Starting phenix.real_space_refine on Thu Jul 2 08:24:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k0l_22601/07_2026/7k0l_22601.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0l_22601/07_2026/7k0l_22601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2026/7k0l_22601.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2026/7k0l_22601.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2026/7k0l_22601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2026/7k0l_22601.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2026/7k0l_22601.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k0l_22601/07_2026/7k0l_22601.cif" } resolution = 3.4 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= -0.003 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 44 5.16 5 C 4877 2.51 5 N 1293 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 7619 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3284 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3883 Classifications: {'peptide': 492} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 474} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 409 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'PLP': 1, 'VRP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 1.43, per 1000 atoms: 0.19 Number of scatterers: 7619 At special positions: 0 Unit cell: (95.475, 96.48, 115.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 1 15.00 O 1404 8.00 N 1293 7.00 C 4877 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 324.6 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 52.3% alpha, 11.1% 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 53 through 64 Processing helix chain 'A' and resid 77 through 81 Processing helix chain 'A' and resid 114 through 129 Processing helix chain 'A' and resid 142 through 157 removed outlier: 3.713A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 179 removed outlier: 3.501A pdb=" N THR A 170 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.515A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 361 through 378 removed outlier: 3.660A pdb=" N GLN A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 Processing helix chain 'A' and resid 453 through 472 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 126 removed outlier: 4.704A pdb=" N TYR B 122 " --> pdb=" O PHE B 118 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.612A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.526A pdb=" N GLU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Proline residue: B 247 - end of helix removed outlier: 3.570A pdb=" N VAL B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.614A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 402 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 457 removed outlier: 3.865A pdb=" N GLU B 437 " --> pdb=" O SER B 433 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.528A pdb=" N ILE B 479 " --> pdb=" O MET B 475 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 30 through 56 removed outlier: 3.542A pdb=" N PHE C 55 " --> pdb=" O THR C 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 4.060A pdb=" N VAL A 94 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.690A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386 removed outlier: 4.437A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.995A pdb=" N ILE B 148 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LYS B 168 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLU B 150 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 166 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 10.291A pdb=" N GLN B 152 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 9.404A pdb=" N GLY B 164 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.681A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B 259 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.501A pdb=" N ARG B 507 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1137 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: 1.22 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2465 1.34 - 1.46: 1174 1.46 - 1.58: 4063 1.58 - 1.70: 2 1.70 - 1.82: 71 Bond restraints: 7775 Sorted by residual: bond pdb=" N ASN B 120 " pdb=" CA ASN B 120 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.13e+00 bond pdb=" N GLU B 119 " pdb=" CA GLU B 119 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.84e+00 bond pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.71e+00 bond pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.25e-02 6.40e+03 