Starting phenix.real_space_refine on Fri Aug 22 15:26:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8q_38156/08_2025/8x8q_38156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8q_38156/08_2025/8x8q_38156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8x8q_38156/08_2025/8x8q_38156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8q_38156/08_2025/8x8q_38156.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x8q_38156/08_2025/8x8q_38156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8q_38156/08_2025/8x8q_38156.map" } resolution = 3.14 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= -0.000 sd= 0.011 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 Zn 1 6.06 5 S 22 5.16 5 C 3155 2.51 5 N 844 2.21 5 O 927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4949 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3855 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 459} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 1093 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 141, 1091 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 141, 1091 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1114 Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4251 SG CYS F 56 46.939 48.744 46.154 1.00140.53 S ATOM 4265 SG CYS F 58 44.589 46.461 47.821 1.00142.47 S ATOM 4726 SG CYS F 116 43.515 50.172 47.323 1.00148.89 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="ZN ZN F 201 " occ=0.44 Time building chain proxies: 1.33, per 1000 atoms: 0.27 Number of scatterers: 4949 At special positions: 0 Unit cell: (72.98, 84.46, 92.66, 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) Zn 1 29.99 S 22 16.00 O 927 8.00 N 844 7.00 C 3155 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=0, symmetry=0 Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 241.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" ND1 HIS F 118 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 56 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 58 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 116 " Number of angles added : 3 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 7 sheets defined 45.2% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'B' and resid 23 through 37 Processing helix chain 'B' and resid 45 through 64 Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 78 through 89 removed outlier: 3.653A pdb=" N ASN B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 128 No H-bonds generated for 'chain 'B' and resid 126 through 128' Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 139 through 146 removed outlier: 3.775A pdb=" N GLN B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 152 removed outlier: 3.678A pdb=" N GLN B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 removed outlier: 3.662A pdb=" N ALA B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 179 removed outlier: 3.810A pdb=" N THR B 178 " --> pdb=" O PRO B 174 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 179 " --> pdb=" O TYR B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 190 through 196 Processing helix chain 'B' and resid 201 through 227 removed outlier: 3.973A pdb=" N ASP B 205 " --> pdb=" O GLN B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 240 through 254 Processing helix chain 'B' and resid 317 through 324 Processing helix chain 'B' and resid 349 through 361 removed outlier: 4.022A pdb=" N GLU B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 390 removed outlier: 3.735A pdb=" N MET B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 419 through 441 removed outlier: 3.668A pdb=" N TYR B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 455 Processing helix chain 'B' and resid 458 through 495 Processing helix chain 'F' and resid 24 through 30 removed outlier: 3.661A pdb=" N TRP F 28 " --> pdb=" O THR F 24 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 101 Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 124 removed outlier: 3.962A pdb=" N LEU B 121 " --> pdb=" O CYS B 297 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 129 through 130 Processing sheet with id=AA4, first strand: chain 'B' and resid 278 through 279 removed outlier: 6.082A pdb=" N ASN B 278 " --> pdb=" O ILE B 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 342 removed outlier: 3.571A pdb=" N VAL B 337 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 370 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 341 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER B 366 " --> pdb=" O LEU B 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.500A pdb=" N LEU F 40 " --> pdb=" O ASP F 35 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP F 33 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER F 44 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU F 31 " --> pdb=" O SER F 44 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 71 through 75 removed outlier: 3.690A pdb=" N TYR F 64 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE F 113 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 114 " --> pdb=" O GLY F 122 