181 " --> pdb=" O UNK L 131 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N UNK L 133 " --> pdb=" O UNK L 179 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N UNK L 179 " --> pdb=" O UNK L 133 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N UNK L 135 " --> pdb=" O UNK L 177 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N UNK L 177 " --> pdb=" O UNK L 135 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N UNK L 137 " --> pdb=" O UNK L 175 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N UNK L 175 " --> pdb=" O UNK L 137 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N UNK L 159 " --> pdb=" O SER N 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.306A pdb=" N UNK L 148 " --> pdb=" O UNK L 155 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N UNK L 198 " --> pdb=" O UNK L 203 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N UNK L 203 " --> pdb=" O UNK L 198 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 4 through 8 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.602A pdb=" N UNK H 50 " --> pdb=" O UNK H 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N UNK H 59 " --> pdb=" O UNK H 51 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 45 through 47 removed outlier: 3.594A pdb=" N UNK H 45 " --> pdb=" O UNK H 41 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N UNK H 108 " --> pdb=" O UNK H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.677A pdb=" N UNK H 150 " --> pdb=" O UNK H 181 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N UNK H 181 " --> pdb=" O UNK H 150 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N UNK H 180 " --> pdb=" O UNK H 176 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N UNK H 176 " --> pdb=" O UNK H 180 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N UNK H 182 " --> pdb=" O UNK H 174 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N UNK H 174 " --> pdb=" O UNK H 182 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N UNK H 184 " --> pdb=" O UNK H 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 156 through 160 Processing sheet with id=AB6, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.724A pdb=" N ALA N 33 " --> pdb=" O THR N 99 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1311 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: 0.98 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 3058 1.37 - 1.56: 5603 1.56 - 1.75: 8 1.75 - 1.93: 48 1.93 - 2.12: 6 Bond restraints: 8723 Sorted by residual: bond pdb=" CA TRP B 443 " pdb=" C TRP B 443 " ideal model delta sigma weight residual 1.523 1.459 0.063 1.23e-02 6.61e+03 2.65e+01 bond pdb=" CA LYS B 314 " pdb=" C LYS B 314 " ideal model delta sigma weight residual 1.520 1.459 0.061 1.20e-02 6.94e+03 2.62e+01 bond pdb=" CA SER B 333 " pdb=" C SER B 333 " ideal model delta sigma weight residual 1.520 1.465 0.054 1.12e-02 7.97e+03 2.37e+01 bond pdb=" C PRO B 339 " pdb=" O PRO B 339 " ideal model delta sigma weight residual 1.233 1.187 0.046 1.06e-02 8.90e+03 1.89e+01 bond pdb=" CA GLU B 309 " pdb=" C GLU B 309 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.22e-02 6.72e+03 1.77e+01 ... (remaining 8718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 11305 2.78 - 5.56: 523 5.56 - 8.34: 100 8.34 - 11.11: 36 11.11 - 13.89: 5 Bond angle restraints: 11969 Sorted by residual: angle pdb=" N ASP B 360 " pdb=" CA ASP B 360 " pdb=" C ASP B 360 " ideal model delta sigma weight residual 111.07 122.65 -11.58 1.07e+00 8.73e-01 1.17e+02 angle pdb=" N PHE B 473 " pdb=" CA PHE B 473 " pdb=" C PHE B 473 " ideal model delta sigma weight residual 