Starting phenix.real_space_refine on Fri May 9 16:20:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrm_61760/05_2025/9jrm_61760_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrm_61760/05_2025/9jrm_61760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jrm_61760/05_2025/9jrm_61760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrm_61760/05_2025/9jrm_61760.map" model { file = "/net/cci-nas-00/data/ceres_data/9jrm_61760/05_2025/9jrm_61760_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrm_61760/05_2025/9jrm_61760_neut.cif" } resolution = 3.34 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= 0.002 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 12 5.16 5 C 2088 2.51 5 N 517 2.21 5 O 515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3134 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3090 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 12, 'TRANS': 371} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'GJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.66, per 1000 atoms: 0.85 Number of scatterers: 3134 At special positions: 0 Unit cell: (68, 67, 75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 2 15.00 O 515 8.00 N 517 7.00 C 2088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 337.4 milliseconds 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 726 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 55 through 58 removed outlier: 4.084A pdb=" N GLN A 58 " --> pdb=" O PRO A 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 68 through 91 removed outlier: 4.050A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.975A pdb=" N LEU A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 removed outlier: 3.500A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.527A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 144 removed outlier: 3.717A pdb=" N ILE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 177 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.874A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 262 Processing helix chain 'A' and resid 264 through 293 removed outlier: 3.511A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 327 removed outlier: 3.905A pdb=" N ALA A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 355 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 391 removed outlier: 3.909A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 380 " --> pdb=" O TYR A 376 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 395 through 418 removed outlier: 3.605A pdb=" N VAL A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.556A pdb=" N GLY A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) 234 hydrogen bonds defined for protein. 702 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: 0.82 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.41: 1364 1.41 - 1.59: 1841 1.59 - 1.77: 4 1.77 - 1.95: 16 1.95 - 2.13: 2 Bond restraints: 3227 Sorted by residual: bond pdb=" O9 GJF A 701 " pdb=" P2 GJF A 701 " ideal model delta sigma weight residual 1.602 1.733 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C3 GJF A 701 " pdb=" N8 GJF A 701 " ideal model delta sigma weight residual 1.342 1.448 -0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C7 GJF A 701 " pdb=" C8 GJF A 701 " ideal model delta sigma weight residual 1.534 1.432 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C14 GJF A 701 " pdb=" N7 GJF A 701 " ideal model delta sigma weight residual 1.336 1.438 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C5 GJF A 701 " pdb=" C8 GJF A 701 " ideal model delta sigma weight residual 1.529 1.447 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 3222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 4357 4.00 - 8.00: 33 8.00 - 12.00: 12 12.00 - 15.99: 4 15.99 - 19.99: 1 Bond angle restraints: 4407 Sorted by residual: angle pdb=" O3 GJF A 701 " pdb=" P1 GJF A 701 " pdb=" S1 GJF A 701 " ideal model delta sigma weight residual 97.13 117.12 -19.99 3.00e+00 1.11e-01 4.44e+01 angle pdb=" O5 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" S2 GJF A 701 " ideal model delta sigma weight residual 116.54 101.01 15.53 3.00e+00 1.11e-01 2.68e+01 angle pdb=" O6 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" S2 GJF A 701 " ideal model delta sigma weight residual 98.38 111.04 -12.66 3.00e+00 1.11e-01 1.78e+01 angle pdb=" C6 GJF A 701 " pdb=" O1 GJF A 701 " pdb=" C7 GJF A 701 " ideal model delta sigma weight residual 110.83 98.67 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" O5 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" O6 GJF A 701 " ideal model delta sigma weight residual 117.11 104.97 12.14 3.00e+00 1.11e-01 1.64e+01 ... (remaining 4402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.96: 1643 20.96 - 41.91: 198 41.91 - 62.87: 29 62.87 - 83.83: 2 83.83 - 104.78: 7 Dihedral angle restraints: 1879 sinusoidal: 749 harmonic: 1130 Sorted by residual: dihedral pdb=" C9 GJF A 701 " pdb=" O6 GJF A 701 " pdb=" P2 GJF A 701 " pdb=" S2 GJF A 701 " ideal model delta sinusoidal sigma weight residual -116.32 -11.54 -104.78 1 3.00e+01 1.11e-03 1.34e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 162.41 17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG A 151 " pdb=" CD ARG A 151 " pdb=" NE ARG A 151 " pdb=" CZ ARG A 151 " ideal model delta sinusoidal sigma weight residual -90.00 -134.32 44.32 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 1876 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 502 0.110 - 0.219: 10 0.219 - 0.329: 1 0.329 - 0.438: 2 0.438 - 0.548: 1 Chirality restraints: 516 Sorted by residual: chirality pdb=" P2 GJF A 701 " pdb=" O5 GJF A 701 " pdb=" O6 GJF A 701 " pdb=" O9 GJF A 701 " both_signs ideal model delta sigma weight residual True 