Starting phenix.real_space_refine on Sun Apr 27 07:17:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8q_38156/04_2025/8x8q_38156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8q_38156/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8x8q_38156/04_2025/8x8q_38156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8q_38156/04_2025/8x8q_38156.map" model { file = "/net/cci-nas-00/data/ceres_data/8x8q_38156/04_2025/8x8q_38156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8q_38156/04_2025/8x8q_38156.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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, 'GLU:plan': 4, 'ARG:plan': 2, '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: 4.02, per 1000 atoms: 0.81 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: 1.25 Conformation dependent library (CDL) restraints added in 657.5 milliseconds 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: 0.55 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: 1.26 Time building geometry restraints manager: 1.48 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 17.570 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (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 TRP 0.023 0.002 TRP B 420 HIS 0.005 0.001 HIS F 21 PHE 0.026 0.003 PHE B 220 TYR 0.010 0.001 TYR B 217 ARG 0.004 0.001 ARG B 125 Details of bonding type rmsd hydrogen bonds : bond 0.17006 ( 220) hydrogen bonds : angle 6.64625 ( 633) metal coordination : bond 0.00687 ( 4) metal coordination : angle 4.24612 ( 3) covalent geometry : bond 0.00431 ( 5066) covalent geometry : angle 0.82517 ( 6871) *********************** 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 : 0.630 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: 0.1782 time to fit residues: 12.3179 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 : 0.621 ------------------------------------------------------------------------------- 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 52 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.2823 r_free = 0.2823 target = 0.071854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.063759 restraints weight = 14159.431| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 2.73 r_work: 0.2573 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 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 = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5070 Z= 0.150 Angle : 0.610 6.200 6874 Z= 0.313 Chirality : 0.043 0.185 750 Planarity : 0.004 0.061 887 Dihedral : 3.684 19.810 684 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.76 % Allowed : 12.19 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.33), residues: 619 helix: 0.79 (0.33), residues: 260 sheet: -0.08 (0.66), residues: 70 loop : -0.30 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 420 HIS 0.006 0.001 HIS F 25 PHE 0.018 0.002 PHE B 220 TYR 0.012 0.001 TYR B 217 ARG 0.005 0.001 ARG F 68 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 220) hydrogen bonds : angle 5.19329 ( 633) metal coordination : bond 0.01806 ( 4) metal coordination : angle 4.13630 ( 3) covalent geometry : bond 0.00348 ( 5066) covalent geometry : angle 0.60419 ( 6871) *********************** 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 47 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.592 Fit side-chains REVERT: B 152 MET cc_start: 0.8807 (mtm) cc_final: 0.8389 (mtm) outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.1711 time to fit residues: 10.2996 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 : 0.573 ------------------------------------------------------------------------------- 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 2 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.3980 chunk 55 optimal weight: 0.0970 chunk 58 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.2871 r_free = 0.2871 target = 0.074416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.066214 restraints weight = 14096.740| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.74 r_work: 0.2618 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5070 Z= 0.105 Angle : 0.529 6.084 6874 Z= 0.269 Chirality : 0.041 0.172 750 Planarity : 0.004 0.059 887 Dihedral : 3.591 18.550 684 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.57 % Allowed : 12.95 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.33), residues: 619 helix: 0.89 (0.33), residues: 261 sheet: -0.19 (0.65), residues: 70 loop : -0.22 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 420 HIS 0.003 0.001 HIS F 21 PHE 0.013 0.001 PHE B 189 TYR 0.008 0.001 TYR B 217 ARG 0.004 0.001 ARG F 68 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 220) hydrogen bonds : angle 4.65429 ( 633) metal coordination : bond 0.00853 ( 4) metal coordination : angle 3.82686 ( 3) covalent geometry : bond 0.00229 ( 5066) covalent geometry : angle 0.52275 ( 6871) *********************** 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 46 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.530 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.1668 time to fit residues: 9.9812 Evaluate side-chains 41 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 57 ASN F 117 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.073751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.065643 restraints weight = 14297.190| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.76 r_work: 0.2605 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2633 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2633 r_free = 0.2633 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2633 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1775 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= 0.113 Angle : 0.501 5.578 6874 Z= 0.256 Chirality : 0.040 0.134 750 Planarity : 0.004 0.059 887 Dihedral : 3.533 18.876 684 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.33 % Allowed : 12.76 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.33), residues: 619 helix: 0.93 (0.33), residues: 261 sheet: -0.60 (0.68), residues: 60 loop : -0.32 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 420 HIS 0.004 0.001 