Starting phenix.real_space_refine on Tue Mar 3 23:36:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gz3_34389/03_2026/8gz3_34389.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz3_34389/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gz3_34389/03_2026/8gz3_34389.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz3_34389/03_2026/8gz3_34389.map" model { file = "/net/cci-nas-00/data/ceres_data/8gz3_34389/03_2026/8gz3_34389.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz3_34389/03_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 9 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: 10 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.85, per 1000 atoms: 0.22 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: 0.64 Conformation dependent library (CDL) restraints added in 170.0 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: 0.33 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: 1.57 Time building geometry restraints manager: 0.81 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: 5034 33.02 - 66.04: 70 66.04 - 99.06: 19 99.06 - 132.08: 7 132.08 - 165.09: 2 Dihedral angle restraints: 5132 sinusoidal: 1586 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 5129 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: 1.920 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.420 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 : 15.002 165.095 2822 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 covalent geometry : bond 0.01223 ( 8723) covalent geometry : angle 1.45161 (11969) SS BOND : bond 0.02201 ( 2) SS BOND : angle 3.66878 ( 4) hydrogen bonds : bond 0.16892 ( 460) hydrogen bonds : angle 7.51033 ( 1311) Misc. bond : bond 0.13048 ( 2) link_BETA1-4 : bond 0.00553 ( 2) link_BETA1-4 : angle 3.63524 ( 6) link_NAG-ASN : bond 0.00701 ( 3) link_NAG-ASN : angle 2.21386 ( 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 : 0.270 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: 0.0994 time to fit residues: 18.9662 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 : 0.172 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3547 r_free = 0.3547 target = 0.147244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.137413 restraints weight = 10716.281| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.97 r_work: 0.3232 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.304 8732 Z= 0.139 Angle : 0.631 12.115 11988 Z= 0.296 Chirality : 0.037 0.160 1420 Planarity : 0.004 0.074 1506 Dihedral : 12.097 175.830 1496 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 2.69 % Allowed : 10.90 % Favored : 86.41 % 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: 0.52 (0.29), residues: 777 helix: 1.23 (0.26), residues: 375 sheet: -0.56 (0.44), residues: 128 loop : -0.29 (0.36), residues: 274 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 0.015 0.001 TRP B 337 HIS 0.004 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8723) covalent geometry : angle 0.62743 (11969) SS BOND : bond 0.00611 ( 2) SS BOND : angle 1.40422 ( 4) hydrogen bonds : bond 0.03907 ( 460) hydrogen bonds : angle 4.87263 ( 1311) Misc. bond : bond 0.27651 ( 2) link_BETA1-4 : bond 0.00668 ( 2) link_BETA1-4 : angle 2.21154 ( 6) link_NAG-ASN : bond 0.00536 ( 3) link_NAG-ASN : angle 1.57876 ( 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 106 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.233 Fit side-chains REVERT: B 318 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7983 (mtmm) REVERT: B 381 LYS cc_start: 0.7720 (mttt) cc_final: 0.7181 (tttm) REVERT: B 508 LYS cc_start: 0.7620 (tmtt) cc_final: 0.6995 (tptp) REVERT: B 513 ARG cc_start: 0.7875 (mtt180) cc_final: 0.6589 (mtt180) REVERT: B 537 CYS cc_start: 0.8583 (t) cc_final: 0.8355 (t) REVERT: N 71 SER cc_start: 0.8423 (t) cc_final: 0.8121 (p) REVERT: N 103 ASN cc_start: 0.8113 (t0) cc_final: 0.7758 (t0) outliers start: 17 outliers final: 6 residues processed: 101 average time/residue: 0.1099 time to fit residues: 14.6460 Evaluate side-chains 83 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 52 optimal weight: 0.0570 chunk 67 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3462 r_free = 0.3462 target = 0.140051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.129257 restraints weight = 10815.223| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.07 r_work: 0.3115 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.281 8732 Z= 0.202 Angle : 0.690 15.933 11988 Z= 0.315 Chirality : 0.040 0.182 1420 Planarity : 0.005 0.070 1506 Dihedral : 10.309 131.135 1488 