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY F 122 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY F 133 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY F 127 " --> pdb=" O LEU F 131 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU F 131 " --> pdb=" O GLY F 127 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 633 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.64 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 838 1.32 - 1.44: 1390 1.44 - 1.57: 2805 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 5066 Sorted by residual: bond pdb=" C LEU B 139 " pdb=" N GLY B 140 " ideal model delta sigma weight residual 1.339 1.316 0.024 7.50e-03 1.78e+04 1.01e+01 bond pdb=" C PRO B 500 " pdb=" O PRO B 500 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 8.84e+00 bond pdb=" N PHE B 416 " pdb=" CA PHE B 416 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.04e-02 9.25e+03 8.07e+00 bond pdb=" N ASP B 335 " pdb=" CA ASP B 335 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.21e-02 6.83e+03 7.71e+00 bond pdb=" N LEU B 139 " pdb=" CA LEU B 139 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.31e-02 5.83e+03 7.50e+00 ... (remaining 5061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 6488 1.63 - 3.26: 303 3.26 - 4.89: 61 4.89 - 6.53: 11 6.53 - 8.16: 8 Bond angle restraints: 6871 Sorted by residual: angle pdb=" N LEU B 382 " pdb=" CA LEU B 382 " pdb=" C LEU B 382 " ideal model delta sigma weight residual 111.75 106.21 5.54 1.28e+00 6.10e-01 1.87e+01 angle pdb=" N VAL B 387 " pdb=" CA VAL B 387 " pdb=" C VAL B 387 " ideal model delta sigma weight residual 112.83 108.65 4.18 9.90e-01 1.02e+00 1.79e+01 angle pdb=" C SER B 333 " pdb=" N HIS B 334 " pdb=" CA HIS B 334 " ideal model delta sigma weight residual 123.17 117.18 5.99 1.49e+00 4.50e-01 1.61e+01 angle pdb=" C VAL B 387 " pdb=" N PHE B 388 " pdb=" CA PHE B 388 " ideal model delta sigma weight residual 122.26 115.34 6.92 1.73e+00 3.34e-01 1.60e+01 angle pdb=" N PRO B 500 " pdb=" CA PRO B 500 " pdb=" C PRO B 500 " ideal model delta sigma weight residual 112.47 105.13 7.34 2.06e+00 2.36e-01 1.27e+01 ... (remaining 6866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 2717 17.96 - 35.93: 241 35.93 - 53.89: 48 53.89 - 71.85: 12 71.85 - 89.82: 7 Dihedral angle restraints: 3025 sinusoidal: 1199 harmonic: 1826 Sorted by residual: dihedral pdb=" CB GLU B 118 " pdb=" CG GLU B 118 " pdb=" CD GLU B 118 " pdb=" OE1 GLU B 118 " ideal model delta sinusoidal sigma weight residual 0.00 89.82 -89.82 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP B 192 " pdb=" CB ASP B 192 " pdb=" CG ASP B 192 " pdb=" OD1 ASP B 192 " ideal model delta sinusoidal sigma weight residual -30.00 -84.23 54.23 1 2.00e+01 2.50e-03 9.97e+00 dihedral pdb=" CB GLU B 415 " pdb=" CG GLU B 415 " pdb=" CD GLU B 415 " pdb=" OE1 GLU B 415 " ideal model delta sinusoidal sigma weight residual 0.00 -84.20 84.20 1 3.00e+01 1.11e-03 9.59e+00 ... (remaining 3022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 616 0.060 - 0.120: 105 0.120 - 0.179: 23 0.179 - 0.239: 5 0.239 - 0.299: 1 Chirality restraints: 750 Sorted by residual: chirality pdb=" CB VAL F 137 " pdb=" CA VAL F 137 " pdb=" CG1 VAL F 137 " pdb=" CG2 VAL F 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA VAL B 337 " pdb=" N VAL B 337 " pdb=" C VAL B 337 " pdb=" CB VAL B 337 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE B 377 " pdb=" N ILE B 377 " pdb=" C ILE B 377 " pdb=" CB ILE B 377 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 747 not shown) Planarity restraints: 887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 185 " -0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO B 186 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 186 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 186 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 498 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C PRO B 498 " 0.038 2.00e-02 2.50e+03 pdb=" O PRO B 498 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU B 499 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 137 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C VAL F 137 " 0.029 2.00e-02 2.50e+03 pdb=" O VAL F 137 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG F 138 " -0.010 2.00e-02 2.50e+03 ... (remaining 884 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 812 2.76 - 3.29: 5050 3.29 - 3.83: 8170 3.83 - 4.36: 9485 4.36 - 4.90: 15630 Nonbonded interactions: 39147 Sorted by model distance: nonbonded pdb=" O GLN B 52 " pdb=" OG1 THR B 55 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLU B 58 " pdb=" NZ LYS B 62 " model vdw 2.231 3.120 nonbonded pdb=" O CYS B 277 " pdb=" OH TYR B 313 " model vdw 2.232 3.040 nonbonded pdb=" OE1 GLU B 164 " pdb=" OG SER B 170 " model vdw 2.247 3.040 nonbonded pdb=" ND2 ASN B 278 " pdb=" OE1 GLN B 308 " model vdw 2.252 3.120 ... (remaining 39142 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=0.29 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.240 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 0.055 5070 Z= 