HIS F 25 PHE 0.010 0.001 PHE B 189 TYR 0.010 0.001 TYR B 217 ARG 0.003 0.001 ARG F 20 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 220) hydrogen bonds : angle 4.49572 ( 633) metal coordination : bond 0.01249 ( 4) metal coordination : angle 3.73730 ( 3) covalent geometry : bond 0.00261 ( 5066) covalent geometry : angle 0.49498 ( 6871) *********************** 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: 7 poor density : 40 time to evaluate : 0.576 Fit side-chains REVERT: B 98 MET cc_start: 0.9067 (mmt) cc_final: 0.8330 (mmt) outliers start: 7 outliers final: 4 residues processed: 45 average time/residue: 0.1679 time to fit residues: 10.3150 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 : 0.574 ------------------------------------------------------------------------------- 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 382 LEU Chi-restraints excluded: chain F residue 45 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.2843 r_free = 0.2843 target = 0.072675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.064649 restraints weight = 14224.934| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.66 r_work: 0.2610 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 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 = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5070 Z= 0.117 Angle : 0.491 5.376 6874 Z= 0.252 Chirality : 0.040 0.134 750 Planarity : 0.004 0.058 887 Dihedral : 3.516 18.302 684 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.14 % Allowed : 13.33 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.33), residues: 619 helix: 0.98 (0.33), residues: 260 sheet: -0.54 (0.68), residues: 60 loop : -0.29 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 142 HIS 0.004 0.001 HIS F 25 PHE 0.008 0.001 PHE B 220 TYR 0.009 0.001 TYR B 217 ARG 0.004 0.001 ARG F 138 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 220) hydrogen bonds : angle 4.43310 ( 633) metal coordination : bond 0.01405 ( 4) metal coordination : angle 3.58498 ( 3) covalent geometry : bond 0.00273 ( 5066) covalent geometry : angle 0.48542 ( 6871) *********************** 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 49 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.616 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.1824 time to fit residues: 12.1367 Evaluate side-chains 44 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 337 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 0 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.2795 r_free = 0.2795 target = 0.070693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.062852 restraints weight = 14215.105| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 2.64 r_work: 0.2564 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2578 r_free = 0.2578 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5070 Z= 0.164 Angle : 0.517 6.397 6874 Z= 0.267 Chirality : 0.042 0.142 750 Planarity : 0.004 0.058 887 Dihedral : 3.640 19.894 684 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.14 % Allowed : 14.29 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.33), residues: 619 helix: 0.91 (0.33), residues: 260 sheet: -0.74 (0.64), residues: 70 loop : -0.19 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 142 HIS 0.006 0.001 HIS F 25 PHE 0.012 0.002 PHE F 76 TYR 0.010 0.001 TYR B 143 ARG 0.004 0.001 ARG F 138 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 220) hydrogen bonds : angle 4.50943 ( 633) metal coordination : bond 0.02389 ( 4) metal coordination : angle 3.67373 ( 3) covalent geometry : bond 0.00392 ( 5066) covalent geometry : angle 0.51131 ( 6871) *********************** 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 47 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.733 Fit side-chains REVERT: B 493 MET cc_start: 0.7195 (mmt) cc_final: 0.6429 (mmt) outliers start: 6 outliers final: 3 residues processed: 47 average time/residue: 0.2097 time to fit residues: 13.6980 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 : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 337 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: 2.9990 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- 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 = 0.2845 r_free = 0.2845 target = 0.072856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.064929 restraints weight = 13900.042| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.62 r_work: 0.2610 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5070 Z= 0.104 Angle : 0.489 6.279 6874 Z= 0.251 Chirality : 0.040 0.165 750 Planarity : 0.004 0.057 887 Dihedral : 3.546 17.157 684 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.52 % Allowed : 14.48 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.33), residues: 619 helix: 0.96 (0.33), residues: 260 sheet: -0.74 (0.64), residues: 70 loop : -0.09 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 142 HIS 0.003 0.001 HIS F 25 PHE 0.009 0.001 PHE F 76 TYR 0.007 0.001 TYR B 217 ARG 0.004 0.000 ARG F 138 Details of bonding type rmsd hydrogen bonds : bond 0.03519 ( 220) hydrogen bonds : angle 4.34448 ( 633) metal coordination : bond 0.00781 ( 4) metal coordination : angle 2.89048 ( 3) covalent geometry : bond 0.00238 ( 5066) covalent geometry : angle 0.48519 ( 6871) *********************** 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 50 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.699 Fit side-chains REVERT: B 98 MET cc_start: 0.9106 (mmt) cc_final: 0.8327 (mmt) outliers start: 8 outliers final: 5 residues processed: 50 average time/residue: 0.1879 time to fit residues: 13.0108 Evaluate side-chains 46 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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 B residue 366 SER 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 32 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.2849 r_free = 0.2849 target = 0.073343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.065365 restraints weight = 14109.784| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.65 r_work: 0.2625 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- 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 = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5070 Z= 0.103 Angle : 0.486 8.004 6874 Z= 0.249 Chirality : 0.041 0.218 750 Planarity : 0.004 0.057 887 Dihedral : 3.501 16.318 684 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.95 % Allowed : 15.