5.54e+00 bond pdb=" C18 VRP B 602 " pdb=" C19 VRP B 602 " ideal model delta sigma weight residual 1.538 1.572 -0.034 2.00e-02 2.50e+03 2.94e+00 ... (remaining 7770 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 10164 1.49 - 2.99: 289 2.99 - 4.48: 41 4.48 - 5.98: 7 5.98 - 7.47: 5 Bond angle restraints: 10506 Sorted by residual: angle pdb=" CB MET B 285 " pdb=" CG MET B 285 " pdb=" SD MET B 285 " ideal model delta sigma weight residual 112.70 120.17 -7.47 3.00e+00 1.11e-01 6.21e+00 angle pdb=" N ASN B 120 " pdb=" CA ASN B 120 " pdb=" C ASN B 120 " ideal model delta sigma weight residual 113.16 110.18 2.98 1.24e+00 6.50e-01 5.79e+00 angle pdb=" C TYR B 176 " pdb=" N ASN B 177 " pdb=" CA ASN B 177 " ideal model delta sigma weight residual 121.54 126.08 -4.54 1.91e+00 2.74e-01 5.64e+00 angle pdb=" CA CYS A 133 " pdb=" C CYS A 133 " pdb=" N GLY A 134 " ideal model delta sigma weight residual 115.67 118.55 -2.88 1.23e+00 6.61e-01 5.50e+00 angle pdb=" CA GLU B 119 " pdb=" C GLU B 119 " pdb=" O GLU B 119 " ideal model delta sigma weight residual 120.55 118.10 2.45 1.06e+00 8.90e-01 5.34e+00 ... (remaining 10501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.52: 4421 22.52 - 45.03: 230 45.03 - 67.55: 14 67.55 - 90.07: 3 90.07 - 112.58: 1 Dihedral angle restraints: 4669 sinusoidal: 1885 harmonic: 2784 Sorted by residual: dihedral pdb=" C5A PLP B 601 " pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " pdb=" O1P PLP B 601 " ideal model delta sinusoidal sigma weight residual 76.43 -170.99 -112.58 1 2.00e+01 2.50e-03 3.32e+01 dihedral pdb=" CA THR B 400 " pdb=" C THR B 400 " pdb=" N HIS B 401 " pdb=" CA HIS B 401 " ideal model delta harmonic sigma weight residual -180.00 -164.35 -15.65 0 5.00e+00 4.00e-02 9.80e+00 dihedral pdb=" CB GLU B 197 " pdb=" CG GLU B 197 " pdb=" CD GLU B 197 " pdb=" OE1 GLU B 197 " ideal model delta sinusoidal sigma weight residual 0.00 80.48 -80.48 1 3.00e+01 1.11e-03 8.90e+00 ... (remaining 4666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 884 0.044 - 0.087: 189 0.087 - 0.131: 82 0.131 - 0.174: 3 0.174 - 0.218: 1 Chirality restraints: 1159 Sorted by residual: chirality pdb=" C18 VRP B 602 " pdb=" C17 VRP B 602 " pdb=" C19 VRP B 602 " pdb=" O28 VRP B 602 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ASN B 177 " pdb=" N ASN B 177 " pdb=" C ASN B 177 " pdb=" CB ASN B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE A 242 " pdb=" N ILE A 242 " pdb=" C ILE A 242 " pdb=" CB ILE A 242 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1156 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 498 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO B 499 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 499 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 499 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.03e+00 pdb=" N PRO B 413 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 469 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 470 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " -0.023 5.00e-02 4.00e+02 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 125 2.69 - 3.24: 7377 3.24 - 3.80: 11385 3.80 - 4.35: 14945 4.35 - 4.90: 26010 Nonbonded interactions: 59842 Sorted by model distance: nonbonded pdb=" OH TYR B 176 " pdb=" O24 VRP B 602 " model vdw 2.141 3.040 nonbonded pdb=" OD2 ASP B 259 " pdb=" OH TYR B 318 " model vdw 2.187 3.040 nonbonded pdb=" OG SER A 401 " pdb=" OD2 ASP A 408 " model vdw 2.246 3.040 nonbonded pdb=" NE2 HIS B 263 " pdb=" O27 VRP B 602 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR A 402 " pdb=" OD1 ASP A 408 " model vdw 2.300 3.040 ... (remaining 59837 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.650 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.050 Find NCS groups from input model: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 : 0.004 0.116 7776 Z= 0.227 Angle : 0.601 7.474 10506 Z= 0.360 Chirality : 0.042 0.218 1159 Planarity : 0.004 0.061 1348 Dihedral : 12.593 112.583 2891 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.09 (0.27), residues: 958 helix: 1.86 (0.25), residues: 432 sheet: 0.64 (0.48), residues: 124 loop : -0.49 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 95 TYR 0.023 0.001 TYR A 166 PHE 0.012 0.001 PHE A 209 TRP 0.011 0.001 TRP A 64 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 ( 7775) covalent geometry : angle 0.60143 / 0.36 (10506) hydrogen bonds : bond 0.16052 / 11.93 ( 398) hydrogen bonds : angle 5.93674 / 4.39 ( 1137) Misc. bond : bond 0.11625 / 6.