Starting phenix.real_space_refine on Tue Jan 14 01:30:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8q_38156/01_2025/8x8q_38156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8q_38156/01_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_38156/01_2025/8x8q_38156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8q_38156/01_2025/8x8q_38156.map" model { file = "/net/cci-nas-00/data/ceres_data/8x8q_38156/01_2025/8x8q_38156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8q_38156/01_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-5571/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: 4.12, per 1000 atoms: 0.83 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: 1.28 Conformation dependent library (CDL) restraints added in 747.7 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: 1.34 Time building geometry restraints manager: 1.50 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: 1.290 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.470 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.910 ------------------------------------------------------------------------------- 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 5066 Z= 0.286 Angle : 0.825 8.157 6871 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 *********************** 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 : 0.661 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: 0.2363 time to fit residues: 16.1432 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 : 0.656 ------------------------------------------------------------------------------- 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 = 28)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.063758 restraints weight = 14159.432| |-----------------------------------------------------------------------------| 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 : 0.003 0.033 5066 Z= 0.225 Angle : 0.604 6.200 6871 Z= 0.312 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 *********************** 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 : 0.614 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: 0.1820 time to fit residues: 11.0459 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 : 0.541 ------------------------------------------------------------------------------- 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: 0.7980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.2856 r_free = 0.2856 target = 0.073930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.065815 restraints weight = 14131.304| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 2.74 r_work: 0.2607 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 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 = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5066 Z= 0.159 Angle : 0.526 6.155 6871 Z= 0.270 Chirality : 0.041 0.200 750 Planarity : 0.004 0.060 887 Dihedral : 3.607 19.007 684 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.57 % Allowed : 12.57 % Favored : 86.86 % 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: 0.31 (0.33), residues: 619 helix: 0.85 (0.33), residues: 261 sheet: -0.01 (0.66), residues: 68 loop : -0.23 (0.34), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 420 HIS 0.003 0.001 HIS F 21 PHE 0.013 0.001 PHE B 220 TYR 0.008 0.001 TYR B 217 ARG 0.004 0.001 ARG F 68 *********************** 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 : 0.557 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.1802 time to fit residues: 10.7711 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 : 0.615 ------------------------------------------------------------------------------- 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: 9.9990 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.0980 chunk 21 optimal weight: 0.0270 chunk 26 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 overall best weight: 0.4038 ------------------------------------------------------------------------------- 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 = 0.2882 r_free = 0.2882 target = 0.075101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.067073 restraints weight = 14178.319| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.68 r_work: 0.2647 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 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 = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5066 Z= 0.137 Angle : 0.489 5.696 6871 Z= 0.251 Chirality : 0.040 0.132 750 Planarity : 0.004 0.058 887 Dihedral : 3.494 17.371 684 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.33 % Allowed : 13.14 % 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: 0.26 (0.33), residues: 619 helix: 0.98 (0.33), residues: 260 sheet: -0.59 (0.68), residues: 60 loop : -0.29 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 420 HIS 0.003 0.001 HIS F 21 PHE 0.009 0.001 PHE B 220 TYR 0.010 0.001 TYR B 217 ARG 0.003 0.000 ARG F 20 *********************** 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 48 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.619 Fit side-chains REVERT: F 76 PHE cc_start: 0.9139 (p90) cc_final: 0.8890 (p90) outliers start: 7 outliers final: 3 residues processed: 47 average time/residue: 0.1613 time to fit residues: 10.3381 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 : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 60 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.2867 r_free = 0.2867 target = 0.074678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.066761 restraints weight = 14070.177| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.66 r_work: 0.2629 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5066 Z= 0.152 Angle : 0.478 5.381 6871 Z= 0.247 Chirality : 0.040 0.132 750 Planarity : 0.004 0.056 887 Dihedral : 3.457 17.936 684 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.33 % Allowed : 12.95 % Favored : 85.71 % 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: 0.32 (0.33), residues: 619 helix: 1.02 (0.33), residues: 260 sheet: -0.54 (0.68), residues: 60 loop : -0.25 (0.33), residues: 299 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 B 207 TYR 0.008 0.001 TYR B 217 ARG 0.003 0.000 ARG F 20 *********************** 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: 7 poor density : 42 time to evaluate : 0.573 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.1671 time to fit residues: 10.9215 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 : 0.525 ------------------------------------------------------------------------------- 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 0 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 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 = 0.2797 r_free = 0.2797 target = 0.070759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.062953 restraints weight = 14287.940| |-----------------------------------------------------------------------------| r_work (start): 0.2650 rms_B_bonded: 2.63 r_work: 0.2570 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5066 Z= 0.261 Angle : 0.516 5.507 6871 Z= 0.269 Chirality : 0.042 0.138 750 Planarity : 0.004 0.057 887 Dihedral : 3.657 20.361 684 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.14 % Allowed : 13.71 % Favored : 85.14 % 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: 