Starting phenix.real_space_refine on Wed Oct 9 20:42:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/10_2024/8vzn_43683.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/10_2024/8vzn_43683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/10_2024/8vzn_43683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/10_2024/8vzn_43683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/10_2024/8vzn_43683.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vzn_43683/10_2024/8vzn_43683.cif" } resolution = 2.77 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= 0.033 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3068 2.51 5 N 748 2.21 5 O 814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 4656 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3246 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 15, 'TRANS': 401} Chain breaks: 1 Chain: "B" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 933 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "C" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 470 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain breaks: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'CHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.05, per 1000 atoms: 0.87 Number of scatterers: 4656 At special positions: 0 Unit cell: (73.87, 68.06, 118.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 814 8.00 N 748 7.00 C 3068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.05 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: 1.24 Conformation dependent library (CDL) restraints added in 658.1 milliseconds 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1090 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 62.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 106 through 127 removed outlier: 3.504A pdb=" N VAL A 111 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.605A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 158 removed outlier: 3.628A pdb=" N ILE A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 172 through 191 Processing helix chain 'A' and resid 192 through 195 removed outlier: 3.862A pdb=" N LEU A 195 " --> pdb=" O LEU A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 195' Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.503A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.913A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 268 through 295 removed outlier: 3.588A pdb=" N MET A 276 " --> pdb=" O HIS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 312 removed outlier: 3.540A pdb=" N ALA A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.630A pdb=" N ARG A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 353 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 365 through 395 Processing helix chain 'A' and resid 396 through 419 Processing helix chain 'A' and resid 423 through 453 removed outlier: 3.824A pdb=" N VAL A 427 " --> pdb=" O HIS A 423 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 442 " --> pdb=" O MET A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 457 through 488 Processing helix chain 'A' and resid 488 through 508 removed outlier: 3.981A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A 499 " --> pdb=" O PHE A 495 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 removed outlier: 3.771A pdb=" N LYS A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 14 removed outlier: 6.633A pdb=" N GLY B 13 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE B 37 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B 53 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA B 43 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 26 Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.417A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TYR C 50 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 98 " --> pdb=" O GLN C 91 " (cutoff:3.500A) 296 hydrogen bonds defined for protein. 873 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: 1.35 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 690 1.29 - 1.42: 1370 1.42 - 1.55: 2680 1.55 - 1.68: 1 1.68 - 1.81: 41 Bond restraints: 4782 Sorted by residual: bond pdb=" CA TYR A 271 " pdb=" C TYR A 271 " ideal model delta sigma weight residual 1.524 1.432 0.092 1.32e-02 5.74e+03 4.81e+01 bond pdb=" CA ALA A 270 " pdb=" CB ALA A 270 " ideal model delta sigma weight residual 1.529 1.424 0.105 1.78e-02 3.16e+03 3.50e+01 bond pdb=" C ARG A 106 " pdb=" O ARG A 106 " ideal model delta sigma weight residual 1.236 1.163 0.073 1.29e-02 6.01e+03 3.18e+01 bond pdb=" C ILE A 126 " pdb=" O ILE A 126 " ideal model delta sigma weight residual 1.235 1.155 0.080 1.45e-02 4.76e+03 3.04e+01 bond pdb=" C LYS B 102 " pdb=" O LYS B 102 " ideal model delta sigma weight residual 1.234 1.168 0.067 1.22e-02 6.72e+03 3.00e+01 ... (remaining 4777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 5643 2.04 - 4.07: 670 4.07 - 6.11: 138 6.11 - 8.14: 38 8.14 - 10.18: 17 Bond angle restraints: 6506 