2.71 3.26 -0.55 2.00e-01 2.50e+01 7.50e+00 chirality pdb=" C16 GJF A 701 " pdb=" C15 GJF A 701 " pdb=" C17 GJF A 701 " pdb=" O8 GJF A 701 " both_signs ideal model delta sigma weight residual False 2.40 2.75 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C17 GJF A 701 " pdb=" C16 GJF A 701 " pdb=" C18 GJF A 701 " pdb=" O9 GJF A 701 " both_signs ideal model delta sigma weight residual False 2.60 2.25 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 513 not shown) Planarity restraints: 518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 81 " 0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 82 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 82 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 82 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 84 " -0.008 2.00e-02 2.50e+03 8.72e-03 1.33e+00 pdb=" CG PHE A 84 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 84 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 84 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 84 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 84 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 84 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 GJF A 701 " -0.012 2.00e-02 2.50e+03 6.80e-03 1.27e+00 pdb=" C11 GJF A 701 " 0.006 2.00e-02 2.50e+03 pdb=" C12 GJF A 701 " 0.002 2.00e-02 2.50e+03 pdb=" C13 GJF A 701 " 0.002 2.00e-02 2.50e+03 pdb=" C14 GJF A 701 " 0.001 2.00e-02 2.50e+03 pdb=" C6 GJF A 701 " 0.012 2.00e-02 2.50e+03 pdb=" N3 GJF A 701 " -0.014 2.00e-02 2.50e+03 pdb=" N4 GJF A 701 " 0.002 2.00e-02 2.50e+03 pdb=" N5 GJF A 701 " 0.001 2.00e-02 2.50e+03 pdb=" N6 GJF A 701 " 0.001 2.00e-02 2.50e+03 pdb=" N7 GJF A 701 " 0.000 2.00e-02 2.50e+03 ... (remaining 515 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 609 2.76 - 3.30: 3135 3.30 - 3.83: 5568 3.83 - 4.37: 6145 4.37 - 4.90: 10688 Nonbonded interactions: 26145 Sorted by model distance: nonbonded pdb=" O GLN A 172 " pdb=" OG1 THR A 176 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" O LYS A 204 " model vdw 2.236 3.040 nonbonded pdb=" O HIS A 358 " pdb=" OG SER A 361 " model vdw 2.332 3.040 nonbonded pdb=" NE2 GLN A 150 " pdb=" O VAL A 327 " model vdw 2.358 3.120 nonbonded pdb=" O GLN A 433 " pdb=" OG SER A 436 " model vdw 2.363 3.040 ... (remaining 26140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.750 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.990 Find NCS groups from input model: 0.030 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.007 0.131 3227 Z= 0.350 Angle : 1.013 19.992 4407 Z= 0.424 Chirality : 0.056 0.548 516 Planarity : 0.004 0.043 518 Dihedral : 17.940 104.782 1153 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 27.58 % Favored : 72.42 % 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: 0.97 (0.44), residues: 378 helix: 1.15 (0.29), residues: 312 sheet: None (None), residues: 0 loop : -1.61 (0.79), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 331 HIS 0.001 0.001 HIS A 27 PHE 0.020 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.001 0.000 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.10651 ( 234) hydrogen bonds : angle 5.39953 ( 702) covalent geometry : bond 0.00681 ( 3227) covalent geometry : angle 1.01310 ( 4407) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.314 Fit side-chains REVERT: A 66 ASN cc_start: 0.8113 (m110) cc_final: 0.7905 (m110) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1131 time to fit residues: 5.4028 Evaluate side-chains 34 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.188487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153564 restraints weight = 3540.156| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.82 r_work: 0.3620 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3227 Z= 0.143 Angle : 0.565 7.471 4407 Z= 0.276 Chirality : 0.039 0.162 516 Planarity : 0.004 0.044 518 Dihedral : 9.718 79.120 490 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.12 % Allowed : 26.97 % Favored : 70.91 % 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: 1.28 (0.43), residues: 378 helix: 1.35 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.44 (0.80), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.020 0.001 PHE A 84 TYR 0.011 0.001 TYR A 35 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 234) hydrogen bonds : angle 4.10082 ( 702) covalent geometry : bond 0.00318 ( 3227) covalent geometry : angle 0.56489 ( 4407) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.338 Fit side-chains REVERT: A 65 THR cc_start: 0.8967 (p) cc_final: 0.8742 (p) REVERT: A 66 ASN cc_start: 0.7967 (m110) cc_final: 0.7695 (m110) REVERT: A 76 TYR cc_start: 0.8582 (t80) cc_final: 0.8239 (t80) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 0.1065 time to fit residues: 6.1538 Evaluate side-chains 40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.185915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.150485 restraints weight = 3563.207| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.86 r_work: 0.3600 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3227 Z= 0.173 Angle : 0.562 7.502 4407 Z= 0.283 Chirality : 0.040 0.116 516 Planarity : 0.004 0.047 518 Dihedral : 8.817 75.816 490 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.55 % Allowed : 26.36 % Favored : 69.09 % 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: 1.23 (0.43), residues: 378 helix: 1.33 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.55 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.022 0.001 PHE A 84 TYR 0.013 0.001 TYR A 35 ARG 0.002 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 234) hydrogen bonds : angle 4.07098 ( 702) covalent geometry : bond 0.00397 ( 3227) covalent geometry : angle 0.56212 ( 