Starting phenix.real_space_refine on Thu Mar 6 03:24:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vzn_43683/03_2025/8vzn_43683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vzn_43683/03_2025/8vzn_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/cci-nas-00/data/ceres_data/8vzn_43683/03_2025/8vzn_43683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vzn_43683/03_2025/8vzn_43683.map" model { file = "/net/cci-nas-00/data/ceres_data/8vzn_43683/03_2025/8vzn_43683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vzn_43683/03_2025/8vzn_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-5624/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: 4.32, per 1000 atoms: 0.93 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: 1.25 Conformation dependent library (CDL) restraints added in 570.6 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: 0.42 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: 1.25 Time building geometry restraints manager: 1.43 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: 3.760 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.320 Find NCS groups from input model: 0.040 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:14.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.505 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: 1.3472 time to fit residues: 121.4205 Evaluate side-chains 64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.166358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.115715 restraints weight = 4711.664| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.94 r_work: 0.3118 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 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 to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8881 (t80) cc_final: 0.8661 (t80) REVERT: A 253 PHE cc_start: 0.9097 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: A 297 GLU cc_start: 0.7367 (mp0) cc_final: 0.7078 (tp30) REVERT: A 381 MET cc_start: 0.8340 (mtm) cc_final: 0.8115 (mtp) REVERT: A 511 LYS cc_start: 0.8226 (tttt) cc_final: 0.7384 (mttp) outliers start: 7 outliers final: 2 residues processed: 71 average time/residue: 1.2649 time to fit residues: 93.3741 Evaluate side-chains 65 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 6 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 330 ASN A 422 ASN C 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.165851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114906 restraints weight = 4760.140| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.95 r_work: 0.3109 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2458 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= 0.214 Angle : 0.532 6.678 6506 Z= 0.285 Chirality : 0.040 0.151 736 Planarity : 0.005 0.046 795 Dihedral : 4.943 46.237 647 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.40 % Allowed : 15.03 % 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: 0.65 (0.35), residues: 586 helix: 1.46 (0.28), residues: 348 sheet: -1.23 (0.64), residues: 55 loop : -0.97 (0.46), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 108 HIS 0.003 0.001 HIS B 38 PHE 0.017 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 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 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.8869 (t80) cc_final: 0.8617 (t80) REVERT: A 223 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7541 (ttt90) REVERT: A 253 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8654 (m-80) REVERT: A 297 GLU cc_start: 0.7459 (mp0) cc_final: 0.7200 (pm20) REVERT: A 381 MET cc_start: 0.8278 (mtm) cc_final: 0.8068 (mtp) REVERT: A 511 LYS cc_start: 0.8200 (tttt) cc_final: 0.7385 (mttp) outliers start: 7 outliers final: 5 residues processed: 66 average time/residue: 1.2355 time to fit residues: 84.8515 Evaluate side-chains 68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 51 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.166777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115910 restraints weight = 4821.620| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.96 r_work: 0.3124 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2692 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= 0.185 Angle : 0.502 6.485 6506 Z= 0.268 Chirality : 0.040 0.149 736 Planarity : 0.005 0.048 795 Dihedral : 4.753 45.657 647 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.60 % Allowed : 15.03 % Favored : 83.37 % 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: 1.19 (0.35), residues: 586 helix: 1.89 (0.28), residues: 348 sheet: -1.08 (0.63), residues: 55 loop : -0.72 (0.47), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.016 0.001 PHE A 144 TYR 0.025 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** 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 70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.464 Fit side-chains REVERT: A 223 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7549 (ttt90) REVERT: A 297 GLU cc_start: 0.7404 (mp0) cc_final: 0.7156 (pm20) REVERT: A 381 MET cc_start: 0.8268 (mtm) cc_final: 0.8035 (mtp) REVERT: A 446 PHE cc_start: 0.8383 (m-80) cc_final: 0.8154 (m-80) REVERT: A 447 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 511 LYS cc_start: 0.8174 (tttt) cc_final: 0.7384 (mttp) REVERT: B 101 ARG cc_start: 0.8638 (tmt170) cc_final: 0.8327 (tmt170) outliers start: 8 outliers final: 5 residues processed: 66 average time/residue: 1.2126 time to fit residues: 83.3421 Evaluate side-chains 67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 32 VAL 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 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 49 optimal weight: 20.0000 chunk 33 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 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 422 ASN C 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.165933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114988 restraints weight = 4835.304| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.95 r_work: 0.3071 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2801 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= 0.199 Angle : 0.507 6.576 6506 Z= 0.269 Chirality : 0.040 0.151 736 Planarity : 0.004 0.050 795 Dihedral : 4.250 15.793 645 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.80 % Allowed : 14.63 % 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: 1.37 (0.35), residues: 586 helix: 1.94 (0.27), residues: 352 sheet: -0.87 (0.64), residues: 55 loop : -0.53 (0.49), residues: 179 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 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** 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 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7511 (ttt90) REVERT: A 297 GLU cc_start: 0.7373 (mp0) cc_final: 0.7167 (pm20) REVERT: A 381 MET cc_start: 0.8308 (mtm) cc_final: 0.8086 (mtp) REVERT: A 451 GLU cc_start: 0.8897 (tp30) cc_final: 0.8692 (tp30) REVERT: A 511 LYS cc_start: 0.8146 (tttt) cc_final: 0.7325 (mttp) outliers start: 9 outliers final: 6 residues processed: 66 average time/residue: 1.2242 time to fit residues: 84.0773 Evaluate side-chains 65 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 A residue 396 THR 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 44 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.166522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.116279 restraints weight = 4793.612| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.91 r_work: 0.3111 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2923 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= 0.182 Angle : 0.496 6.460 6506 Z= 0.262 Chirality : 0.040 0.150 736 Planarity : 0.004 0.051 795 Dihedral : 4.160 15.658 645 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.80 % Allowed : 15.43 % 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: 1.50 (0.36), residues: 586 helix: 2.06 (0.27), residues: 352 sheet: -0.64 (0.64), residues: 55 loop : -0.59 (0.49), residues: 179 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 0.015 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 518 *********************** 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 69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7572 (ttt90) REVERT: A 381 MET cc_start: 0.8304 (mtm) cc_final: 0.8076 (mtp) REVERT: A 444 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.7989 (mt) REVERT: A 511 LYS cc_start: 0.8172 (tttt) cc_final: 0.7349 (mttp) outliers start: 9 outliers final: 5 residues processed: 65 average time/residue: 1.3075 time to fit residues: 88.3366 Evaluate side-chains 66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 A residue 444 LEU 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 17 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.164341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.113724 restraints weight = 4809.101| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.92 r_work: 0.3085 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2922 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= 0.231 Angle : 0.525 6.596 6506 Z= 0.277 Chirality : 0.041 0.154 736 Planarity : 0.005 0.050 795 Dihedral : 4.270 17.071 645 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.40 % Allowed : 16.03 % Favored : 82.57 % 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: 1.52 (0.36), residues: 586 helix: 1.97 (0.27), residues: 352 sheet: -0.55 (0.65), residues: 55 loop : -0.38 (0.51), residues: 179 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 0.017 0.002 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 518 *********************** 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 68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7564 (ttt90) REVERT: A 297 GLU cc_start: 0.7313 (pm20) cc_final: 0.6889 (tp30) REVERT: A 381 MET cc_start: 0.8320 (mtm) cc_final: 0.8097 (mtp) REVERT: A 446 PHE cc_start: 0.8407 (m-80) cc_final: 0.8151 (m-80) REVERT: A 511 LYS cc_start: 0.8179 (tttt) cc_final: 0.7332 (mttp) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 1.1989 time to fit residues: 79.9755 Evaluate side-chains 66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 30 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 chunk 56 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3817 r_free = 0.3817 target = 0.166444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.116086 restraints weight = 4798.386| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.91 r_work: 0.3115 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3020 