0.234 Angle : 0.830 8.157 6874 Z= 0.462 Chirality : 0.052 0.299 750 Planarity : 0.005 0.060 887 Dihedral : 14.724 89.817 1849 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.57 % Allowed : 12.76 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.16 (0.34), residues: 619 helix: 0.88 (0.33), residues: 253 sheet: -0.32 (0.77), residues: 56 loop : -0.38 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 125 TYR 0.010 0.001 TYR B 217 PHE 0.026 0.003 PHE B 220 TRP 0.023 0.002 TRP B 420 HIS 0.005 0.001 HIS F 21 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 5066) covalent geometry : angle 0.82517 ( 6871) hydrogen bonds : bond 0.17006 ( 220) hydrogen bonds : angle 6.64625 ( 633) metal coordination : bond 0.00687 ( 4) metal coordination : angle 4.24612 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.120 Fit side-chains REVERT: B 493 MET cc_start: 0.7427 (mmt) cc_final: 0.6616 (mmt) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.0679 time to fit residues: 4.6432 Evaluate side-chains 44 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.072111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.063977 restraints weight = 14290.185| |-----------------------------------------------------------------------------| r_work (start): 0.2658 rms_B_bonded: 2.76 r_work: 0.2575 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5070 Z= 0.145 Angle : 0.609 6.338 6874 Z= 0.311 Chirality : 0.043 0.180 750 Planarity : 0.004 0.061 887 Dihedral : 3.677 17.119 684 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.95 % Allowed : 11.81 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.22 (0.33), residues: 619 helix: 0.79 (0.33), residues: 260 sheet: -0.08 (0.66), residues: 70 loop : -0.29 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 68 TYR 0.012 0.001 TYR B 217 PHE 0.018 0.002 PHE B 220 TRP 0.014 0.001 TRP B 420 HIS 0.006 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5066) covalent geometry : angle 0.60283 ( 6871) hydrogen bonds : bond 0.04424 ( 220) hydrogen bonds : angle 5.15311 ( 633) metal coordination : bond 0.01758 ( 4) metal coordination : angle 4.10164 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.199 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.0600 time to fit residues: 3.7592 Evaluate side-chains 42 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain F residue 105 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 17 optimal weight: 0.3980 chunk 60 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 257 GLN F 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.072437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.064446 restraints weight = 14232.718| |-----------------------------------------------------------------------------| r_work (start): 0.2677 rms_B_bonded: 2.66 r_work: 0.2596 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5070 Z= 0.119 Angle : 0.535 6.054 6874 Z= 0.273 Chirality : 0.042 0.165 750 Planarity : 0.004 0.059 887 Dihedral : 3.609 19.953 684 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.95 % Allowed : 11.62 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.29 (0.33), residues: 619 helix: 0.86 (0.32), residues: 261 sheet: -0.03 (0.66), residues: 68 loop : -0.27 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 20 TYR 0.008 0.001 TYR B 217 PHE 0.013 0.001 PHE B 189 TRP 0.009 0.001 TRP B 420 HIS 0.004 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5066) covalent geometry : angle 0.52884 ( 6871) hydrogen bonds : bond 0.03939 ( 220) hydrogen bonds : angle 4.69540 ( 633) metal coordination : bond 0.01355 ( 4) metal coordination : angle 3.85266 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.136 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 45 average time/residue: 0.0600 time to fit residues: 3.6251 Evaluate side-chains 42 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain F residue 45 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.0470 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 54 optimal weight: 0.0670 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 117 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.074807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.066845 restraints weight = 13882.015| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.64 r_work: 0.2646 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5070 Z= 0.095 Angle : 0.493 5.721 6874 Z= 0.251 Chirality : 0.040 0.134 750 Planarity : 0.004 0.057 887 Dihedral : 3.491 16.635 684 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.14 % Allowed : 12.57 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.29 (0.33), residues: 619 helix: 1.02 (0.33), residues: 260 sheet: -0.57 (0.68), residues: 60 loop : -0.29 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 20 TYR 0.010 0.001 TYR B 217 PHE 0.010 0.001 PHE B 189 TRP 0.006 0.001 TRP B 420 HIS 0.003 0.001 HIS F 21 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 5066) covalent geometry : angle 0.48767 ( 6871) hydrogen bonds : bond 0.03427 ( 220) hydrogen bonds : angle 4.41264 ( 633) metal coordination : bond 0.00668 ( 4) metal coordination : angle 3.64686 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.134 Fit side-chains REVERT: F 76 PHE cc_start: 0.9142 (p90) cc_final: 0.8914 (p90) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.0635 time to fit residues: 3.9421 Evaluate side-chains 43 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 343 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 0.0000 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.072925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.064908 restraints weight = 14231.187| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.66 r_work: 0.2619 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5070 Z= 0.114 Angle : 0.489 5.308 6874 Z= 0.251 Chirality : 0.040 0.133 750 Planarity : 0.004 0.057 887 Dihedral : 3.476 18.651 684 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.14 % Allowed : 12.95 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.30 (0.33), residues: 619 helix: 1.03 (0.33), residues: 260 sheet: -0.54 (0.69), residues: 60 loop : -0.30 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 138 TYR 0.008 0.001 TYR B 217 PHE 0.008 0.001 PHE B 207 TRP 0.007 0.001 TRP F 142 HIS 0.004 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5066) covalent geometry : angle 0.48301 ( 6871) hydrogen bonds : bond 0.03627 ( 220) hydrogen bonds : angle 4.37054 ( 633) metal coordination : bond 0.01373 ( 4) metal coordination : angle 3.57405 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.186 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.0592 time to fit residues: 3.6726 Evaluate side-chains 43 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain F residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.072689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.064691 restraints weight = 14381.795| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 2.67 r_work: 0.2598 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5070 Z= 0.116 Angle : 0.489 6.067 6874 Z= 0.250 Chirality : 0.040 0.143 750 Planarity : 0.004 0.056 887 Dihedral : 3.496 17.632 684 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.33 % Allowed : 13.33 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.32 (0.33), residues: 619 helix: 1.02 (0.33), residues: 260 sheet: -0.51 (0.69), residues: 60 loop : -0.27 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 138 TYR 0.008 0.001 TYR B 217 PHE 0.010 0.001 PHE F 76 TRP 0.007 0.001 TRP F 142 HIS 0.004 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5066) covalent geometry : angle 0.48341 ( 6871) hydrogen bonds : bond 0.03606 ( 220) hydrogen bonds : angle 4.32115 ( 633) metal coordination : bond 0.01453 ( 4) metal coordination : angle 3.42874 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.135 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.0717 time to fit residues: 4.6245 Evaluate side-chains 44 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain F residue 45 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS F 57 ASN F 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.071063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.063110 restraints weight = 14268.528| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.64 r_work: 0.2570 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5070 Z= 0.158 Angle : 0.511 6.913 6874 Z= 0.263 Chirality : 0.042 0.180 750 Planarity : 0.004 0.056 887 Dihedral : 3.615 19.071 684 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.14 % Allowed : 14.48 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.27 (0.33), residues: 619 helix: 0.96 (0.33), residues: 259 sheet: -0.76 (0.64), residues: 70 loop : -0.18 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 138 TYR 0.009 0.001 TYR F 72 PHE 0.014 0.002 PHE F 76 TRP 0.009 0.001 TRP F 142 HIS 0.006 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 5066) covalent geometry : angle 0.50594 ( 6871) hydrogen bonds : bond 0.03967 ( 220) hydrogen bonds : angle 4.45750 ( 633) metal coordination : bond 0.01998 ( 4) metal coordination : angle 3.33426 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.190 Fit side-chains REVERT: B 493 MET cc_start: 0.7260 (mmt) cc_final: 0.6432 (mmt) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.0553 time to fit residues: 3.5712 Evaluate side-chains 43 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain F residue 45 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS F 57 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.072376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.064415 restraints weight = 14346.671| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 2.67 r_work: 0.2594 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5070 Z= 0.113 Angle : 0.496 7.679 6874 Z= 0.254 Chirality : 0.041 0.207 750 Planarity : 0.004 0.057 887 Dihedral : 3.581 16.645 684 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.76 % Allowed : 15.43 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.37 (0.33), residues: 619 helix: 1.05 (0.33), residues: 257 sheet: -0.73 (0.64), residues: 70 loop : -0.12 