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.77 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: 0.42 (0.29), residues: 777 helix: 1.05 (0.26), residues: 376 sheet: -0.74 (0.44), residues: 129 loop : -0.09 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 92 TYR 0.016 0.002 TYR B 29 PHE 0.019 0.002 PHE B 454 TRP 0.019 0.002 TRP B 337 HIS 0.008 0.002 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8723) covalent geometry : angle 0.68649 (11969) SS BOND : bond 0.01344 ( 2) SS BOND : angle 1.29936 ( 4) hydrogen bonds : bond 0.04083 ( 460) hydrogen bonds : angle 4.77132 ( 1311) Misc. bond : bond 0.22822 ( 2) link_BETA1-4 : bond 0.00421 ( 2) link_BETA1-4 : angle 2.17308 ( 6) link_NAG-ASN : bond 0.00437 ( 3) link_NAG-ASN : angle 1.79361 ( 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 96 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.273 Fit side-chains REVERT: B 318 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8228 (mtmm) REVERT: B 381 LYS cc_start: 0.7810 (mttt) cc_final: 0.7282 (tttm) REVERT: B 508 LYS cc_start: 0.7595 (tmtt) cc_final: 0.6945 (tptp) REVERT: B 513 ARG cc_start: 0.7964 (mtt180) cc_final: 0.6992 (mtt180) REVERT: B 537 CYS cc_start: 0.8611 (t) cc_final: 0.8368 (t) REVERT: N 71 SER cc_start: 0.8420 (t) cc_final: 0.8129 (m) outliers start: 22 outliers final: 12 residues processed: 90 average time/residue: 0.1057 time to fit residues: 12.7093 Evaluate side-chains 78 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 VAL 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: 3.9990 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 0.0570 chunk 79 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 112 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3492 r_free = 0.3492 target = 0.142606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.131137 restraints weight = 10896.506| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.11 r_work: 0.3159 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.202 8732 Z= 0.105 Angle : 0.560 13.839 11988 Z= 0.255 Chirality : 0.035 0.166 1420 Planarity : 0.003 0.061 1506 Dihedral : 9.441 126.637 1488 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.53 % Allowed : 12.80 % Favored : 84.68 % 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: 1.40 (0.26), residues: 375 sheet: -0.68 (0.44), residues: 129 loop : 0.04 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.010 0.001 TYR A 37 PHE 0.016 0.001 PHE B 454 TRP 0.010 0.001 TRP B 337 HIS 0.010 0.001 HIS B 449 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8723) covalent geometry : angle 0.55734 (11969) SS BOND : bond 0.01057 ( 2) SS BOND : angle 1.24265 ( 4) hydrogen bonds : bond 0.03273 ( 460) hydrogen bonds : angle 4.42721 ( 1311) Misc. bond : bond 0.17425 ( 2) link_BETA1-4 : bond 0.00463 ( 2) link_BETA1-4 : angle 1.96871 ( 6) link_NAG-ASN : bond 0.00319 ( 3) link_NAG-ASN : angle 1.39720 ( 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 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.260 Fit side-chains REVERT: A 12 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: B 33 TYR cc_start: 0.8909 (m-80) cc_final: 0.8625 (m-80) REVERT: B 199 ARG cc_start: 0.6599 (tmt170) cc_final: 0.5936 (ttp80) REVERT: B 318 LYS cc_start: 0.8393 (mtpp) cc_final: 0.8095 (mtmm) REVERT: B 336 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7370 (mm-30) REVERT: B 381 LYS cc_start: 0.7611 (mttt) cc_final: 0.7078 (tttm) REVERT: B 406 LEU cc_start: 0.8645 (mt) cc_final: 0.8437 (mp) REVERT: B 508 LYS cc_start: 0.7549 (tmtt) cc_final: 0.6922 (tptp) REVERT: B 513 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7014 (mtt-85) REVERT: B 537 CYS cc_start: 0.8582 (t) cc_final: 0.8374 (t) REVERT: N 71 SER cc_start: 0.8243 (t) cc_final: 0.7928 (m) outliers start: 16 outliers final: 7 residues processed: 87 average time/residue: 0.1042 time to fit residues: 12.1792 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 : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU 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 B residue 523 ILE 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: 1.9990 chunk 24 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3429 r_free = 0.3429 target = 0.137270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.121737 restraints weight = 11025.910| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.64 r_work: 0.3006 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.277 8732 Z= 0.222 Angle : 0.690 16.415 11988 Z= 0.311 Chirality : 0.039 0.183 1420 Planarity : 0.004 0.055 1506 Dihedral : 8.964 115.463 1488 