111.07 121.39 -10.32 1.07e+00 8.73e-01 9.31e+01 angle pdb=" N GLY B 560 " pdb=" CA GLY B 560 " pdb=" C GLY B 560 " ideal model delta sigma weight residual 111.93 122.35 -10.42 1.15e+00 7.56e-01 8.22e+01 angle pdb=" N GLU B 336 " pdb=" CA GLU B 336 " pdb=" C GLU B 336 " ideal model delta sigma weight residual 109.59 123.48 -13.89 1.61e+00 3.86e-01 7.45e+01 angle pdb=" N LEU B 211 " pdb=" CA LEU B 211 " pdb=" C LEU B 211 " ideal model delta sigma weight residual 113.20 103.52 9.68 1.21e+00 6.83e-01 6.40e+01 ... (remaining 11964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.02: 4896 33.02 - 66.04: 66 66.04 - 99.06: 10 99.06 - 132.08: 3 132.08 - 165.09: 2 Dihedral angle restraints: 4977 sinusoidal: 1431 harmonic: 3546 Sorted by residual: dihedral pdb=" C2C HEM B 603 " pdb=" C3C HEM B 603 " pdb=" CAC HEM B 603 " pdb=" CBC HEM B 603 " ideal model delta sinusoidal sigma weight residual 0.00 -51.11 51.11 2 1.00e+01 1.00e-02 2.91e+01 dihedral pdb=" O5' FAD B 601 " pdb=" O3P FAD B 601 " pdb=" P FAD B 601 " pdb=" PA FAD B 601 " ideal model delta sinusoidal sigma weight residual 298.23 133.14 165.09 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C LYS B 306 " pdb=" N LYS B 306 " pdb=" CA LYS B 306 " pdb=" CB LYS B 306 " ideal model delta harmonic sigma weight residual -122.60 -133.51 10.91 0 2.50e+00 1.60e-01 1.91e+01 ... (remaining 4974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1196 0.118 - 0.236: 171 0.236 - 0.355: 35 0.355 - 0.473: 15 0.473 - 0.591: 3 Chirality restraints: 1420 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.65e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.74e+01 chirality pdb=" CA LYS B 306 " pdb=" N LYS B 306 " pdb=" C LYS B 306 " pdb=" CB LYS B 306 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.73e+00 ... (remaining 1417 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS B 119 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C HIS B 119 " -0.079 2.00e-02 2.50e+03 pdb=" O HIS B 119 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU B 120 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 16 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C GLY N 16 " -0.075 2.00e-02 2.50e+03 pdb=" O GLY N 16 " 0.029 2.00e-02 2.50e+03 pdb=" N SER N 17 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK L 84 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C UNK L 84 " -0.073 2.00e-02 2.50e+03 pdb=" O UNK L 84 " 0.028 2.00e-02 2.50e+03 pdb=" N UNK L 85 " 0.025 2.00e-02 2.50e+03 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 291 2.69 - 3.25: 8053 3.25 - 3.80: 13290 3.80 - 4.35: 16665 4.35 - 4.90: 28156 Nonbonded interactions: 66455 Sorted by model distance: nonbonded pdb=" NE2 HIS B 222 " pdb="FE HEM B 602 " model vdw 2.142 3.080 nonbonded pdb=" O GLY B 179 " pdb=" OG1 THR B 183 " model vdw 2.213 3.040 nonbonded pdb=" O TYR N 100 " pdb=" OH TYR N 105 " model vdw 2.281 3.040 nonbonded pdb=" O THR N 32 " pdb=" NH2 ARG N 72 " model vdw 2.313 3.120 nonbonded pdb=" O ALA A 101 " pdb=" OG1 THR A 107 " model vdw 2.316 3.040 ... (remaining 66450 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'H' and resid 4 through 219) selection = chain 'L' } 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: 1.850 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.012 0.199 8732 Z= 0.746 Angle : 1.456 13.893 11988 Z= 0.816 Chirality : 0.098 0.591 1420 Planarity : 0.008 0.081 1506 Dihedral : 13.722 165.095 2667 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.74 % Allowed : 8.53 % Favored : 89.73 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.28), residues: 777 helix: 