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 138 TYR 0.007 0.001 TYR B 217 PHE 0.012 0.001 PHE F 76 TRP 0.007 0.001 TRP F 142 HIS 0.003 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5066) covalent geometry : angle 0.49213 ( 6871) hydrogen bonds : bond 0.03575 ( 220) hydrogen bonds : angle 4.33911 ( 633) metal coordination : bond 0.00858 ( 4) metal coordination : angle 2.80709 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.197 Fit side-chains REVERT: B 98 MET cc_start: 0.9124 (mmt) cc_final: 0.8356 (mmt) outliers start: 4 outliers final: 4 residues processed: 42 average time/residue: 0.0623 time to fit residues: 3.5567 Evaluate side-chains 41 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain F residue 45 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.072925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.065008 restraints weight = 14307.018| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.67 r_work: 0.2611 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5070 Z= 0.110 Angle : 0.490 7.947 6874 Z= 0.251 Chirality : 0.041 0.251 750 Planarity : 0.004 0.056 887 Dihedral : 3.530 16.532 684 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.76 % Allowed : 16.00 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.42 (0.33), residues: 619 helix: 1.08 (0.33), residues: 257 sheet: -0.72 (0.64), residues: 70 loop : -0.06 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 138 TYR 0.007 0.001 TYR B 217 PHE 0.012 0.001 PHE F 76 TRP 0.007 0.001 TRP F 142 HIS 0.003 0.001 HIS F 25 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5066) covalent geometry : angle 0.48723 ( 6871) hydrogen bonds : bond 0.03520 ( 220) hydrogen bonds : angle 4.30883 ( 633) metal coordination : bond 0.00960 ( 4) metal coordination : angle 2.74414 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.197 Fit side-chains REVERT: B 98 MET cc_start: 0.9123 (mmt) cc_final: 0.8345 (mmt) outliers start: 4 outliers final: 4 residues processed: 41 average time/residue: 0.0792 time to fit residues: 4.2701 Evaluate side-chains 40 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain F residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 49 optimal weight: 0.0980 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.074136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.066395 restraints weight = 14523.274| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.67 r_work: 0.2643 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5070 Z= 0.094 Angle : 0.484 8.345 6874 Z= 0.247 Chirality : 0.041 0.256 750 Planarity : 0.004 0.055 887 Dihedral : 3.477 16.698 684 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.57 % Allowed : 16.38 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.53 (0.34), residues: 619 helix: 1.12 (0.33), residues: 258 sheet: -0.73 (0.64), residues: 70 loop : 0.06 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.007 0.001 TYR B 217 PHE 0.010 0.001 PHE F 76 TRP 0.006 0.001 TRP B 427 HIS 0.002 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 5066) covalent geometry : angle 0.48082 ( 6871) hydrogen bonds : bond 0.03244 ( 220) hydrogen bonds : angle 4.20315 ( 633) metal coordination : bond 0.00443 ( 4) metal coordination : angle 2.51384 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.157 Fit side-chains REVERT: B 98 MET cc_start: 0.9075 (mmt) cc_final: 0.8305 (mmt) REVERT: B 380 GLN cc_start: 0.9041 (tp40) cc_final: 0.8799 (tp40) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.0665 time to fit residues: 3.6701 Evaluate side-chains 37 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 0.0030 chunk 9 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 38 optimal weight: 0.0070 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 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 = 0.2896 r_free = 0.2896 target = 0.075263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.067417 restraints weight = 14507.952| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.71 r_work: 0.2674 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2677 r_free = 0.2677 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5070 Z= 0.091 Angle : 0.477 8.158 6874 Z= 0.244 Chirality : 0.040 0.248 750 Planarity : 0.004 0.054 887 Dihedral : 3.365 15.345 683 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.76 % Allowed : 16.00 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 aren not related in a simple way. whole: 0.61 (0.34), residues: 619 helix: 1.19 (0.33), residues: 259 sheet: -0.64 (0.65), residues: 70 loop : 0.08 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 336 TYR 0.008 0.001 TYR B 241 PHE 0.009 0.001 PHE B 207 TRP 0.005 0.001 TRP B 427 HIS 0.002 0.001 HIS F 71 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 5066) covalent geometry : angle 0.47395 ( 6871) hydrogen bonds : bond 0.03172 ( 220) hydrogen bonds : angle 4.15627 ( 633) metal coordination : bond 0.00403 ( 4) metal coordination : angle 2.45144 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1137.85 seconds wall clock time: 20 minutes 10.21 seconds (1210.21 seconds total)