Starting phenix.real_space_refine on Fri Dec 27 09:51:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqo_60386/12_2024/8zqo_60386.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqo_60386/12_2024/8zqo_60386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqo_60386/12_2024/8zqo_60386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqo_60386/12_2024/8zqo_60386.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqo_60386/12_2024/8zqo_60386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqo_60386/12_2024/8zqo_60386.cif" } resolution = 2.8 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= -0.001 sd= 0.063 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: 6 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 2683 2.51 5 N 607 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4032 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 3959 Classifications: {'peptide': 515} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 492} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 34 Unusual residues: {' CL': 1, ' NA': 2, 'HC6': 1} Classifications: {'undetermined': 4, 'water': 1} Link IDs: {None: 4} Time building chain proxies: 3.40, per 1000 atoms: 0.84 Number of scatterers: 4032 At special positions: 0 Unit cell: (85, 75.65, 91.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 20 16.00 Na 2 11.00 O 719 8.00 N 607 7.00 C 2683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 301 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 653.7 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.742A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 removed outlier: 3.521A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.704A pdb=" N GLY A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.553A pdb=" N ALA A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.540A pdb=" N TRP A 84 " --> pdb=" O GLY A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.520A pdb=" N LYS A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 4.622A pdb=" N PHE A 118 " --> pdb=" O MET A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 130 through 157 removed outlier: 4.301A pdb=" N ALA A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.602A pdb=" N TYR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 208 removed outlier: 3.844A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix removed outlier: 3.601A pdb=" N SER A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 262 removed outlier: 4.342A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 285 Processing helix chain 'A' and resid 285 through 297 removed outlier: 3.610A pdb=" N ILE A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.543A pdb=" N THR A 303 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 328 removed outlier: 3.674A pdb=" N CYS A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 363 removed outlier: 3.693A pdb=" N SER A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 401 through 427 removed outlier: 4.159A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.546A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 478 through 504 removed outlier: 3.503A pdb=" N LEU A 482 " --> pdb=" O PRO A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 512 282 hydrogen bonds defined for protein. 828 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: 1.04 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 601 1.31 - 1.43: 1178 1.43 - 1.56: 2328 1.56 - 1.68: 1 1.68 - 1.81: 35 Bond restraints: 4143 Sorted by residual: bond pdb=" C LEU A 97 " pdb=" O LEU A 97 " ideal model delta sigma weight residual 1.237 1.180 0.056 1.19e-02 7.06e+03 2.23e+01 bond pdb=" CA LEU A 97 " pdb=" C LEU A 97 " ideal model delta sigma weight residual 1.524 1.466 0.057 1.29e-02 6.01e+03 1.97e+01 bond pdb=" CAJ HC6 A 603 " pdb=" CAM HC6 A 603 " ideal model delta sigma weight residual 1.475 1.404 0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N VAL A 402 " pdb=" CA VAL A 402 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.47e+00 bond pdb=" N GLN A 370 " pdb=" CA GLN A 370 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 6.86e+00 ... (remaining 4138 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 5505 1.80 - 3.59: 112 3.59 - 5.39: 28 5.39 - 7.18: 11 7.18 - 8.98: 9 Bond angle restraints: 5665 Sorted by residual: angle pdb=" O ALA A 26 " pdb=" C ALA A 26 " pdb=" N TRP A 27 " ideal model delta sigma weight residual 122.12 118.41 3.71 1.06e+00 8.90e-01 1.22e+01 angle pdb=" CA ALA A 26 " pdb=" C ALA A 26 " pdb=" N TRP A 27 " ideal model delta sigma weight residual 117.30 120.98 -3.68 1.16e+00 7.43e-01 1.01e+01 angle pdb=" N VAL A 63 " pdb=" CA VAL A 63 " pdb=" C VAL A 63 " ideal model delta sigma weight residual 109.34 115.74 -6.40 2.08e+00 2.31e-01 9.47e+00 angle pdb=" O ILE A 96 " pdb=" C ILE A 96 " pdb=" N LEU A 97 " ideal model delta sigma weight residual 121.87 118.94 2.93 9.70e-01 1.06e+00 9.12e+00 angle pdb=" N GLY A 64 " pdb=" CA GLY A 64 " pdb=" C GLY A 64 " ideal model delta sigma weight residual 112.64 117.89 -5.25 1.74e+00 3.30e-01 9.10e+00 ... (remaining 5660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 2188 21.89 - 43.78: 172 43.78 - 65.67: 39 65.67 - 87.57: 10 87.57 - 109.46: 4 Dihedral angle restraints: 2413 sinusoidal: 932 harmonic: 1481 Sorted by residual: dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.25 109.46 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.85 107.47 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C6 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O4 BMA B 3 " ideal model delta sinusoidal sigma weight residual -163.34 -59.86 -103.48 1 3.00e+01 1.11e-03 1.32e+01 ... (remaining 2410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 596 0.070 - 0.140: 58 0.140 - 0.210: 4 0.210 - 0.280: 1 0.280 - 0.350: 1 Chirality restraints: 660 Sorted by residual: chirality pdb=" CAD HC6 A 603 " pdb=" CAC HC6 A 603 " pdb=" CAG HC6 A 603 " pdb=" OAE HC6 A 603 " both_signs ideal model delta sigma weight residual False 2.61 2.26 