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.255 Fit side-chains REVERT: B 472 MET cc_start: 0.8708 (mmm) cc_final: 0.8463 (mmm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0674 time to fit residues: 6.1870 Evaluate side-chains 56 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081565 restraints weight = 16378.350| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.29 r_work: 0.3084 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7776 Z= 0.146 Angle : 0.509 6.642 10506 Z= 0.274 Chirality : 0.042 0.148 1159 Planarity : 0.004 0.055 1348 Dihedral : 5.252 73.889 1075 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.50 % Allowed : 5.35 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.27), residues: 958 helix: 1.95 (0.25), residues: 445 sheet: 0.55 (0.46), residues: 131 loop : -0.48 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.025 0.001 TYR A 166 PHE 0.013 0.001 PHE A 209 TRP 0.009 0.001 TRP C 32 HIS 0.006 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7775) covalent geometry : angle 0.50915 / 0.27 (10506) hydrogen bonds : bond 0.04823 / 3.36 ( 398) hydrogen bonds : angle 4.69573 / 3.46 ( 1137) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.180 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 56 average time/residue: 0.0625 time to fit residues: 5.1423 Evaluate side-chains 58 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 74 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.095490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.082871 restraints weight = 16209.247| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.30 r_work: 0.3107 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7776 Z= 0.111 Angle : 0.469 6.652 10506 Z= 0.252 Chirality : 0.041 0.140 1159 Planarity : 0.004 0.051 1348 Dihedral : 4.973 83.389 1075 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.87 % Allowed : 6.10 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.27), residues: 958 helix: 2.08 (0.25), residues: 445 sheet: 0.45 (0.45), residues: 129 loop : -0.48 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 136 TYR 0.017 0.001 TYR A 166 PHE 0.011 0.001 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7775) covalent geometry : angle 0.46892 / 0.25 (10506) hydrogen bonds : bond 0.04041 / 2.76 ( 398) hydrogen bonds : angle 4.47494 / 3.30 ( 1137) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.329 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 63 average time/residue: 0.0687 time to fit residues: 6.3510 Evaluate side-chains 63 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 503 ILE Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081844 restraints weight = 16404.035| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.29 r_work: 0.3090 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7776 Z= 0.139 Angle : 0.471 6.666 10506 Z= 0.253 Chirality : 0.041 0.140 1159 Planarity : 0.004 0.050 1348 Dihedral : 4.774 82.123 1075 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.00 % Allowed : 7.97 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.27), residues: 958 helix: 2.08 (0.25), residues: 445 sheet: 0.38 (0.45), residues: 131 loop : -0.46 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 95 TYR 0.017 0.001 TYR A 166 PHE 0.013 0.001 PHE A 209 TRP 0.009 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 7775) covalent geometry : angle 0.47078 / 0.25 (10506) hydrogen bonds : bond 0.04153 / 2.84 ( 398) hydrogen bonds : angle 4.38360 / 3.24 ( 1137) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.188 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 59 average time/residue: 0.0549 time to fit residues: 5.0280 Evaluate side-chains 61 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082570 restraints weight = 16326.607| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.30 r_work: 0.3104 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7776 Z= 0.114 Angle : 0.454 6.608 10506 Z= 0.243 Chirality : 0.040 0.138 1159 Planarity : 0.004 0.048 1348 Dihedral : 4.491 72.223 1075 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.00 % Allowed : 8.84 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.27), residues: 958 helix: 2.15 (0.25), residues: 445 sheet: 0.35 (0.45), residues: 129 loop : -0.45 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 136 TYR 0.014 0.001 TYR A 166 PHE 0.012 0.001 PHE A 209 TRP 0.009 0.001 TRP C 32 HIS 0.004 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 7775) covalent geometry : angle 0.45399 / 0.24 (10506) hydrogen