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.16 % Allowed : 14.06 % Favored : 82.78 % 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: 0.56 (0.29), residues: 777 helix: 1.08 (0.26), residues: 377 sheet: -0.65 (0.44), residues: 129 loop : 0.10 (0.37), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 198 TYR 0.015 0.002 TYR B 29 PHE 0.014 0.002 PHE B 62 TRP 0.018 0.002 TRP B 337 HIS 0.008 0.002 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 8723) covalent geometry : angle 0.68693 (11969) SS BOND : bond 0.01022 ( 2) SS BOND : angle 1.61136 ( 4) hydrogen bonds : bond 0.04026 ( 460) hydrogen bonds : angle 4.64590 ( 1311) Misc. bond : bond 0.21678 ( 2) link_BETA1-4 : bond 0.00264 ( 2) link_BETA1-4 : angle 1.69407 ( 6) link_NAG-ASN : bond 0.00366 ( 3) link_NAG-ASN : angle 1.79565 ( 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 88 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.296 Fit side-chains REVERT: A 8 MET cc_start: 0.8751 (mmt) cc_final: 0.8401 (mmt) REVERT: B 318 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8258 (mtmt) REVERT: B 381 LYS cc_start: 0.7687 (mttt) cc_final: 0.7252 (tttm) REVERT: B 397 ASP cc_start: 0.7965 (p0) cc_final: 0.7641 (p0) REVERT: B 508 LYS cc_start: 0.7568 (tmtt) cc_final: 0.6919 (tptp) REVERT: B 513 ARG cc_start: 0.7946 (mtt180) cc_final: 0.6970 (mtt180) REVERT: B 537 CYS cc_start: 0.8624 (t) cc_final: 0.8421 (t) REVERT: N 83 MET cc_start: 0.9087 (mtm) cc_final: 0.8876 (mtp) outliers start: 20 outliers final: 9 residues processed: 82 average time/residue: 0.0953 time to fit residues: 10.6527 Evaluate side-chains 78 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 449 HIS Chi-restraints excluded: chain B residue 523 ILE Chi-restraints excluded: chain B residue 530 THR 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: 10.0000 chunk 70 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3451 r_free = 0.3451 target = 0.139139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.124365 restraints weight = 10942.332| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.44 r_work: 0.3072 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.220 8732 Z= 0.145 Angle : 0.606 14.924 11988 Z= 0.273 Chirality : 0.036 0.172 1420 Planarity : 0.003 0.046 1506 Dihedral : 8.727 110.574 1488 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.53 % Allowed : 14.53 % Favored : 82.94 % 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: 0.72 (0.30), residues: 777 helix: 1.24 (0.26), residues: 379 sheet: -0.56 (0.44), residues: 129 loop : 0.11 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 118 TYR 0.011 0.001 TYR B 29 PHE 0.013 0.001 PHE B 454 TRP 0.012 0.001 TRP B 337 HIS 0.006 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8723) covalent geometry : angle 0.60369 (11969) SS BOND : bond 0.00853 ( 2) SS BOND : angle 1.38621 ( 4) hydrogen bonds : bond 0.03500 ( 460) hydrogen bonds : angle 4.46377 ( 1311) Misc. bond : bond 0.18852 ( 2) link_BETA1-4 : bond 0.00264 ( 2) link_BETA1-4 : angle 1.60764 ( 6) link_NAG-ASN : bond 0.00267 ( 3) link_NAG-ASN : angle 1.53317 ( 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 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.272 Fit side-chains REVERT: A 8 MET cc_start: 0.8740 (mmt) cc_final: 0.8421 (mmt) REVERT: B 318 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8296 (mtmt) REVERT: B 336 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7469 (mm-30) REVERT: B 381 LYS cc_start: 0.7687 (mttt) cc_final: 0.7143 (tttm) REVERT: B 508 LYS cc_start: 0.7543 (tmtt) cc_final: 0.6878 (tptp) REVERT: B 513 ARG cc_start: 0.7893 (mtt180) cc_final: 0.7067 (mtt-85) REVERT: B 537 CYS cc_start: 0.8721 (t) cc_final: 0.8494 (t) outliers start: 16 outliers final: 8 residues processed: 82 average time/residue: 0.0929 time to fit residues: 10.3430 Evaluate side-chains 75 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 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 N residue 28 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: 10.0000 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3436 r_free = 0.3436 target = 0.137859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.123377 restraints weight = 11081.964| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.53 r_work: 0.3037 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.236 8732 Z= 0.184 Angle : 0.647 15.733 11988 Z= 0.290 Chirality : 0.038 0.172 1420 Planarity : 0.004 0.046 1506 Dihedral : 8.783 107.452 1488 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.53 % Allowed : 15.01 % Favored : 82.46 % 