0.25 (0.33), residues: 619 helix: 0.91 (0.33), residues: 260 sheet: -0.69 (0.64), residues: 70 loop : -0.18 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 142 HIS 0.006 0.001 HIS F 25 PHE 0.011 0.002 PHE F 76 TYR 0.010 0.001 TYR F 72 ARG 0.004 0.001 ARG F 138 *********************** 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 46 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.586 Fit side-chains REVERT: B 493 MET cc_start: 0.7270 (mmt) cc_final: 0.6472 (mmt) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.1657 time to fit residues: 10.4434 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 : 0.542 ------------------------------------------------------------------------------- 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 366 SER 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: 3.9990 chunk 32 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.2787 r_free = 0.2787 target = 0.069839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.061993 restraints weight = 14196.060| |-----------------------------------------------------------------------------| r_work (start): 0.2636 rms_B_bonded: 2.65 r_work: 0.2557 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2475 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2491 r_free = 0.2491 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5066 Z= 0.278 Angle : 0.530 6.863 6871 Z= 0.274 Chirality : 0.043 0.211 750 Planarity : 0.004 0.058 887 Dihedral : 3.734 19.805 684 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.95 % Allowed : 14.86 % Favored : 84.19 % 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 (0.33), residues: 619 helix: 0.83 (0.33), residues: 260 sheet: -0.79 (0.64), residues: 70 loop : -0.21 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 142 HIS 0.007 0.001 HIS F 25 PHE 0.013 0.002 PHE F 76 TYR 0.010 0.001 TYR F 72 ARG 0.003 0.001 ARG F 138 *********************** 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 43 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.594 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 43 average time/residue: 0.1751 time to fit residues: 10.1143 Evaluate side-chains 43 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.2790 r_free = 0.2790 target = 0.070477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.062635 restraints weight = 14369.781| |-----------------------------------------------------------------------------| r_work (start): 0.2625 rms_B_bonded: 2.66 r_work: 0.2545 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5066 Z= 0.249 Angle : 0.527 7.760 6871 Z= 0.271 Chirality : 0.042 0.211 750 Planarity : 0.004 0.057 887 Dihedral : 3.742 18.902 684 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.14 % Allowed : 15.62 % 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: 0.13 (0.33), residues: 619 helix: 0.80 (0.33), residues: 260 sheet: -0.87 (0.64), residues: 70 loop : -0.20 (0.34), 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 0.011 0.002 PHE F 76 TYR 0.009 0.001 TYR F 72 ARG 0.003 0.000 ARG F 138 *********************** 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 43 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.654 Fit side-chains REVERT: B 493 MET cc_start: 0.7286 (mmt) cc_final: 0.6525 (mmt) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.1998 time to fit residues: 11.8490 Evaluate side-chains 42 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 0.0060 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- 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 = 0.072334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.064532 restraints weight = 14287.452| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.65 r_work: 0.2610 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 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 = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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 : 0.002 0.027 5066 Z= 0.160 Angle : 0.503 8.418 6871 Z= 0.258 Chirality : 0.041 0.242 750 Planarity : 0.004 0.057 887 Dihedral : 3.619 16.850 684 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.95 % Allowed : 16.57 % Favored : 82.48 % 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: 0.18 (0.33), residues: 619 helix: 0.75 (0.33), residues: 266 sheet: -0.82 (0.64), residues: 70 loop : -0.10 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 122 HIS 0.003 0.001 HIS F 71 PHE 0.008 0.001 PHE F 76 TYR 0.008 0.001 TYR B 217 ARG 0.003 0.000 ARG B 336 *********************** 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: 5 poor density : 38 time to evaluate : 0.527 Fit side-chains REVERT: B 98 MET cc_start: 0.9117 (mmt) cc_final: 0.8287 (mmt) REVERT: B 493 MET cc_start: 0.7147 (mmt) cc_final: 0.6248 (mmt) outliers start: 5 outliers final: 5 residues processed: 43 average time/residue: 0.1741 time to fit residues: 10.0836 Evaluate side-chains 41 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 437 LEU 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: 0.7980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.2821 r_free = 0.2821 target = 0.071876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.063919 restraints weight = 14284.900| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.67 r_work: 0.2588 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5066 Z= 0.200 Angle : 0.516 8.672 6871 Z= 0.264 Chirality : 0.042 0.263 750 Planarity : 0.004 0.057 887 Dihedral : 3.636 17.433 684 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.95 % Allowed : 16.38 % Favored : 82.67 % 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: 0.17 (0.33), residues: 619 helix: 0.73 (0.33), residues: 266 sheet: -0.83 (0.64), residues: 70 loop : -0.08 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 142 HIS 0.005 0.001 HIS F 25 PHE 0.009 0.001 PHE F 76 TYR 0.008 0.001 TYR F 72 ARG 0.003 0.000 ARG B 336 ********************** 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 41 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 1.052 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 0.2007 time to fit residues: 11.3964 Evaluate side-chains 41 residues out of total 542 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 437 LEU 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: 0.7980 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 58 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.072996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.065018 restraints weight = 14263.169| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.70 r_work: 0.2607 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5066 Z= 0.166 Angle : 0.504 8.681 6871 Z= 0.258 Chirality : 0.041 0.256 750 Planarity : 0.004 0.056 887 Dihedral : 3.592 16.723 684 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.95 % Allowed : 16.38 % Favored : 82.67 % 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: 0.25 (0.33), residues: 619 helix: 0.78 (0.33), residues: 266 sheet: -0.80 (0.64), residues: 70 loop : -0.01 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 142 HIS 0.003 0.001 HIS F 25 PHE 0.008 0.001 PHE F 76 TYR 0.007 0.001 TYR B 217 ARG 0.003 0.000 ARG B 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2696.45 seconds wall clock time: 50 minutes 1.41 seconds (3001.41 seconds total)