Sorted by residual: angle pdb=" O CYS A 120 " pdb=" C CYS A 120 " pdb=" N ASN A 121 " ideal model delta sigma weight residual 122.12 114.16 7.96 1.06e+00 8.90e-01 5.64e+01 angle pdb=" N ALA C 33 " pdb=" CA ALA C 33 " pdb=" C ALA C 33 " ideal model delta sigma weight residual 110.88 101.31 9.57 1.28e+00 6.10e-01 5.59e+01 angle pdb=" C GLN B 16 " pdb=" CA GLN B 16 " pdb=" CB GLN B 16 " ideal model delta sigma weight residual 108.68 118.86 -10.18 1.39e+00 5.18e-01 5.36e+01 angle pdb=" CA TRP A 425 " pdb=" C TRP A 425 " pdb=" O TRP A 425 " ideal model delta sigma weight residual 120.24 112.37 7.87 1.11e+00 8.12e-01 5.03e+01 angle pdb=" N TYR A 454 " pdb=" CA TYR A 454 " pdb=" CB TYR A 454 " ideal model delta sigma weight residual 110.42 118.54 -8.12 1.18e+00 7.18e-01 4.74e+01 ... (remaining 6501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 2475 17.85 - 35.70: 210 35.70 - 53.55: 35 53.55 - 71.41: 13 71.41 - 89.26: 8 Dihedral angle restraints: 2741 sinusoidal: 1026 harmonic: 1715 Sorted by residual: dihedral pdb=" CD ARG B 70 " pdb=" NE ARG B 70 " pdb=" CZ ARG B 70 " pdb=" NH1 ARG B 70 " ideal model delta sinusoidal sigma weight residual 0.00 88.68 -88.68 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CD ARG B 114 " pdb=" NE ARG B 114 " pdb=" CZ ARG B 114 " pdb=" NH1 ARG B 114 " ideal model delta sinusoidal sigma weight residual 0.00 87.99 -87.99 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CD ARG A 107 " pdb=" NE ARG A 107 " pdb=" CZ ARG A 107 " pdb=" NH1 ARG A 107 " ideal model delta sinusoidal sigma weight residual 0.00 86.98 -86.98 1 1.00e+01 1.00e-02 9.09e+01 ... (remaining 2738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 459 0.067 - 0.134: 198 0.134 - 0.201: 59 0.201 - 0.268: 17 0.268 - 0.335: 3 Chirality restraints: 736 Sorted by residual: chirality pdb=" CB VAL C 34 " pdb=" CA VAL C 34 " pdb=" CG1 VAL C 34 " pdb=" CG2 VAL C 34 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA SER A 104 " pdb=" N SER A 104 " pdb=" C SER A 104 " pdb=" CB SER A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LYS C 40 " pdb=" N LYS C 40 " pdb=" C LYS C 40 " pdb=" CB LYS C 40 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 733 not shown) Planarity restraints: 795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 70 " 1.103 9.50e-02 1.11e+02 4.94e-01 1.47e+02 pdb=" NE ARG B 70 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 70 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG B 70 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 70 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 107 " -1.098 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 107 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 107 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 107 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 107 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 114 " 1.089 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG B 114 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 114 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 114 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 114 " 0.015 2.00e-02 2.50e+03 ... (remaining 792 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1640 2.84 - 3.36: 4385 3.36 - 3.87: 8138 3.87 - 4.39: 9851 4.39 - 4.90: 16081 Nonbonded interactions: 40095 Sorted by model distance: nonbonded pdb=" O LEU A 195 " pdb=" OH TYR B 104 " model vdw 2.330 3.040 nonbonded pdb=" O THR A 175 " pdb=" OG1 THR A 179 " model vdw 2.335 3.040 nonbonded pdb=" OH TYR A 128 " pdb=" OG1 THR A 203 " model vdw 2.369 3.040 nonbonded pdb=" O ALA A 449 " pdb=" OG1 THR A 453 " model vdw 2.379 3.040 nonbonded pdb=" N LYS B 102 " pdb=" O LYS B 102 " model vdw 2.414 2.496 ... (remaining 40090 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.090 Process input model: 16.540 Find NCS groups from input model: 0.050 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 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 : 0.015 0.105 4782 Z= 0.967 Angle : 1.531 10.176 6506 Z= 1.057 Chirality : 0.084 0.335 736 Planarity : 0.039 0.494 795 Dihedral : 15.045 89.256 1645 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.81 % Allowed : 8.82 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.34 (0.29), residues: 586 helix: -1.97 (0.23), residues: 348 sheet: -2.12 (0.55), residues: 67 loop : -2.28 (0.42), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 121 HIS 0.008 0.003 HIS B 112 PHE 0.026 0.004 PHE A 436 TYR 0.019 0.003 TYR A 117 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.534 Fit side-chains REVERT: A 102 LYS cc_start: 0.6915 (tttm) cc_final: 0.6684 (ttmm) REVERT: A 253 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.7334 (t80) REVERT: A 381 MET cc_start: 0.8352 (mtm) cc_final: 0.8152 (mtp) REVERT: A 511 LYS cc_start: 0.8079 (tttt) cc_final: 0.7517 (mttp) REVERT: B 106 TRP cc_start: 0.8598 (OUTLIER) cc_final: 0.8396 (t-100) outliers start: 14 outliers final: 1 residues processed: 87 