bonds : bond 0.03772 / 2.58 ( 398) hydrogen bonds : angle 4.30334 / 3.18 ( 1137) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: B 505 GLU cc_start: 0.8332 (mp0) cc_final: 0.8024 (mp0) outliers start: 8 outliers final: 7 residues processed: 65 average time/residue: 0.0609 time to fit residues: 5.9202 Evaluate side-chains 65 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 91 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 79 optimal weight: 0.0370 chunk 80 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.096041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.083468 restraints weight = 16267.753| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.29 r_work: 0.3121 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7776 Z= 0.097 Angle : 0.435 6.559 10506 Z= 0.232 Chirality : 0.040 0.142 1159 Planarity : 0.004 0.048 1348 Dihedral : 4.264 64.163 1075 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.37 % Allowed : 9.34 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.27), residues: 958 helix: 2.22 (0.25), residues: 444 sheet: 0.34 (0.45), residues: 131 loop : -0.40 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 105 TYR 0.011 0.001 TYR C 50 PHE 0.012 0.001 PHE A 168 TRP 0.008 0.001 TRP C 32 HIS 0.002 0.000 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7775) covalent geometry : angle 0.43457 / 0.23 (10506) hydrogen bonds : bond 0.03416 / 2.35 ( 398) hydrogen bonds : angle 4.24425 / 3.14 ( 1137) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 77 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8034 (m170) REVERT: A 469 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7504 (mp-120) REVERT: B 505 GLU cc_start: 0.8285 (mp0) cc_final: 0.7849 (mp0) outliers start: 11 outliers final: 7 residues processed: 69 average time/residue: 0.0533 time to fit residues: 5.4925 Evaluate side-chains 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 47 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.082951 restraints weight = 16304.314| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.29 r_work: 0.3109 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7776 Z= 0.118 Angle : 0.454 6.599 10506 Z= 0.242 Chirality : 0.041 0.136 1159 Planarity : 0.004 0.048 1348 Dihedral : 4.197 58.257 1075 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.62 % Allowed : 9.84 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.27), residues: 958 helix: 2.26 (0.25), residues: 438 sheet: 0.28 (0.44), residues: 131 loop : -0.46 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 507 TYR 0.013 0.001 TYR C 50 PHE 0.012 0.001 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7775) covalent geometry : angle 0.45409 / 0.24 (10506) hydrogen bonds : bond 0.03666 / 2.51 ( 398) hydrogen bonds : angle 4.25248 / 3.16 ( 1137) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 77 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.8066 (m170) REVERT: A 469 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7542 (mp-120) REVERT: B 321 GLU cc_start: 0.8881 (tp30) cc_final: 0.8620 (tp30) REVERT: B 505 GLU cc_start: 0.8281 (mp0) cc_final: 0.7910 (mp0) outliers start: 13 outliers final: 8 residues processed: 68 average time/residue: 0.0507 time to fit residues: 5.3583 Evaluate side-chains 69 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 57 optimal weight: 0.0060 chunk 61 optimal weight: 0.0000 chunk 92 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 79 optimal weight: 0.0470 chunk 77 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.097468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084975 restraints weight = 16178.671| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.29 r_work: 0.3144 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7776 Z= 0.085 Angle : 0.435 6.740 10506 Z= 0.231 Chirality : 0.040 0.144 1159 Planarity : 0.004 0.048 1348 Dihedral : 4.013 53.409 1075 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.12 % Allowed : 10.21 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.47 (0.27), residues: 958 helix: 2.34 (0.25), residues: 439 sheet: 0.30 (0.44), residues: 131 loop : -0.37 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 459 TYR 0.008 0.001 TYR C 50 PHE 0.010 0.001 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.002 0.000 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 ( 7775) covalent geometry : angle 0.43527 / 0.23 (10506) hydrogen bonds : bond 0.03041 / 2.09 ( 398) hydrogen bonds : angle 4.20486 / 3.13 ( 