0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LEU A 482 " pdb=" N LEU A 482 " pdb=" C LEU A 482 " pdb=" CB LEU A 482 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.48e-01 ... (remaining 657 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAJ HC6 A 603 " -0.037 2.00e-02 2.50e+03 1.98e-02 7.83e+00 pdb=" CAM HC6 A 603 " 0.038 2.00e-02 2.50e+03 pdb=" CAN HC6 A 603 " 0.004 2.00e-02 2.50e+03 pdb=" CAO HC6 A 603 " 0.003 2.00e-02 2.50e+03 pdb=" CAP HC6 A 603 " -0.000 2.00e-02 2.50e+03 pdb=" CAQ HC6 A 603 " -0.002 2.00e-02 2.50e+03 pdb=" CAR HC6 A 603 " 0.009 2.00e-02 2.50e+03 pdb=" CAS HC6 A 603 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 457 " 0.039 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO A 458 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 458 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 458 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 451 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 452 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 452 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 452 " 0.027 5.00e-02 4.00e+02 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 82 2.70 - 3.25: 3911 3.25 - 3.80: 6225 3.80 - 4.35: 7865 4.35 - 4.90: 13854 Nonbonded interactions: 31937 Sorted by model distance: nonbonded pdb=" OD2 ASP A 188 " pdb="NA NA A 602 " model vdw 2.155 2.470 nonbonded pdb=" OG SER A 350 " pdb="NA NA A 602 " model vdw 2.173 2.470 nonbonded pdb=" OG SER A 346 " pdb="NA NA A 601 " model vdw 2.189 2.470 nonbonded pdb=" O VAL A 63 " pdb="NA NA A 601 " model vdw 2.232 2.470 nonbonded pdb=" OH TYR A 433 " pdb=" OD1 ASP A 512 " model vdw 2.236 3.040 ... (remaining 31932 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: 0.690 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 4143 Z= 0.301 Angle : 0.758 8.976 5665 Z= 0.392 Chirality : 0.046 0.350 660 Planarity : 0.006 0.071 683 Dihedral : 17.768 109.457 1477 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.20 % Allowed : 16.39 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.88 (0.39), residues: 513 helix: 1.82 (0.28), residues: 374 sheet: -3.68 (1.45), residues: 10 loop : 0.08 (0.57), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.018 0.001 TYR A 175 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 5 outliers final: 2 residues processed: 44 average time/residue: 1.0574 time to fit residues: 48.7059 Evaluate side-chains 36 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 373 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 43 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8565 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4143 Z= 0.180 Angle : 0.582 8.038 5665 Z= 0.287 Chirality : 0.039 0.165 660 Planarity : 0.005 0.037 683 Dihedral : 11.844 74.022 657 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.41 % Allowed : 16.87 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.28 (0.39), residues: 513 helix: 2.17 (0.28), residues: 365 sheet: -3.75 (1.38), residues: 10 loop : 0.23 (0.58), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 27 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.017 0.001 TYR A 67 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 268 THR cc_start: 0.7741 (OUTLIER) cc_final: 0.7537 (m) REVERT: A 395 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8369 (ttp) outliers start: 10 outliers final: 4 residues processed: 43 average time/residue: 1.0758 time to fit residues: 48.3714 Evaluate side-chains 41 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8573 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4143 Z= 0.179 Angle : 0.559 8.026 5665 Z= 0.277 Chirality : 0.039 0.155 660 Planarity : 0.004 0.037 683 Dihedral : 9.385 61.699 654 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.65 % Allowed : 16.63 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.35 (0.39), residues: 513 helix: 2.20 (0.27), residues: 371 sheet: -3.77 (1.37), residues: 10 loop : 0.23 (0.59), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 27 HIS 0.002 0.001 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.017 0.001 TYR A 67 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.8002 (t60) cc_final: 0.7430 (t-100) REVERT: A 395 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8305 (mtm) outliers start: 11 outliers final: 6 residues processed: 46 average time/residue: 1.0623 time to fit residues: 51.1316 Evaluate side-chains 43 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 34 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8559 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4143 Z= 0.167 Angle : 0.537 8.207 5665 Z= 0.268 Chirality : 0.038 0.124 660 Planarity : 0.004 0.037 683 Dihedral : 8.455 58.693 654 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.65 % Allowed : 17.11 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.42 (0.39), residues: 513 helix: 2.24 (0.27), residues: 372 sheet: -3.74 (1.38), residues: 10 loop : 0.26 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.016 0.001 TYR A 67 ARG 0.002 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7970 (t60) cc_final: 0.7412 (t-100) outliers start: 11 outliers final: 8 residues processed: 43 average time/residue: 1.0308 time to fit residues: 46.3752 Evaluate side-chains 42 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.0070 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 12 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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: 0.8529 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4143 Z= 0.145 Angle : 0.511 8.097 5665 Z= 0.255 Chirality : 0.037 0.118 660 Planarity : 0.004 0.035 683 Dihedral : 7.759 55.164 654 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.41 % Allowed : 17.35 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.55 (0.39), residues: 513 helix: 2.34 (0.27), residues: 372 sheet: -3.68 (1.38), residues: 10 loop : 0.30 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.015 0.001 TYR A 67 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7942 (t60) cc_final: 0.7387 (t-100) outliers start: 10 outliers final: 7 residues processed: 44 average time/residue: 0.9929 time to fit residues: 45.7556 Evaluate side-chains 41 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 12 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.8575 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4143 Z= 0.180 Angle : 0.547 8.171 5665 Z= 0.274 Chirality : 0.039 0.128 660 Planarity : 0.004 0.038 683 Dihedral : 7.731 57.806 654 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.17 % Allowed : 17.11 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.36 (0.39), residues: 513 helix: 2.21 (0.27), residues: 371 sheet: -3.65 (1.36), residues: 10 loop : 0.21 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.018 0.001 TYR A 67 ARG 0.003 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7971 (t60) cc_final: 0.7397 (t-100) outliers start: 9 outliers final: 6 residues processed: 42 average time/residue: 1.1074 time to fit residues: 48.5830 Evaluate side-chains 41 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8566 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4143 Z= 0.171 Angle : 0.532 7.985 5665 Z= 0.267 Chirality : 0.038 0.119 660 Planarity : 0.004 0.037 683 Dihedral : 7.393 57.227 654 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.93 % Allowed : 17.83 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.44 (0.39), residues: 513 helix: 2.25 (0.27), residues: 372 sheet: -3.66 (1.38), residues: 10 loop : 0.26 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.017 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 27 TRP cc_start: 0.7975 (t60) cc_final: 0.7398 (t-100) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 1.1607 time to fit residues: 49.5915 Evaluate side-chains 41 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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: 0.8594 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4143 Z= 0.201 Angle : 0.561 8.023 5665 Z= 0.283 Chirality : 0.039 0.139 660 Planarity : 0.004 0.039 683 Dihedral : 7.438 59.629 654 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.69 % Allowed : 18.07 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.26 (0.39), residues: 513 helix: 2.14 (0.27), residues: 371 sheet: -3.69 (1.36), residues: 10 loop : 0.16 (0.58), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.008 0.001 PHE A 479 TYR 0.018 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.445 Fit side-chains REVERT: A 27 TRP cc_start: 0.7984 (t60) cc_final: 0.7393 (t-100) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 1.0683 time to fit residues: 49.1860 Evaluate side-chains 41 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 50 optimal weight: 0.0030 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 overall best weight: 0.6590 ------------------------------------------------------------------------------- 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: 0.8558 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4143 Z= 0.159 Angle : 0.523 7.956 5665 Z= 0.263 Chirality : 0.038 0.118 660 Planarity : 0.004 0.036 683 Dihedral : 7.032 56.635 654 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.20 % Allowed : 18.55 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.42 (0.39), residues: 513 helix: 2.26 (0.27), residues: 372 sheet: -3.64 (1.38), residues: 10 loop : 0.21 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.016 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.440 Fit side-chains REVERT: A 27 TRP cc_start: 0.7960 (t60) cc_final: 0.7411 (t-100) REVERT: A 314 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8051 (mp0) outliers start: 5 outliers final: 6 residues processed: 39 average time/residue: 1.2167 time to fit residues: 49.4946 Evaluate side-chains 40 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 395 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 4 optimal weight: 0.0010 chunk 31 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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: 0.8533 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4143 Z= 0.146 Angle : 0.509 7.958 5665 Z= 0.255 Chirality : 0.037 0.122 660 Planarity : 0.004 0.035 683 Dihedral : 6.651 56.606 654 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.45 % Allowed : 18.55 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.53 (0.39), residues: 513 helix: 2.34 (0.27), residues: 372 sheet: -3.68 (1.38), residues: 10 loop : 0.24 (0.59), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.007 0.001 PHE A 479 TYR 0.016 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.453 Fit side-chains REVERT: A 27 TRP cc_start: 0.7911 (t60) cc_final: 0.7357 (t-100) REVERT: A 314 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8044 (mp0) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 1.0783 time to fit residues: 44.2790 Evaluate side-chains 37 residues out of total 415 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 391 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 32 optimal weight: 0.0010 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.129908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.098566 restraints weight = 4605.653| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.74 r_work: 0.2769 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4143 Z= 0.166 Angle : 0.523 7.916 5665 Z= 0.263 Chirality : 0.038 0.117 660 Planarity : 0.004 0.037 683 Dihedral : 6.722 55.774 654 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.20 % Allowed : 18.80 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.45 (0.39), residues: 513 helix: 2.29 (0.27), residues: 372 sheet: -3.68 (1.38), residues: 10 loop : 0.19 (0.58), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 228 HIS 0.001 0.000 HIS A 162 PHE 0.009 0.001 PHE A 479 TYR 0.017 0.001 TYR A 67 ARG 0.004 0.000 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1609.49 seconds wall clock time: 29 minutes 26.11 seconds (1766.11 seconds total)