0.60 (0.25), residues: 377 sheet: -0.40 (0.44), residues: 123 loop : -0.88 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 31 TYR 0.020 0.003 TYR B 476 PHE 0.025 0.003 PHE B 62 TRP 0.021 0.003 TRP B 361 HIS 0.007 0.002 HIS B 239 Details of bonding type rmsd/Z covalent geometry : bond 0.01223 / 0.75 ( 8723) covalent geometry : angle 1.45161 / 0.82 (11969) SS BOND : bond 0.02201 / 1.05 ( 2) SS BOND : angle 3.66878 / 1.85 ( 4) hydrogen bonds : bond 0.16892 / 11.75 ( 460) hydrogen bonds : angle 7.51033 / 5.53 ( 1311) Misc. bond : bond 0.13048 / 6.74 ( 2) link_BETA1-4 : bond 0.00553 / 0.26 ( 2) link_BETA1-4 : angle 3.63524 / 2.05 ( 6) link_NAG-ASN : bond 0.00701 / 0.34 ( 3) link_NAG-ASN : angle 2.21386 / 1.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.318 Fit side-chains REVERT: A 73 MET cc_start: 0.8197 (mmm) cc_final: 0.7860 (mmm) REVERT: B 92 ARG cc_start: 0.7449 (mtp180) cc_final: 0.7229 (mtt-85) REVERT: B 203 GLU cc_start: 0.8167 (tt0) cc_final: 0.7752 (pm20) REVERT: B 234 GLU cc_start: 0.7225 (tt0) cc_final: 0.6967 (mp0) REVERT: B 246 GLN cc_start: 0.8374 (mm110) cc_final: 0.8108 (mm-40) REVERT: B 465 MET cc_start: 0.9042 (mmt) cc_final: 0.8805 (mmt) REVERT: B 513 ARG cc_start: 0.7976 (mtt180) cc_final: 0.6964 (mtt-85) REVERT: B 537 CYS cc_start: 0.9172 (t) cc_final: 0.8887 (t) REVERT: N 65 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8487 (tttm) REVERT: N 71 SER cc_start: 0.7953 (t) cc_final: 0.7361 (p) outliers start: 11 outliers final: 5 residues processed: 141 average time/residue: 0.1000 time to fit residues: 19.1795 Evaluate side-chains 94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 330 PRO Chi-restraints excluded: chain B residue 530 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.145536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.135148 restraints weight = 10825.489| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.13 r_work: 0.3226 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.311 8732 Z= 0.142 Angle : 0.628 12.814 11988 Z= 0.295 Chirality : 0.037 0.164 1420 Planarity : 0.004 0.077 1506 Dihedral : 10.505 174.470 1341 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.53 % Allowed : 10.58 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.29), residues: 777 helix: 1.21 (0.25), residues: 379 sheet: -0.55 (0.44), residues: 128 loop : -0.34 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 118 TYR 0.012 0.001 TYR B 201 PHE 0.021 0.002 PHE B 62 TRP 0.014 0.001 TRP B 337 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 8723) covalent geometry : angle 0.62504 / 0.29 (11969) SS BOND : bond 0.02831 / 1.35 ( 2) SS BOND : angle 1.64077 / 0.93 ( 4) hydrogen bonds : bond 0.03982 / 2.77 ( 460) hydrogen bonds : angle 4.88960 / 3.58 ( 1311) Misc. bond : bond 0.28462 / 14.42 ( 2) link_BETA1-4 : bond 0.00572 / 0.28 ( 2) link_BETA1-4 : angle 1.64228 / 0.86 ( 6) link_NAG-ASN : bond 0.00478 / 0.25 ( 3) link_NAG-ASN : angle 1.62040 / 0.89 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.284 Fit side-chains REVERT: B 103 MET cc_start: 0.8970 (mtp) cc_final: 0.8744 (mtm) REVERT: B 318 LYS cc_start: 0.8314 (mtpp) cc_final: 0.8034 (mtmm) REVERT: B 381 LYS cc_start: 0.7778 (mttt) cc_final: 0.7207 (tttm) REVERT: B 508 LYS cc_start: 0.7614 (tmtt) cc_final: 0.6983 (tptp) REVERT: B 513 ARG cc_start: 0.7879 (mtt180) cc_final: 0.6595 (mtt180) REVERT: B 537 CYS cc_start: 0.8630 (t) cc_final: 0.8412 (t) REVERT: N 71 SER cc_start: 0.8452 (t) cc_final: 0.8163 (p) REVERT: N 103 ASN cc_start: 0.8127 (t0) cc_final: 0.7780 (t0) outliers start: 16 outliers final: 7 residues processed: 100 