1137) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.8802 (mmt) cc_final: 0.8575 (mmp) REVERT: A 469 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7465 (mp-120) REVERT: B 86 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7878 (t80) REVERT: B 505 GLU cc_start: 0.8258 (mp0) cc_final: 0.7939 (mp0) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.0545 time to fit residues: 6.1673 Evaluate side-chains 68 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.083029 restraints weight = 16211.790| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.27 r_work: 0.3111 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7776 Z= 0.131 Angle : 0.475 7.084 10506 Z= 0.250 Chirality : 0.041 0.139 1159 Planarity : 0.004 0.048 1348 Dihedral : 4.020 48.444 1075 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.25 % Allowed : 10.21 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.27), residues: 958 helix: 2.26 (0.25), residues: 439 sheet: 0.26 (0.44), residues: 131 loop : -0.40 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 507 TYR 0.013 0.001 TYR C 50 PHE 0.012 0.001 PHE A 209 TRP 0.007 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 7775) covalent geometry : angle 0.47546 / 0.25 (10506) hydrogen bonds : bond 0.03735 / 2.56 ( 398) hydrogen bonds : angle 4.23922 / 3.16 ( 1137) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.176 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.8753 (mmt) cc_final: 0.8483 (mmp) REVERT: A 226 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7597 (tp) REVERT: A 469 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7570 (mp-120) REVERT: B 86 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7847 (t80) outliers start: 10 outliers final: 5 residues processed: 65 average time/residue: 0.0513 time to fit residues: 5.3270 Evaluate side-chains 67 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.082823 restraints weight = 16193.615| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.28 r_work: 0.3107 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7776 Z= 0.124 Angle : 0.475 7.095 10506 Z= 0.249 Chirality : 0.041 0.147 1159 Planarity : 0.004 0.048 1348 Dihedral : 3.975 42.342 1075 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.25 % Allowed : 10.34 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.27), residues: 958 helix: 2.25 (0.25), residues: 438 sheet: 0.21 (0.44), residues: 131 loop : -0.41 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 507 TYR 0.014 0.001 TYR C 50 PHE 0.012 0.001 PHE A 209 TRP 0.009 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 ( 7775) covalent geometry : angle 0.47466 / 0.25 (10506) hydrogen bonds : bond 0.03704 / 2.53 ( 398) hydrogen bonds : angle 4.25069 / 3.18 ( 1137) Misc. bond : bond 0.00007 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 214 MET cc_start: 0.8786 (mmt) cc_final: 0.8459 (mmp) REVERT: A 226 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7564 (tp) REVERT: A 469 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7533 (mp-120) REVERT: B 86 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7790 (t80) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.0488 time to fit residues: 5.1586 Evaluate side-chains 69 residues out of total 815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 86 TYR Chi-restraints excluded: chain B residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 68 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.0870 chunk 3 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088594 restraints weight = 15996.081| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.14 r_work: 0.3222 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7776 Z= 0.133 Angle : 0.485 7.638 10506 Z= 0.254 Chirality : 0.041 0.140 1159 Planarity : 0.004 0.050 1348 Dihedral : 3.953 37.134 1075 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.37 % Allowed : 10.09 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.33 (0.27), residues: 958 helix: 2.21 (0.25), residues: 439 sheet: 0.18 (0.44), residues: 131 loop : -0.40 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 507 TYR 0.014 0.001 TYR C 50 PHE 0.012 0.001 PHE A 209 TRP 0.008 0.001 TRP C 32 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 7775) covalent geometry : angle 0.48532 / 0.25 (10506) hydrogen bonds : bond 0.03888 / 2.65 ( 398) hydrogen bonds : angle 4.24378 / 3.17 ( 1137) Misc. bond : bond 0.00008 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1434.27 seconds wall clock time: 25 minutes 20.96 seconds (1520.96 seconds total)