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: 0.62 (0.29), residues: 777 helix: 1.14 (0.26), residues: 381 sheet: -0.53 (0.45), residues: 123 loop : 0.00 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 73 TYR 0.013 0.002 TYR B 29 PHE 0.014 0.002 PHE B 215 TRP 0.015 0.002 TRP B 337 HIS 0.007 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8723) covalent geometry : angle 0.64423 (11969) SS BOND : bond 0.00452 ( 2) SS BOND : angle 1.47180 ( 4) hydrogen bonds : bond 0.03762 ( 460) hydrogen bonds : angle 4.51549 ( 1311) Misc. bond : bond 0.19579 ( 2) link_BETA1-4 : bond 0.00311 ( 2) link_BETA1-4 : angle 1.54010 ( 6) link_NAG-ASN : bond 0.00296 ( 3) link_NAG-ASN : angle 1.59766 ( 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 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.276 Fit side-chains REVERT: A 8 MET cc_start: 0.8710 (mmt) cc_final: 0.8416 (mmt) REVERT: B 199 ARG cc_start: 0.6289 (tmt170) cc_final: 0.5512 (ttp80) REVERT: B 318 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8193 (mtmt) REVERT: B 381 LYS cc_start: 0.7644 (mttt) cc_final: 0.7159 (tttm) REVERT: B 508 LYS cc_start: 0.7671 (tmtt) cc_final: 0.6961 (tptp) REVERT: B 513 ARG cc_start: 0.7851 (mtt180) cc_final: 0.7036 (mtt-85) outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 0.0951 time to fit residues: 10.3379 Evaluate side-chains 81 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain B residue 98 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 449 HIS Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 96 CYS 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: 0.6980 chunk 27 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3464 r_free = 0.3464 target = 0.140168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.125885 restraints weight = 10855.905| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.44 r_work: 0.3080 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 8732 Z= 0.118 Angle : 0.566 13.943 11988 Z= 0.255 Chirality : 0.035 0.159 1420 Planarity : 0.003 0.043 1506 Dihedral : 8.528 107.470 1488 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.90 % Allowed : 16.11 % Favored : 81.99 % 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: 0.84 (0.30), residues: 777 helix: 1.41 (0.26), residues: 379 sheet: -0.50 (0.44), residues: 124 loop : 0.04 (0.38), residues: 274 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 0.009 0.001 TRP B 424 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8723) covalent geometry : angle 0.56396 (11969) SS BOND : bond 0.00361 ( 2) SS BOND : angle 1.22549 ( 4) hydrogen bonds : bond 0.03274 ( 460) hydrogen bonds : angle 4.31858 ( 1311) Misc. bond : bond 0.16139 ( 2) link_BETA1-4 : bond 0.00379 ( 2) link_BETA1-4 : angle 1.51269 ( 6) link_NAG-ASN : bond 0.00209 ( 3) link_NAG-ASN : angle 1.29851 ( 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 86 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.267 Fit side-chains REVERT: A 8 MET cc_start: 0.8738 (mmt) cc_final: 0.8369 (mmt) REVERT: A 12 GLU cc_start: 0.8470 (mp0) cc_final: 0.8192 (mp0) REVERT: B 199 ARG cc_start: 0.6506 (tmt170) cc_final: 0.5795 (ttp80) REVERT: B 318 LYS cc_start: 0.8551 (mtpp) cc_final: 0.8287 (mtmt) REVERT: B 336 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7464 (mm-30) REVERT: B 381 LYS cc_start: 0.7755 (mttt) cc_final: 0.7172 (tttm) REVERT: B 508 LYS cc_start: 0.7531 (tmtt) cc_final: 0.6853 (tptp) REVERT: B 513 ARG cc_start: 0.7827 (mtt180) cc_final: 0.6882 (mtt-85) outliers start: 12 outliers final: 10 residues processed: 82 average time/residue: 0.1063 time to fit residues: 11.7191 Evaluate side-chains 74 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 474 LEU Chi-restraints excluded: chain B residue 530 THR 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: 10.0000 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 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: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3398 r_free = 0.3398 target = 0.134633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.119076 restraints weight = 11047.099| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.57 r_work: 0.2976 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.319 8732 Z= 0.361 Angle : 0.816 16.931 11988 Z= 0.371 Chirality : 0.045 0.182 1420 Planarity : 0.005 0.074 1506 Dihedral : 9.184 105.229 1488 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.69 % Allowed : 16.27 % Favored : 81.04 % 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: 0.15 (0.29), residues: 777 helix: 0.75 (0.25), residues: 381 sheet: -0.72 (0.44), residues: 122 loop : -0.22 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 73 TYR 0.021 0.003 TYR N 80 PHE 0.017 0.003 PHE B 563 TRP 0.018 0.003 TRP B 337 HIS 0.010 0.002 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00847 ( 8723) covalent geometry : angle 0.81356 (11969) SS BOND : bond 0.00378 ( 2) SS BOND : angle 1.90943 ( 4) hydrogen bonds : bond 0.04689 ( 460) hydrogen bonds : angle 4.92189 ( 1311) Misc. bond : bond 0.24981 ( 2) link_BETA1-4 : bond 0.00405 ( 2) link_BETA1-4 : angle 1.53338 ( 6) link_NAG-ASN : bond 0.00504 ( 3) link_NAG-ASN : angle 2.04757 ( 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 83 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.201 Fit side-chains REVERT: B 199 ARG cc_start: 0.6335 (tmt170) cc_final: 0.6042 (tmt170) REVERT: B 318 LYS cc_start: 0.8493 (mtpp) cc_final: 0.8260 (mtmt) REVERT: B 397 ASP cc_start: 0.7973 (p0) cc_final: 0.7210 (p0) REVERT: B 401 TYR cc_start: 0.8121 (m-10) cc_final: 0.7910 (m-80) REVERT: B 513 ARG cc_start: 0.7905 (mtt180) cc_final: 0.7080 (mtt-85) outliers start: 17 outliers final: 11 residues processed: 77 average time/residue: 0.0959 time to fit residues: 9.9711 Evaluate side-chains 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 9 optimal weight: 0.3980 chunk 106 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3451 r_free = 0.3451 target = 0.139066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.124996 restraints weight = 10865.252| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.38 r_work: 0.3074 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.217 8732 Z= 0.135 Angle : 0.604 14.355 11988 Z= 0.271 Chirality : 0.036 0.151 1420 Planarity : 0.003 0.045 1506 Dihedral : 8.641 105.907 1488 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.11 % Allowed : 17.85 % Favored : 81.04 % 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: 0.56 (0.29), residues: 777 helix: 1.19 (0.26), residues: 379 sheet: -0.71 (0.44), residues: 124 loop : -0.07 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 290 TYR 0.021 0.001 TYR N 80 PHE 0.012 0.001 PHE B 454 TRP 0.010 0.001 TRP B 424 HIS 0.005 0.001 HIS B 115 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8723) covalent geometry : angle 0.60144 (11969) SS BOND : bond 0.00401 ( 2) SS BOND : angle 1.25765 ( 4) hydrogen bonds : bond 0.03453 ( 460) hydrogen bonds : angle 4.48939 ( 1311) Misc. bond : bond 0.18942 ( 2) link_BETA1-4 : bond 0.00565 ( 2) link_BETA1-4 : angle 1.66420 ( 6) link_NAG-ASN : bond 0.00218 ( 3) link_NAG-ASN : angle 1.37859 ( 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 76 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.229 Fit side-chains REVERT: A 8 MET cc_start: 0.8718 (mmt) cc_final: 0.8446 (mmt) REVERT: B 199 ARG cc_start: 0.6458 (tmt170) cc_final: 0.5690 (ttp80) REVERT: B 318 LYS cc_start: 0.8550 (mtpp) cc_final: 0.8317 (mtmt) REVERT: B 508 LYS cc_start: 0.7675 (tmtt) cc_final: 0.6902 (tptp) REVERT: B 513 ARG cc_start: 0.7859 (mtt180) cc_final: 0.6730 (mtt180) REVERT: N 6 GLU cc_start: 0.7980 (mp0) cc_final: 0.7612 (mp0) outliers start: 7 outliers final: 6 residues processed: 74 average time/residue: 0.1058 time to fit residues: 10.6865 Evaluate side-chains 70 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 111 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3451 r_free = 0.3451 target = 0.139050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.126537 restraints weight = 10924.451| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.21 r_work: 0.3109 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 8732 Z= 0.136 Angle : 0.593 14.203 11988 Z= 0.268 Chirality : 0.036 0.153 1420 Planarity : 0.003 0.045 1506 Dihedral : 8.423 102.157 1488 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.42 % Allowed : 17.54 % Favored : 81.04 % 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: 1.36 (0.26), residues: 379 sheet: -0.58 (0.44), residues: 123 loop : -0.03 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 290 TYR 0.012 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 covalent geometry : bond 0.00320 ( 8723) covalent geometry : angle 0.59104 (11969) SS BOND : bond 0.00376 ( 2) SS BOND : angle 1.35613 ( 4) hydrogen bonds : bond 0.03407 ( 460) hydrogen bonds : angle 4.37416 ( 1311) Misc. bond : bond 0.17537 ( 2) link_BETA1-4 : bond 0.00323 ( 2) link_BETA1-4 : angle 1.48704 ( 6) link_NAG-ASN : bond 0.00196 ( 3) link_NAG-ASN : angle 1.34033 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1752.62 seconds wall clock time: 30 minutes 41.43 seconds (1841.43 seconds total)