average time/residue: 0.1134 time to fit residues: 15.4355 Evaluate side-chains 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 HIS ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.140427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.130466 restraints weight = 10755.996| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 0.95 r_work: 0.3116 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.302 8732 Z= 0.234 Angle : 0.715 16.043 11988 Z= 0.329 Chirality : 0.041 0.165 1420 Planarity : 0.005 0.073 1506 Dihedral : 9.397 132.902 1335 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 3.48 % Allowed : 11.22 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.29), residues: 777 helix: 0.95 (0.26), residues: 376 sheet: -0.73 (0.44), residues: 129 loop : -0.16 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 92 TYR 0.016 0.002 TYR B 29 PHE 0.018 0.002 PHE B 454 TRP 0.020 0.002 TRP B 337 HIS 0.008 0.002 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.23 ( 8723) covalent geometry : angle 0.71172 / 0.33 (11969) SS BOND : bond 0.01336 / 0.64 ( 2) SS BOND : angle 1.80081 / 0.99 ( 4) hydrogen bonds : bond 0.04301 / 3.03 ( 460) hydrogen bonds : angle 4.87009 / 3.56 ( 1311) Misc. bond : bond 0.24095 / 12.44 ( 2) link_BETA1-4 : bond 0.00301 / 0.14 ( 2) link_BETA1-4 : angle 1.50040 / 0.80 ( 6) link_NAG-ASN : bond 0.00453 / 0.22 ( 3) link_NAG-ASN : angle 1.90649 / 1.01 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.275 Fit side-chains REVERT: A 12 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: A 35 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7961 (mm-40) REVERT: B 318 LYS cc_start: 0.8424 (mtpp) cc_final: 0.8167 (mtmm) REVERT: B 381 LYS cc_start: 0.7840 (mttt) cc_final: 0.7289 (tttm) REVERT: B 508 LYS cc_start: 0.7673 (tmtt) cc_final: 0.6973 (tptp) REVERT: B 513 ARG cc_start: 0.7956 (mtt180) cc_final: 0.6984 (mtt180) REVERT: B 537 CYS cc_start: 0.8565 (t) cc_final: 0.8331 (t) REVERT: N 71 SER cc_start: 0.8495 (t) cc_final: 0.8242 (m) outliers start: 22 outliers final: 10 residues processed: 90 average time/residue: 0.1109 time to fit residues: 13.4934 Evaluate side-chains 81 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 0.0070 chunk 79 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.140103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.126642 restraints weight = 11000.326| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.41 r_work: 0.3103 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.224 8732 Z= 0.121 Angle : 0.585 14.443 11988 Z= 0.266 Chirality : 0.035 0.151 1420 Planarity : 0.004 0.062 1506 Dihedral : 8.682 127.841 1333 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.69 % Allowed : 12.48 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.30), residues: 777 helix: 1.26 (0.26), residues: 375 sheet: -0.64 (0.44), residues: 128 loop : 0.09 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.010 0.001 TYR B 280 PHE 0.016 0.001 PHE B 454 TRP 0.011 0.001 TRP B 337 HIS 0.008 0.001 HIS B 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8723) covalent geometry : angle 0.58216 / 0.27 (11969) SS BOND : bond 0.00720 / 0.35 ( 2) SS BOND : angle 1.30145 / 0.74 ( 4) hydrogen bonds : bond 0.03442 / 2.41 ( 460) hydrogen bonds : angle 4.51759 / 3.27 ( 1311) Misc. bond : bond 0.19312 / 9.86 ( 2) link_BETA1-4 : bond 0.00321 / 0.16 ( 2) link_BETA1-4 : angle 1.41592 / 0.75 ( 6) link_NAG-ASN : bond 0.00312 / 0.16 ( 3) link_NAG-ASN : angle 1.51408 / 0.84 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.248 Fit side-chains REVERT: A 35 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7969 (mm-40) REVERT: B 318 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8166 (mtmm) REVERT: B 336 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7407 (mm-30) REVERT: B 381 LYS cc_start: 0.7803 (mttt) cc_final: 0.7185 (tttm) REVERT: B 508 LYS cc_start: 0.7573 (tmtt) cc_final: 0.6911 (tptp) REVERT: B 513 ARG cc_start: 0.7953 (mtt180) cc_final: 0.6903 (mtt180) REVERT: B 537 CYS cc_start: 0.8737 (t) cc_final: 0.8497 (t) REVERT: N 71 SER cc_start: 0.8352 (t) cc_final: 0.8077 (m) outliers start: 17 outliers final: 7 residues processed: 84 average time/residue: 0.1131 time to fit residues: 12.8172 Evaluate side-chains 79 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 40 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.138962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.125208 restraints weight = 10947.838| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.42 r_work: 0.3062 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.249 8732 Z= 0.181 Angle : 0.634 15.651 11988 Z= 0.286 Chirality : 0.037 0.154 1420 Planarity : 0.004 0.056 1506 Dihedral : 8.362 120.457 1333 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.84 % Allowed : 13.90 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 777 helix: 1.17 (0.26), residues: 377 sheet: -0.63 (0.44), residues: 129 loop : 0.10 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 118 TYR 0.013 0.002 TYR B 29 PHE 0.014 0.002 PHE B 215 TRP 0.015 0.001 TRP B 337 HIS 0.007 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 8723) covalent geometry : angle 0.63121 / 0.29 (11969) SS BOND : bond 0.00330 / 0.17 ( 2) SS BOND : angle 1.52285 / 0.85 ( 4) hydrogen bonds : bond 0.03742 / 2.62 ( 460) hydrogen bonds : angle 4.53493 / 3.28 ( 1311) Misc. bond : bond 0.20166 / 10.38 ( 2) link_BETA1-4 : bond 0.00385 / 0.19 ( 2) link_BETA1-4 : angle 1.42459 / 0.75 ( 6) link_NAG-ASN : bond 0.00306 / 0.15 ( 3) link_NAG-ASN : angle 1.60438 / 0.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.270 Fit side-chains REVERT: A 8 MET cc_start: 0.8709 (mmt) cc_final: 0.8477 (mmt) REVERT: A 35 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8000 (mm-40) REVERT: B 318 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8270 (mtmm) REVERT: B 381 LYS cc_start: 0.7820 (mttt) cc_final: 0.7180 (tttm) REVERT: B 508 LYS cc_start: 0.7555 (tmtt) cc_final: 0.6881 (tptp) REVERT: B 513 ARG cc_start: 0.7970 (mtt180) cc_final: 0.7124 (mtt-85) REVERT: B 537 CYS cc_start: 0.8782 (t) cc_final: 0.8554 (t) REVERT: N 71 SER cc_start: 0.8587 (t) cc_final: 0.8368 (m) outliers start: 18 outliers final: 11 residues processed: 80 average time/residue: 0.1074 time to fit residues: 11.7532 Evaluate side-chains 80 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.0060 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.138984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.124880 restraints weight = 10966.265| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.45 r_work: 0.3068 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.211 8732 Z= 0.150 Angle : 0.593 14.521 11988 Z= 0.268 Chirality : 0.036 0.145 1420 Planarity : 0.003 0.045 1506 Dihedral : 7.927 114.473 1333 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.37 % Allowed : 14.53 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.30), residues: 777 helix: 1.30 (0.26), residues: 379 sheet: -0.57 (0.44), residues: 129 loop : 0.10 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 118 TYR 0.011 0.001 TYR B 201 PHE 0.013 0.001 PHE B 454 TRP 0.013 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 8723) covalent geometry : angle 0.59052 / 0.27 (11969) SS BOND : bond 0.00634 / 0.31 ( 2) SS BOND : angle 1.32126 / 0.74 ( 4) hydrogen bonds : bond 0.03494 / 2.44 ( 460) hydrogen bonds : angle 4.43050 / 3.19 ( 1311) Misc. bond : bond 0.18244 / 9.31 ( 2) link_BETA1-4 : bond 0.00375 / 0.18 ( 2) link_BETA1-4 : angle 1.38928 / 0.73 ( 6) link_NAG-ASN : bond 0.00222 / 0.11 ( 3) link_NAG-ASN : angle 1.43079 / 0.