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.33), residues: 619 helix: 0.99 (0.33), residues: 260 sheet: -0.70 (0.64), residues: 70 loop : 0.01 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 142 HIS 0.003 0.001 HIS F 25 PHE 0.009 0.001 PHE F 76 TYR 0.007 0.001 TYR B 217 ARG 0.004 0.000 ARG F 138 Details of bonding type rmsd hydrogen bonds : bond 0.03410 ( 220) hydrogen bonds : angle 4.31383 ( 633) metal coordination : bond 0.00836 ( 4) metal coordination : angle 2.70261 ( 3) covalent geometry : bond 0.00235 ( 5066) covalent geometry : angle 0.48236 ( 6871) *********************** 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 45 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.616 Fit side-chains REVERT: B 98 MET cc_start: 0.9111 (mmt) cc_final: 0.8319 (mmt) outliers start: 5 outliers final: 4 residues processed: 45 average time/residue: 0.1855 time to fit residues: 11.4130 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 : 0.615 ------------------------------------------------------------------------------- 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 22 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 35 optimal weight: 0.4980 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.2858 r_free = 0.2858 target = 0.073197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.065419 restraints weight = 14198.004| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 2.61 r_work: 0.2635 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2637 r_free = 0.2637 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5070 Z= 0.101 Angle : 0.493 7.981 6874 Z= 0.250 Chirality : 0.041 0.241 750 Planarity : 0.004 0.056 887 Dihedral : 3.482 15.735 684 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.76 % Allowed : 16.38 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.33), residues: 619 helix: 1.01 (0.33), residues: 260 sheet: -0.72 (0.64), residues: 70 loop : 0.07 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 142 HIS 0.003 0.001 HIS F 25 PHE 0.008 0.001 PHE B 207 TYR 0.007 0.001 TYR B 217 ARG 0.004 0.000 ARG B 336 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 220) hydrogen bonds : angle 4.28263 ( 633) metal coordination : bond 0.00738 ( 4) metal coordination : angle 2.80770 ( 3) covalent geometry : bond 0.00228 ( 5066) covalent geometry : angle 0.48944 ( 6871) *********************** 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 43 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.704 Fit side-chains REVERT: B 98 MET cc_start: 0.9110 (mmt) cc_final: 0.8323 (mmt) outliers start: 4 outliers final: 4 residues processed: 43 average time/residue: 0.2631 time to fit residues: 16.0099 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 : 0.674 ------------------------------------------------------------------------------- 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 51 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.073528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.065753 restraints weight = 14428.812| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.62 r_work: 0.2638 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2353 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= 0.100 Angle : 0.488 8.364 6874 Z= 0.248 Chirality : 0.041 0.262 750 Planarity : 0.004 0.055 887 Dihedral : 3.448 15.607 684 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.95 % Allowed : 15.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.34), residues: 619 helix: 1.05 (0.33), residues: 260 sheet: -0.68 (0.64), residues: 70 loop : 0.09 (0.35), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 142 HIS 0.003 0.001 HIS F 25 PHE 0.008 0.001 PHE B 207 TYR 0.007 0.001 TYR B 217 ARG 0.004 0.000 ARG F 138 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 220) hydrogen bonds : angle 4.26552 ( 633) metal coordination : bond 0.00744 ( 4) metal coordination : angle 2.75215 ( 3) covalent geometry : bond 0.00228 ( 5066) covalent geometry : angle 0.48441 ( 6871) ********************** 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 44 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.920 Fit side-chains REVERT: B 98 MET cc_start: 0.9102 (mmt) cc_final: 0.8319 (mmt) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 0.2003 time to fit residues: 12.2639 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 : 0.659 ------------------------------------------------------------------------------- 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 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.2851 r_free = 0.2851 target = 0.072884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.065052 restraints weight = 14458.749| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.67 r_work: 0.2622 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- 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 = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5070 Z= 0.109 Angle : 0.496 8.426 6874 Z= 0.252 Chirality : 0.041 0.259 750 Planarity : 0.004 0.054 887 Dihedral : 3.453 16.088 684 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.95 % Allowed : 16.19 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.34), residues: 619 helix: 1.06 (0.33), residues: 259 sheet: -0.70 (0.65), residues: 70 loop : 0.09 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 142 HIS 0.004 0.001 HIS F 25 PHE 0.008 0.001 PHE B 207 TYR 0.007 0.001 TYR B 217 ARG 0.004 0.000 ARG F 138 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 220) hydrogen bonds : angle 4.27845 ( 633) metal coordination : bond 0.01098 ( 4) metal coordination : angle 2.89693 ( 3) covalent geometry : bond 0.00252 ( 5066) covalent geometry : angle 0.49259 ( 6871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2901.67 seconds wall clock time: 52 minutes 12.96 seconds (3132.96 seconds total)