Starting phenix.real_space_refine on Mon Jun 24 20:46:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8q_38156/06_2024/8x8q_38156.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8q_38156/06_2024/8x8q_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8q_38156/06_2024/8x8q_38156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8q_38156/06_2024/8x8q_38156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8q_38156/06_2024/8x8q_38156.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8q_38156/06_2024/8x8q_38156.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 4.41, per 1000 atoms: 0.89 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 - 3.50 Amino acid : False - 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: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.48 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: 1.28 Time building geometry restraints manager: 1.94 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: 98.18 - 105.38: 85 105.38 - 112.57: 2527 112.57 - 119.77: 1820 119.77 - 126.97: 2375 126.97 - 134.16: 64 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 2.440 nonbonded pdb=" OE1 GLU B 58 " pdb=" NZ LYS B 62 " model vdw 2.231 2.520 nonbonded pdb=" O CYS B 277 " pdb=" OH TYR B 313 " model vdw 2.232 2.440 nonbonded pdb=" OE1 GLU B 164 " pdb=" OG SER B 170 " model vdw 2.247 2.440 nonbonded pdb=" ND2 ASN B 278 " pdb=" OE1 GLN B 308 " model vdw 2.252 2.520 ... (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 ========== 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.410 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.900 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.598 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: 0.1715 time to fit residues: 11.6559 Evaluate side-chains 44 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 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 F 57 ASN F 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5066 Z= 0.175 Angle : 0.580 6.692 6871 Z= 0.294 Chirality : 0.042 0.186 750 Planarity : 0.004 0.060 887 Dihedral : 3.575 17.596 684 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.95 % Allowed : 11.62 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.33), residues: 262 sheet: 0.05 (0.66), residues: 70 loop : -0.26 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 420 HIS 0.004 0.001 HIS F 25 PHE 0.018 0.002 PHE B 220 TYR 0.011 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 50 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.566 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.2233 time to fit residues: 14.0118 Evaluate side-chains 44 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 437 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5066 Z= 0.171 Angle : 0.515 5.933 6871 Z= 0.263 Chirality : 0.041 0.202 750 Planarity : 0.004 0.058 887 Dihedral : 3.512 19.777 684 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.95 % Allowed : 12.00 % 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: 0.46 (0.33), residues: 619 helix: 1.01 (0.33), residues: 262 sheet: 0.08 (0.66), residues: 68 loop : -0.20 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 420 HIS 0.004 0.001 HIS F 25 PHE 0.013 0.002 PHE B 220 TYR 0.009 0.001 TYR B 288 ARG 0.004 0.000 ARG F 20 *********************** 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 45 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.593 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 45 average time/residue: 0.1885 time to fit residues: 11.3826 Evaluate side-chains 40 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 45 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1696 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= 0.209 Angle : 0.497 5.379 6871 Z= 0.257 Chirality : 0.041 0.134 750 Planarity : 0.004 0.059 887 Dihedral : 3.523 19.354 684 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.52 % Allowed : 13.14 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.33), residues: 619 helix: 1.04 (0.33), residues: 261 sheet: -0.28 (0.64), residues: 70 loop : -0.21 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 142 HIS 0.005 0.001 HIS F 25 PHE 0.010 0.002 PHE B 220 TYR 0.009 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 50 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.575 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.1418 time to fit residues: 9.6284 Evaluate side-chains 44 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 B residue 437 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 34 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5066 Z= 0.148 Angle : 0.470 5.332 6871 Z= 0.242 Chirality : 0.039 0.133 750 Planarity : 0.004 0.056 887 Dihedral : 3.417 17.229 684 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.33 % Allowed : 13.33 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.33), residues: 619 helix: 1.15 (0.33), residues: 260 sheet: -0.26 (0.64), residues: 70 loop : -0.13 (0.34), 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 B 220 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 fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.589 Fit side-chains REVERT: F 76 PHE cc_start: 0.9095 (p90) cc_final: 0.8842 (p90) outliers start: 7 outliers final: 2 residues processed: 48 average time/residue: 0.1638 time to fit residues: 10.6772 Evaluate side-chains 42 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 321 PHE Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 0.0970 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- 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 F 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2007 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= 0.158 Angle : 0.472 5.975 6871 Z= 0.242 Chirality : 0.040 0.162 750 Planarity : 0.004 0.055 887 Dihedral : 3.422 17.470 684 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.95 % Allowed : 14.10 % Favored : 84.95 % 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: 0.55 (0.33), residues: 619 helix: 1.17 (0.33), residues: 260 sheet: -0.40 (0.63), residues: 70 loop : -0.07 (0.35), residues: 289 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 