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.285 Fit side-chains REVERT: A 35 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7972 (mm-40) REVERT: B 318 LYS cc_start: 0.8534 (mtpp) cc_final: 0.8220 (mtmt) REVERT: B 336 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7499 (mm-30) REVERT: B 381 LYS cc_start: 0.7783 (mttt) cc_final: 0.7175 (tttm) REVERT: B 508 LYS cc_start: 0.7538 (tmtt) cc_final: 0.6863 (tptp) REVERT: B 513 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7084 (mtt-85) REVERT: B 537 CYS cc_start: 0.8779 (t) cc_final: 0.8559 (t) REVERT: N 71 SER cc_start: 0.8596 (t) cc_final: 0.8374 (m) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 0.1079 time to fit residues: 13.0017 Evaluate side-chains 78 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 94 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.137658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.123923 restraints weight = 11072.023| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.38 r_work: 0.3047 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.245 8732 Z= 0.200 Angle : 0.655 15.709 11988 Z= 0.295 Chirality : 0.038 0.148 1420 Planarity : 0.004 0.047 1506 Dihedral : 8.026 112.190 1333 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.00 % Allowed : 14.85 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.29), residues: 777 helix: 1.13 (0.26), residues: 381 sheet: -0.53 (0.45), residues: 123 loop : -0.07 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 73 TYR 0.014 0.002 TYR B 29 PHE 0.015 0.002 PHE B 215 TRP 0.016 0.002 TRP B 337 HIS 0.007 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 ( 8723) covalent geometry : angle 0.65286 / 0.29 (11969) SS BOND : bond 0.00376 / 0.19 ( 2) SS BOND : angle 1.54702 / 0.87 ( 4) hydrogen bonds : bond 0.03839 / 2.69 ( 460) hydrogen bonds : angle 4.54561 / 3.29 ( 1311) Misc. bond : bond 0.20281 / 10.41 ( 2) link_BETA1-4 : bond 0.00311 / 0.15 ( 2) link_BETA1-4 : angle 1.39473 / 0.73 ( 6) link_NAG-ASN : bond 0.00275 / 0.13 ( 3) link_NAG-ASN : angle 1.58474 / 0.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.283 Fit side-chains REVERT: A 35 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7976 (mm-40) REVERT: B 318 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8337 (mtmt) REVERT: B 381 LYS cc_start: 0.7819 (mttt) cc_final: 0.7314 (tttm) REVERT: B 508 LYS cc_start: 0.7652 (tmtt) cc_final: 0.6904 (tptp) REVERT: B 513 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7069 (mtt-85) REVERT: B 537 CYS cc_start: 0.8737 (t) cc_final: 0.8516 (t) outliers start: 19 outliers final: 12 residues processed: 82 average time/residue: 0.1085 time to fit residues: 12.1676 Evaluate side-chains 85 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 116 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.140215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.127560 restraints weight = 10812.273| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.23 r_work: 0.3104 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 8732 Z= 0.131 Angle : 0.585 14.282 11988 Z= 0.264 Chirality : 0.035 0.144 1420 Planarity : 0.003 0.045 1506 Dihedral : 7.770 107.254 1333 