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= 0.187 Angle : 0.505 6.440 6506 Z= 0.265 Chirality : 0.041 0.169 736 Planarity : 0.004 0.052 795 Dihedral : 4.142 15.719 645 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.40 % Allowed : 16.63 % Favored : 81.96 % 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: 2.08 (0.27), residues: 352 sheet: -0.45 (0.66), residues: 55 loop : -0.55 (0.50), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.003 0.001 HIS B 38 PHE 0.015 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 518 *********************** 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 to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7565 (ttt90) REVERT: A 297 GLU cc_start: 0.7424 (pm20) cc_final: 0.6934 (tp30) REVERT: A 381 MET cc_start: 0.8287 (mtm) cc_final: 0.8065 (mtp) REVERT: A 446 PHE cc_start: 0.8391 (m-80) cc_final: 0.8173 (m-80) REVERT: A 447 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7743 (mm-30) REVERT: A 451 GLU cc_start: 0.8892 (tp30) cc_final: 0.8505 (tp30) REVERT: A 511 LYS cc_start: 0.8186 (tttt) cc_final: 0.7328 (mttp) outliers start: 7 outliers final: 5 residues processed: 62 average time/residue: 1.1870 time to fit residues: 76.8503 Evaluate side-chains 65 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.165438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.114859 restraints weight = 4779.194| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.91 r_work: 0.3056 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3035 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= 0.217 Angle : 0.527 6.606 6506 Z= 0.276 Chirality : 0.041 0.185 736 Planarity : 0.005 0.052 795 Dihedral : 4.201 16.284 645 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.40 % Allowed : 17.03 % Favored : 81.56 % 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: 2.03 (0.27), residues: 352 sheet: -0.40 (0.65), residues: 55 loop : -0.36 (0.51), residues: 179 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 0.001 0.000 ARG A 518 *********************** 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 68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7517 (ttt90) REVERT: A 297 GLU cc_start: 0.7426 (pm20) cc_final: 0.6838 (tp30) REVERT: A 381 MET cc_start: 0.8288 (mtm) cc_final: 0.8080 (mtp) REVERT: A 446 PHE cc_start: 0.8352 (m-80) cc_final: 0.8131 (m-80) REVERT: A 447 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7669 (mm-30) REVERT: A 511 LYS cc_start: 0.8148 (tttt) cc_final: 0.7258 (mttp) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 1.2124 time to fit residues: 80.8207 Evaluate side-chains 66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 27 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.164897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114358 restraints weight = 4772.664| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.89 r_work: 0.3103 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.3044 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= 0.213 Angle : 0.529 8.005 6506 Z= 0.276 Chirality : 0.041 0.197 736 Planarity : 0.005 0.052 795 Dihedral : 4.194 16.175 645 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.20 % Allowed : 17.03 % Favored : 81.76 % 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: 1.64 (0.36), residues: 586 helix: 2.06 (0.28), residues: 351 sheet: -0.41 (0.64), residues: 56 loop : -0.30 (0.50), residues: 179 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 0.015 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.002 0.000 ARG A 326 ********************** 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 67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 223 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7555 (ttt90) REVERT: A 297 GLU cc_start: 0.7477 (pm20) cc_final: 0.6889 (tp30) REVERT: A 381 MET cc_start: 0.8315 (mtm) cc_final: 0.8060 (mtp) REVERT: A 446 PHE cc_start: 0.8424 (m-80) cc_final: 0.8209 (m-80) REVERT: A 451 GLU cc_start: 0.8910 (tp30) cc_final: 0.8555 (tp30) REVERT: A 511 LYS cc_start: 0.8187 (tttt) cc_final: 0.7320 (mttp) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 1.2223 time to fit residues: 81.6113 Evaluate side-chains 67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 54 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN C 28 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.166516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116231 restraints weight = 4743.993| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.90 r_work: 0.3125 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3125 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= 0.178 Angle : 0.498 6.445 6506 Z= 0.263 Chirality : 0.040 0.150 736 Planarity : 0.004 0.052 795 Dihedral : 4.092 15.779 645 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.20 % Allowed : 17.03 % Favored : 81.76 % 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: 1.70 (0.36), residues: 586 helix: 2.10 (0.27), residues: 356 sheet: -0.32 (0.64), residues: 56 loop : -0.39 (0.50), residues: 174 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 0.015 0.001 PHE A 144 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3917.10 seconds wall clock time: 67 minutes 35.54 seconds (4055.54 seconds total)