0.009 0.001 PHE B 220 TYR 0.007 0.001 TYR B 217 ARG 0.003 0.000 ARG F 20 *********************** 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 fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 0.521 Fit side-chains REVERT: F 76 PHE cc_start: 0.9089 (p90) cc_final: 0.8860 (p90) outliers start: 5 outliers final: 5 residues processed: 47 average time/residue: 0.1693 time to fit residues: 10.7074 Evaluate side-chains 45 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 382 LEU 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 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 0.4980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5066 Z= 0.158 Angle : 0.476 6.735 6871 Z= 0.243 Chirality : 0.040 0.175 750 Planarity : 0.004 0.054 887 Dihedral : 3.441 17.061 684 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.33 % Allowed : 14.10 % 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: 0.59 (0.33), residues: 619 helix: 1.21 (0.33), residues: 260 sheet: -0.42 (0.64), residues: 70 loop : -0.04 (0.35), residues: 289 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 B 207 TYR 0.007 0.001 TYR B 217 ARG 0.003 0.000 ARG F 20 *********************** 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 48 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.635 Fit side-chains REVERT: B 98 MET cc_start: 0.9163 (mmt) cc_final: 0.8370 (mmt) REVERT: F 76 PHE cc_start: 0.9062 (p90) cc_final: 0.8840 (p90) outliers start: 7 outliers final: 4 residues processed: 48 average time/residue: 0.1533 time to fit residues: 10.4184 Evaluate side-chains 44 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 HIS F 57 ASN F 117 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5066 Z= 0.170 Angle : 0.482 7.178 6871 Z= 0.245 Chirality : 0.040 0.215 750 Planarity : 0.004 0.054 887 Dihedral : 3.476 17.377 684 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.76 % Allowed : 15.05 % 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: 0.48 (0.33), residues: 619 helix: 1.06 (0.33), residues: 266 sheet: -0.48 (0.64), residues: 70 loop : -0.05 (0.35), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 F 72 ARG 0.003 0.000 ARG F 20 *********************** 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 fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.556 Fit side-chains REVERT: B 98 MET cc_start: 0.9180 (mmt) cc_final: 0.8384 (mmt) REVERT: F 76 PHE cc_start: 0.9071 (p90) cc_final: 0.8854 (p90) outliers start: 4 outliers final: 4 residues processed: 45 average time/residue: 0.1602 time to fit residues: 10.1271 Evaluate side-chains 44 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 40 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5066 Z= 0.149 Angle : 0.478 7.975 6871 Z= 0.243 Chirality : 0.040 0.248 750 Planarity : 0.004 0.054 887 Dihedral : 3.441 16.007 684 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.95 % Allowed : 15.24 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.34), residues: 619 helix: 1.14 (0.33), residues: 265 sheet: -0.48 (0.64), residues: 70 loop : -0.01 (0.35), residues: 284 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 B 207 TYR 0.007 0.001 TYR B 241 ARG 0.003 0.000 ARG F 20 *********************** 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 46 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 0.519 Fit side-chains REVERT: B 98 MET cc_start: 0.9139 (mmt) cc_final: 0.8369 (mmt) outliers start: 5 outliers final: 5 residues processed: 46 average time/residue: 0.1661 time to fit residues: 10.3892 Evaluate side-chains 44 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 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 343 VAL Chi-restraints excluded: chain B residue 366 SER 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 61 optimal weight: 0.9980 chunk 56 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5066 Z= 0.149 Angle : 0.481 8.461 6871 Z= 0.244 Chirality : 0.041 0.258 750 Planarity : 0.004 0.054 887 Dihedral : 3.437 16.268 684 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.14 % Allowed : 15.24 % Favored : 83.62 % 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: 0.70 (0.34), residues: 619 helix: 1.31 (0.33), residues: 259 sheet: -0.49 (0.64), residues: 70 loop : 0.06 (0.35), residues: 290 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 0.011 0.001 PHE F 76 TYR 0.006 0.001 TYR B 217 ARG 0.003 0.000 ARG F 115 ********************** 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 46 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.668 Fit side-chains REVERT: B 98 MET cc_start: 0.9141 (mmt) cc_final: 0.8365 (mmt) outliers start: 6 outliers final: 5 residues processed: 46 average time/residue: 0.1731 time to fit residues: 10.8503 Evaluate side-chains 44 residues out of total 542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 0.0570 chunk 20 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 0.0470 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 0.3980 chunk 35 optimal weight: 0.5980 chunk 56 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 overall best weight: 0.2996 ------------------------------------------------------------------------------- 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 = 0.2896 r_free = 0.2896 target = 0.075237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.067376 restraints weight = 14149.630| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 2.63 r_work: 0.2662 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5066 Z= 0.122 Angle : 0.470 8.099 6871 Z= 0.238 Chirality : 0.040 0.251 750 Planarity : 0.003 0.053 887 Dihedral : 3.363 14.967 684 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.95 % Allowed : 15.24 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.68 (0.34), residues: 619 helix: 1.22 (0.33), residues: 265 sheet: -0.50 (0.64), residues: 70 loop : 0.10 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 427 HIS 0.002 0.000 HIS F 21 PHE 0.008 0.001 PHE B 207 TYR 0.007 0.001 TYR B 241 ARG 0.002 0.000 ARG F 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1462.24 seconds wall clock time: 26 minutes 56.65 seconds (1616.65 seconds total)