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.05 % Allowed : 16.27 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.29), residues: 777 helix: 1.34 (0.26), residues: 379 sheet: -0.45 (0.45), residues: 123 loop : -0.04 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.011 0.001 TYR A 37 PHE 0.012 0.001 PHE B 454 TRP 0.011 0.001 TRP B 337 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 8723) covalent geometry : angle 0.58285 / 0.26 (11969) SS BOND : bond 0.00441 / 0.22 ( 2) SS BOND : angle 1.28472 / 0.72 ( 4) hydrogen bonds : bond 0.03384 / 2.37 ( 460) hydrogen bonds : angle 4.38522 / 3.15 ( 1311) Misc. bond : bond 0.16956 / 8.61 ( 2) link_BETA1-4 : bond 0.00346 / 0.17 ( 2) link_BETA1-4 : angle 1.38418 / 0.72 ( 6) link_NAG-ASN : bond 0.00178 / 0.09 ( 3) link_NAG-ASN : angle 1.30144 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.310 Fit side-chains REVERT: A 12 GLU cc_start: 0.8355 (mp0) cc_final: 0.8148 (mp0) REVERT: A 35 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7946 (mm-40) REVERT: B 199 ARG cc_start: 0.6430 (tmt170) cc_final: 0.5716 (ttp80) REVERT: B 318 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8304 (mtmt) REVERT: B 336 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7458 (mm-30) REVERT: B 381 LYS cc_start: 0.7759 (mttt) cc_final: 0.7165 (tttm) REVERT: B 508 LYS cc_start: 0.7641 (tmtt) cc_final: 0.6909 (tptp) REVERT: B 513 ARG cc_start: 0.7816 (mtt180) cc_final: 0.6876 (mtt-85) outliers start: 13 outliers final: 11 residues processed: 82 average time/residue: 0.1065 time to fit residues: 11.8116 Evaluate side-chains 83 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 292 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.135527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.122468 restraints weight = 11017.425| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.24 r_work: 0.3038 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.318 8732 Z= 0.348 Angle : 0.810 17.118 11988 Z= 0.368 Chirality : 0.044 0.199 1420 Planarity : 0.005 0.073 1506 Dihedral : 8.468 110.321 1333 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.16 % Allowed : 15.64 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.29), residues: 777 helix: 0.76 (0.25), residues: 379 sheet: -0.64 (0.44), residues: 122 loop : -0.26 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 73 TYR 0.020 0.002 TYR B 152 PHE 0.016 0.003 PHE B 215 TRP 0.019 0.003 TRP B 337 HIS 0.010 0.002 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00822 / 0.35 ( 8723) covalent geometry : angle 0.80788 / 0.37 (11969) SS BOND : bond 0.00390 / 0.20 ( 2) SS BOND : angle 1.91658 / 1.05 ( 4) hydrogen bonds : bond 0.04670 / 3.27 ( 460) hydrogen bonds : angle 4.92084 / 3.57 ( 1311) Misc. bond : bond 0.25224 / 13.03 ( 2) link_BETA1-4 : bond 0.00203 / 0.10 ( 2) link_BETA1-4 : angle 1.36136 / 0.72 ( 6) link_NAG-ASN : bond 0.00477 / 0.23 ( 3) link_NAG-ASN : angle 1.98299 / 1.05 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.305 Fit side-chains REVERT: A 35 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7857 (mm-40) REVERT: B 199 ARG cc_start: 0.6376 (tmt170) cc_final: 0.6107 (tmt170) REVERT: B 397 ASP cc_start: 0.8126 (p0) cc_final: 0.7524 (p0) REVERT: B 513 ARG cc_start: 0.7912 (mtt180) cc_final: 0.7092 (mtt-85) outliers start: 20 outliers final: 15 residues processed: 81 average time/residue: 0.1046 time to fit residues: 11.6534 Evaluate side-chains 85 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 428 CYS Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 449 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 552 