4407) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 34 time to evaluate : 0.331 Fit side-chains REVERT: A 40 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7012 (mp10) outliers start: 15 outliers final: 9 residues processed: 46 average time/residue: 0.0952 time to fit residues: 6.1037 Evaluate side-chains 43 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 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 358 HIS A 431 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.188014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152298 restraints weight = 3643.806| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.92 r_work: 0.3613 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3227 Z= 0.149 Angle : 0.549 7.554 4407 Z= 0.273 Chirality : 0.039 0.114 516 Planarity : 0.004 0.045 518 Dihedral : 8.324 74.194 490 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.15 % Allowed : 26.67 % Favored : 68.18 % 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: 1.38 (0.43), residues: 378 helix: 1.43 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.51 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.020 0.001 PHE A 84 TYR 0.012 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.03850 ( 234) hydrogen bonds : angle 4.01453 ( 702) covalent geometry : bond 0.00340 ( 3227) covalent geometry : angle 0.54877 ( 4407) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 35 time to evaluate : 0.320 Fit side-chains REVERT: A 40 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: A 76 TYR cc_start: 0.8597 (t80) cc_final: 0.8209 (t80) REVERT: A 89 TYR cc_start: 0.7759 (t80) cc_final: 0.7525 (t80) outliers start: 17 outliers final: 13 residues processed: 49 average time/residue: 0.0936 time to fit residues: 6.3465 Evaluate side-chains 48 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 35 optimal weight: 0.0770 chunk 19 optimal weight: 0.7980 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.189254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.154185 restraints weight = 3528.470| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.83 r_work: 0.3643 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3227 Z= 0.124 Angle : 0.521 7.590 4407 Z= 0.260 Chirality : 0.038 0.111 516 Planarity : 0.004 0.043 518 Dihedral : 7.912 72.007 490 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.55 % Allowed : 27.88 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.44), residues: 378 helix: 1.63 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.44 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 27 PHE 0.018 0.001 PHE A 84 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 234) hydrogen bonds : angle 3.90717 ( 702) covalent geometry : bond 0.00273 ( 3227) covalent geometry : angle 0.52106 ( 4407) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.308 Fit side-chains REVERT: A 40 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7001 (mp10) REVERT: A 130 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7435 (mmm) outliers start: 15 outliers final: 12 residues processed: 40 average time/residue: 0.0985 time to fit residues: 5.5836 Evaluate side-chains 45 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.184467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.148588 restraints weight = 3662.208| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.86 r_work: 0.3614 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3227 Z= 0.157 Angle : 0.556 7.701 4407 Z= 0.276 Chirality : 0.039 0.117 516 Planarity : 0.004 0.046 518 Dihedral : 7.896 70.634 490 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.76 % Allowed : 26.36 % Favored : 67.88 % 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: 1.59 (0.44), residues: 378 helix: 1.58 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.45 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.021 0.001 PHE A 84 TYR 0.013 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 234) hydrogen bonds : angle 3.96984 ( 702) covalent geometry : bond 0.00361 ( 3227) covalent geometry : angle 0.55565 ( 4407) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.317 Fit side-chains REVERT: A 40 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: A 76 TYR cc_start: 0.8567 (t80) cc_final: 0.8197 (t80) REVERT: A 130 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7597 (mmm) outliers start: 19 outliers final: 14 residues processed: 50 average time/residue: 0.0972 time to fit residues: 6.7639 Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150867 restraints weight = 3529.018| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.80 r_work: 0.3594 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3227 Z= 0.169 Angle : 0.575 7.789 4407 Z= 0.284 Chirality : 0.040 0.158 516 Planarity : 0.004 0.046 518 Dihedral : 7.907 69.932 490 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.45 % Allowed : 26.36 % Favored : 68.18 % 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: 1.49 (0.43), residues: 378 helix: 1.51 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.50 (0.83), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.022 0.001 PHE A 84 TYR 0.013 0.001 TYR A 35 ARG 0.001 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 234) hydrogen bonds : angle 4.01883 ( 702) covalent geometry : bond 0.00392 ( 3227) covalent geometry : angle 0.57535 ( 4407) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.306 Fit side-chains REVERT: A 40 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: A 76 TYR cc_start: 0.8630 (t80) cc_final: 0.8313 (t80) REVERT: A 130 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7738 (mmm) outliers start: 18 outliers final: 14 residues processed: 49 average time/residue: 0.0972 time to fit residues: 6.5719 Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.185323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.149622 restraints weight = 3577.688| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.84 r_work: 0.3625 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3227 Z= 0.138 Angle : 0.555 7.781 4407 Z= 0.272 Chirality : 0.039 0.162 516 Planarity : 0.004 0.044 518 Dihedral : 7.725 69.226 490 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.76 % Allowed : 26.97 % Favored : 67.27 % 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: 1.71 (0.44), residues: 378 helix: 1.67 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.47 (0.81), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 289 PHE 0.019 0.001 PHE A 84 TYR 0.012 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 234) hydrogen bonds : angle 3.96223 ( 702) covalent geometry : bond 0.00311 ( 3227) covalent geometry : angle 0.55518 ( 4407) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 35 time to evaluate : 0.327 Fit side-chains REVERT: A 40 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: A 76 TYR cc_start: 0.8563 (t80) cc_final: 0.8199 (t80) REVERT: A 130 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7604 (mmm) outliers start: 19 outliers final: 14 residues processed: 50 average time/residue: 0.0965 time to fit residues: 6.6836 Evaluate side-chains 51 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 35 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 6 optimal weight: 0.3980 chunk 17 optimal weight: 0.0870 chunk 32 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.190543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154838 restraints weight = 3605.002| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.88 r_work: 0.3644 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3227 Z= 0.118 Angle : 0.539 8.032 4407 Z= 0.263 Chirality : 0.038 0.163 516 Planarity : 0.004 0.043 518 Dihedral : 7.466 67.903 490 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.55 % Allowed : 27.88 % Favored : 67.58 % 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: 1.94 (0.44), residues: 378 helix: 1.83 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.41 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 289 PHE 0.017 0.001 PHE A 84 TYR 0.010 0.001 TYR A 35 ARG 0.001 0.000 ARG A 333 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 234) hydrogen bonds : angle 3.85611 ( 702) covalent geometry : bond 0.00257 ( 3227) covalent geometry : angle 0.53864 ( 4407) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 25 time to evaluate : 0.408 Fit side-chains REVERT: A 40 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: A 130 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.7473 (mmm) outliers start: 15 outliers final: 10 residues processed: 37 average time/residue: 0.0926 time to fit residues: 4.7760 Evaluate side-chains 37 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 25 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.186982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151868 restraints weight = 3508.918| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.81 r_work: 0.3608 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3227 Z= 0.162 Angle : 0.579 8.469 4407 Z= 0.283 Chirality : 0.040 0.163 516 Planarity : 0.004 0.045 518 Dihedral : 7.581 67.147 490 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.24 % Allowed : 28.48 % Favored : 67.27 % 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: 1.77 (0.43), residues: 378 helix: 1.70 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.41 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.022 0.001 PHE A 84 TYR 0.013 0.001 TYR A 35 ARG 0.001 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 234) hydrogen bonds : angle 3.96080 ( 702) covalent geometry : bond 0.00375 ( 3227) covalent geometry : angle 0.57867 ( 4407) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 756 Ramachandran restraints generated. 378 Oldfield, 0 Emsley, 378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.302 Fit side-chains REVERT: A 40 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7027 (mp10) REVERT: A 76 TYR cc_start: 0.8584 (t80) cc_final: 0.8281 (t80) REVERT: A 130 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7655 (mmm) outliers start: 14 outliers final: 12 residues processed: 46 average time/residue: 0.1074 time to fit residues: 6.7201 Evaluate side-chains 50 residues out of total 330 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 36 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 331 TRP Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 35 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.187680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.152384 restraints weight = 3578.247| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.84 r_work: 0.3617 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3227 Z= 0.143 Angle : 0.566 8.413 4407 Z= 0.276 Chirality : 0.039 0.163 516 Planarity : 0.004 0.044 518 Dihedral : 7.503 66.517 490 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.24 % Allowed : 28.48 % Favored : 67.27 % 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: 1.84 (0.43), residues: 378 helix: 1.76 (0.29), residues: 313 sheet: None (None), residues: 0 loop : -1.39 (0.82), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.001 HIS A 27 PHE 0.020 0.001 PHE A 84 TYR 0.012 0.001 TYR A 35 ARG 0.001 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 234) hydrogen bonds : angle 3.93885 ( 702) covalent geometry : bond 0.00326 ( 3227) covalent geometry : angle 0.56604 ( 4407) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.94 seconds wall clock time: 28 minutes 13.32 seconds (1693.32 seconds total)