average time/residue: 1.5749 time to fit residues: 141.8179 Evaluate side-chains 64 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain B residue 106 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 355 ASN A 422 ASN C 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4782 Z= 0.216 Angle : 0.572 7.467 6506 Z= 0.310 Chirality : 0.041 0.153 736 Planarity : 0.005 0.048 795 Dihedral : 5.947 53.011 651 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.40 % Allowed : 13.83 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.53 (0.34), residues: 586 helix: 0.46 (0.27), residues: 352 sheet: -1.23 (0.61), residues: 65 loop : -1.55 (0.45), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.002 0.001 HIS B 38 PHE 0.018 0.002 PHE A 144 TYR 0.025 0.001 TYR A 117 ARG 0.005 0.001 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8557 (t80) cc_final: 0.8328 (t80) REVERT: A 253 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8681 (m-80) REVERT: A 381 MET cc_start: 0.8180 (mtm) cc_final: 0.7958 (mtp) REVERT: A 511 LYS cc_start: 0.8094 (tttt) cc_final: 0.7500 (mttp) outliers start: 7 outliers final: 2 residues processed: 71 average time/residue: 1.2359 time to fit residues: 91.3738 Evaluate side-chains 65 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 40 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.0670 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.0370 chunk 39 optimal weight: 0.8980 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 330 ASN A 422 ASN C 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4782 Z= 0.149 Angle : 0.497 6.523 6506 Z= 0.265 Chirality : 0.039 0.146 736 Planarity : 0.004 0.045 795 Dihedral : 4.748 48.036 647 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.00 % Allowed : 15.03 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.35), residues: 586 helix: 1.62 (0.28), residues: 349 sheet: -1.18 (0.63), residues: 55 loop : -1.11 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.002 0.001 HIS B 38 PHE 0.015 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8504 (t80) cc_final: 0.8259 (t80) REVERT: A 223 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7345 (ttt90) REVERT: A 253 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8737 (m-80) REVERT: A 381 MET cc_start: 0.8079 (mtm) cc_final: 0.7853 (mtp) REVERT: A 511 LYS cc_start: 0.8088 (tttt) cc_final: 0.7489 (mttp) outliers start: 5 outliers final: 3 residues processed: 66 average time/residue: 1.3865 time to fit residues: 95.1910 Evaluate side-chains 64 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.0470 chunk 56 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 15 optimal weight: 0.0670 chunk 46 optimal weight: 0.3980 chunk 31 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4782 Z= 0.151 Angle : 0.487 6.434 6506 Z= 0.258 Chirality : 0.039 0.145 736 Planarity : 0.004 0.047 795 Dihedral : 4.610 46.789 647 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.20 % Allowed : 15.63 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.35), residues: 586 helix: 2.01 (0.28), residues: 349 sheet: -1.10 (0.63), residues: 54 loop : -0.82 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.002 0.001 HIS B 38 PHE 0.014 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.536 Fit side-chains REVERT: A 157 TYR cc_start: 0.8470 (t80) cc_final: 0.8235 (t80) REVERT: A 223 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7393 (ttt90) REVERT: A 253 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8747 (m-80) REVERT: A 381 MET cc_start: 0.8087 (mtm) cc_final: 0.7873 (mtp) REVERT: A 447 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 511 LYS cc_start: 0.8063 (tttt) cc_final: 0.7489 (mttp) outliers start: 6 outliers final: 3 residues processed: 66 average time/residue: 1.3932 time to fit residues: 95.7939 Evaluate side-chains 63 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4782 Z= 0.204 Angle : 0.510 6.545 6506 Z= 0.271 Chirality : 0.040 0.151 736 Planarity : 0.004 0.049 795 Dihedral : 4.712 45.006 647 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.60 % Allowed : 14.83 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.36), residues: 586 helix: 1.99 (0.27), residues: 351 sheet: -0.80 (0.63), residues: 55 loop : -0.61 (0.49), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 108 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 516 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7405 (ttt90) REVERT: A 253 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8652 (m-80) REVERT: A 511 LYS cc_start: 0.8086 (tttt) cc_final: 0.7498 (mttp) outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 1.3817 time to fit residues: 90.6844 Evaluate side-chains 65 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN C 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4782 Z= 0.175 Angle : 0.494 6.451 6506 Z= 0.261 Chirality : 0.040 0.149 736 Planarity : 0.004 0.052 795 Dihedral : 4.597 44.561 647 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.00 % Allowed : 15.03 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.36), residues: 586 helix: 2.08 (0.27), residues: 355 sheet: -0.57 (0.64), residues: 55 loop : -0.60 (0.50), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.002 0.001 HIS B 38 PHE 0.015 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 515 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7407 (ttt90) REVERT: A 511 LYS cc_start: 0.8056 (tttt) cc_final: 0.7494 (mttp) outliers start: 10 outliers final: 5 residues processed: 66 average time/residue: 1.4399 time to fit residues: 98.9460 Evaluate side-chains 66 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4782 Z= 0.201 Angle : 0.516 6.509 6506 Z= 0.272 Chirality : 0.041 0.172 736 Planarity : 0.005 0.052 795 Dihedral : 4.177 15.899 645 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.40 % Allowed : 15.83 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.36), residues: 586 helix: 2.05 (0.27), residues: 355 sheet: -0.38 (0.65), residues: 55 loop : -0.36 (0.52), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.001 PHE A 144 TYR 0.023 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7422 (ttt90) REVERT: A 447 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 511 LYS cc_start: 0.8077 (tttt) cc_final: 0.7477 (mttp) outliers start: 7 outliers final: 5 residues processed: 65 average time/residue: 1.4353 time to fit residues: 96.8823 Evaluate side-chains 67 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 61 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS A 330 ASN C 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4782 Z= 0.245 Angle : 0.537 6.620 6506 Z= 0.282 Chirality : 0.042 0.188 736 Planarity : 0.005 0.052 795 Dihedral : 4.288 17.914 645 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.40 % Allowed : 15.83 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.57 (0.36), residues: 586 helix: 2.00 (0.28), residues: 351 sheet: -0.31 (0.65), residues: 55 loop : -0.41 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.555 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7391 (ttt90) REVERT: A 511 LYS cc_start: 0.8092 (tttt) cc_final: 0.7470 (mttp) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 1.3766 time to fit residues: 89.0021 Evaluate side-chains 64 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4782 Z= 0.227 Angle : 0.531 7.873 6506 Z= 0.278 Chirality : 0.042 0.193 736 Planarity : 0.005 0.054 795 Dihedral : 4.250 17.027 645 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.20 % Allowed : 16.63 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.60 (0.36), residues: 586 helix: 2.02 (0.27), residues: 353 sheet: -0.23 (0.65), residues: 55 loop : -0.42 (0.51), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7376 (ttt90) REVERT: A 451 GLU cc_start: 0.8719 (tp30) cc_final: 0.8412 (tp30) REVERT: A 511 LYS cc_start: 0.8077 (tttt) cc_final: 0.7441 (mttp) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 1.4196 time to fit residues: 90.1273 Evaluate side-chains 63 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.1980 chunk 46 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4782 Z= 0.170 Angle : 0.504 7.916 6506 Z= 0.263 Chirality : 0.040 0.196 736 Planarity : 0.004 0.054 795 Dihedral : 4.083 15.380 645 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.20 % Allowed : 16.43 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.36), residues: 586 helix: 2.14 (0.27), residues: 355 sheet: -0.29 (0.64), residues: 56 loop : -0.43 (0.51), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.014 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 516 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1172 Ramachandran restraints generated. 586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7408 (ttt90) REVERT: A 447 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7454 (mm-30) REVERT: A 511 LYS cc_start: 0.8074 (tttt) cc_final: 0.7438 (mttp) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 1.3909 time to fit residues: 88.3565 Evaluate side-chains 64 residues out of total 499 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 92 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.165322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.114710 restraints weight = 4812.589| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.92 r_work: 0.3094 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4782 Z= 0.221 Angle : 0.518 6.557 6506 Z= 0.274 Chirality : 0.041 0.154 736 Planarity : 0.005 0.054 795 Dihedral : 4.190 16.123 645 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.40 % Allowed : 16.23 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.67 (0.36), residues: 586 helix: 2.04 (0.27), residues: 354 sheet: -0.24 (0.64), residues: 56 loop : -0.30 (0.51), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 189 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.01 seconds wall clock time: 44 minutes 6.75 seconds (2646.75 seconds total)