SER Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 0.5980 chunk 106 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 52 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.138948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.126354 restraints weight = 10890.520| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.22 r_work: 0.3102 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.214 8732 Z= 0.127 Angle : 0.599 14.243 11988 Z= 0.270 Chirality : 0.035 0.162 1420 Planarity : 0.003 0.047 1506 Dihedral : 7.886 104.383 1333 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.74 % Allowed : 17.06 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.29), residues: 777 helix: 1.22 (0.26), residues: 377 sheet: -0.65 (0.44), residues: 124 loop : -0.10 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 118 TYR 0.011 0.001 TYR A 37 PHE 0.013 0.001 PHE B 454 TRP 0.011 0.001 TRP B 424 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8723) covalent geometry : angle 0.59683 / 0.27 (11969) SS BOND : bond 0.00441 / 0.22 ( 2) SS BOND : angle 1.31575 / 0.73 ( 4) hydrogen bonds : bond 0.03443 / 2.40 ( 460) hydrogen bonds : angle 4.51146 / 3.25 ( 1311) Misc. bond : bond 0.18742 / 9.55 ( 2) link_BETA1-4 : bond 0.00323 / 0.16 ( 2) link_BETA1-4 : angle 1.45886 / 0.76 ( 6) link_NAG-ASN : bond 0.00202 / 0.10 ( 3) link_NAG-ASN : angle 1.29554 / 0.72 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1554 Ramachandran restraints generated. 777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.290 Fit side-chains REVERT: A 35 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.7823 (mm-40) REVERT: A 73 MET cc_start: 0.8127 (tpt) cc_final: 0.7796 (tpt) REVERT: B 199 ARG cc_start: 0.6347 (tmt170) cc_final: 0.5590 (ttp80) REVERT: B 508 LYS cc_start: 0.7681 (tmtt) cc_final: 0.6923 (tptp) REVERT: B 513 ARG cc_start: 0.7829 (mtt180) cc_final: 0.6694 (mtt180) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.0975 time to fit residues: 10.3816 Evaluate side-chains 79 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 312 MET Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain N residue 101 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 111 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.137255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.125009 restraints weight = 10977.366| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.18 r_work: 0.3088 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.245 8732 Z= 0.206 Angle : 0.661 15.352 11988 Z= 0.299 Chirality : 0.038 0.162 1420 Planarity : 0.004 0.048 1506 Dihedral : 7.945 100.401 1333 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.05 % Allowed : 16.43 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.29), residues: 777 helix: 1.14 (0.26), residues: 377 sheet: -0.69 (0.43), residues: 124 loop : -0.13 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 118 TYR 0.018 0.002 TYR N 80 PHE 0.014 0.002 PHE B 215 TRP 0.014 0.002 TRP B 337 HIS 0.007 0.001 HIS B 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 ( 8723) covalent geometry : angle 0.65870 / 0.30 (11969) SS BOND : bond 0.00392 / 0.20 ( 2) SS BOND : angle 1.69532 / 0.94 ( 4) hydrogen bonds : bond 0.03846 / 2.69 ( 460) hydrogen bonds : angle 4.58868 / 3.31 ( 1311) Misc. bond : bond 0.20454 / 10.49 ( 2) link_BETA1-4 : bond 0.00253 / 0.13 ( 2) link_BETA1-4 : angle 1.38871 / 0.73 ( 6) link_NAG-ASN : bond 0.00277 / 0.13 ( 3) link_NAG-ASN : angle 1.50982 / 0.83 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2033.30 seconds wall clock time: 35 minutes 42.02 seconds (2142.02 seconds total)