Starting phenix.real_space_refine on Wed Mar 5 15:15:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pij_17683/03_2025/8pij_17683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pij_17683/03_2025/8pij_17683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pij_17683/03_2025/8pij_17683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pij_17683/03_2025/8pij_17683.map" model { file = "/net/cci-nas-00/data/ceres_data/8pij_17683/03_2025/8pij_17683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pij_17683/03_2025/8pij_17683.cif" } resolution = 2.9 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= 0.022 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 1 5.49 5 S 10 5.16 5 C 1362 2.51 5 N 376 2.21 5 O 442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2191 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'G3P': 1, 'WKE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.46, per 1000 atoms: 1.58 Number of scatterers: 2191 At special positions: 0 Unit cell: (71.61, 65.1, 117.18, 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 10 16.00 P 1 15.00 O 442 8.00 N 376 7.00 C 1362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 111 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 273.4 milliseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 530 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 24.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.511A pdb=" N LEU A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.404A pdb=" N TYR A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.844A pdb=" N TYR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.906A pdb=" N THR B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 3.727A pdb=" N SER A 79 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 121 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.556A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.582A pdb=" N VAL B 14 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 125 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 36 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG B 40 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 222 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: 0.55 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 619 1.33 - 1.45: 377 1.45 - 1.57: 1215 1.57 - 1.69: 1 1.69 - 1.81: 14 Bond restraints: 2226 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA MET B 116 " pdb=" C MET B 116 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.25e-02 6.40e+03 6.93e+00 bond pdb=" CA VAL B 110 " pdb=" C VAL B 110 " ideal model delta sigma weight residual 1.523 1.491 0.031 1.28e-02 6.10e+03 5.91e+00 bond pdb=" CA SER B 115 " pdb=" C SER B 115 " ideal model delta sigma weight residual 1.523 1.491 0.033 1.34e-02 5.57e+03 5.89e+00 bond pdb=" CA SER B 112 " pdb=" C SER B 112 " ideal model delta sigma weight residual 1.521 1.497 0.025 1.23e-02 6.61e+03 3.99e+00 ... (remaining 2221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 2968 1.85 - 3.70: 40 3.70 - 5.55: 8 5.55 - 7.40: 2 7.40 - 9.25: 1 Bond angle restraints: 3019 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.90 -9.25 3.00e+00 1.11e-01 9.51e+00 angle pdb=" N ASP B 109 " pdb=" CA ASP B 109 " pdb=" CB ASP B 109 " ideal model delta sigma weight residual 111.65 107.89 3.76 1.40e+00 5.10e-01 7.20e+00 angle pdb=" CA TYR B 113 " pdb=" CB TYR B 113 " pdb=" CG TYR B 113 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.46e+00 angle pdb=" C PHE B 29 " pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " ideal model delta sigma weight residual 110.42 114.66 -4.24 1.99e+00 2.53e-01 4.55e+00 angle pdb=" N SER B 114 " pdb=" CA SER B 114 " pdb=" C SER B 114 " ideal model delta sigma weight residual 109.50 112.74 -3.24 1.58e+00 4.01e-01 4.20e+00 ... (remaining 3014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 1217 24.62 - 49.23: 108 49.23 - 73.84: 26 73.84 - 98.46: 0 98.46 - 123.07: 2 Dihedral angle restraints: 1353 sinusoidal: 524 harmonic: 829 Sorted by residual: dihedral pdb=" C8 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual 173.56 -63.37 -123.07 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O4 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual -63.24 56.71 -119.95 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" N ARG B 47 " pdb=" CA ARG B 47 " pdb=" CB ARG B 47 " pdb=" CG ARG B 47 " ideal model delta sinusoidal sigma weight residual -60.00 -119.62 59.62 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 185 0.023 - 0.046: 77 0.046 - 0.069: 52 0.069 - 0.093: 17 0.093 - 0.116: 18 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA VAL B 81 " pdb=" N VAL B 81 " pdb=" C VAL B 81 " pdb=" CB VAL B 81 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.15e-01 ... (remaining 346 not shown) Planarity restraints: 383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 WKE A 202 " 0.036 2.00e-02 2.50e+03 2.93e-02 1.08e+01 pdb=" C8 WKE A 202 " -0.010 2.00e-02 2.50e+03 pdb=" C9 WKE A 202 " 0.027 2.00e-02 2.50e+03 pdb=" N1 WKE A 202 " -0.046 2.00e-02 2.50e+03 pdb=" O3 WKE A 202 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 108 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C SER B 108 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 108 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP B 109 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WKE A 202 " -0.018 2.00e-02 2.50e+03 1.15e-02 1.66e+00 pdb=" C3 WKE A 202 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" C5 WKE A 202 " 0.011 2.00e-02 2.50e+03 pdb=" O1 WKE A 202 " -0.003 2.00e-02 2.50e+03 ... (remaining 380 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 365 2.76 - 3.30: 1773 3.30 - 3.83: 3372 3.83 - 4.37: 3797 4.37 - 4.90: 6913 Nonbonded interactions: 16220 Sorted by model distance: nonbonded pdb=" O ALA A 31 " pdb=" OG SER A 34 " model vdw 2.231 3.040 nonbonded pdb=" OD2 ASP A 60 " pdb=" OG SER B 108 " model vdw 2.260 3.040 nonbonded pdb=" NH2 ARG B 103 " pdb=" O1 WKE A 202 " model vdw 2.348 3.120 nonbonded pdb=" OG1 THR A 81 " pdb=" O3P G3P A 201 " model vdw 2.355 3.040 nonbonded pdb=" OG SER B 56 " pdb=" O SER B 108 " model vdw 2.356 3.040 ... (remaining 16215 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: 2.560 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 12.360 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:13.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 0.118 2226 Z= 0.304 Angle : 0.578 9.250 3019 Z= 0.290 Chirality : 0.041 0.116 349 Planarity : 0.004 0.031 383 Dihedral : 18.971 123.074 814 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 30.74 % Favored : 65.80 % 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: 0.25 (0.52), residues: 284 helix: 1.24 (0.72), residues: 50 sheet: 0.22 (0.59), residues: 83 loop : -0.14 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 108 HIS 0.000 0.000 HIS A 149 PHE 0.002 0.001 PHE A 119 TYR 0.018 0.001 TYR B 113 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8356 (tt0) cc_final: 0.8044 (tt0) REVERT: B 75 ASP cc_start: 0.8350 (t0) cc_final: 0.7405 (t0) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.8943 time to fit residues: 56.9436 Evaluate side-chains 52 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3045 r_free = 0.3045 target = 0.060184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.039816 restraints weight = 6455.551| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 3.18 r_work: 0.2383 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2226 Z= 0.366 Angle : 0.571 4.973 3019 Z= 0.305 Chirality : 0.044 0.141 349 Planarity : 0.004 0.025 383 Dihedral : 8.732 82.158 350 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.49 % Allowed : 31.17 % Favored : 62.34 % 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: 0.19 (0.52), residues: 284 helix: 1.01 (0.74), residues: 51 sheet: 0.36 (0.55), residues: 92 loop : -0.27 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.009 0.002 PHE B 102 TYR 0.008 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.254 Fit side-chains REVERT: A 41 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: A 126 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8692 (ttt180) REVERT: B 20 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7242 (mp) REVERT: B 75 ASP cc_start: 0.8384 (t0) cc_final: 0.7399 (t70) REVERT: B 84 GLN cc_start: 0.8557 (tp-100) cc_final: 0.8185 (tp40) REVERT: B 85 MET cc_start: 0.8381 (mtt) cc_final: 0.8063 (mtt) REVERT: B 93 THR cc_start: 0.9348 (p) cc_final: 0.9096 (m) outliers start: 15 outliers final: 5 residues processed: 49 average time/residue: 1.0627 time to fit residues: 53.3500 Evaluate side-chains 48 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.041037 restraints weight = 6382.849| |-----------------------------------------------------------------------------| r_work (start): 0.2542 rms_B_bonded: 3.20 r_work: 0.2426 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2317 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2226 Z= 0.177 Angle : 0.498 6.999 3019 Z= 0.260 Chirality : 0.042 0.146 349 Planarity : 0.003 0.025 383 Dihedral : 5.383 52.120 347 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 6.49 % Allowed : 29.87 % Favored : 63.64 % 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: 0.27 (0.51), residues: 284 helix: 1.27 (0.75), residues: 51 sheet: 0.30 (0.52), residues: 92 loop : -0.22 (0.57), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.009 0.001 TYR B 118 ARG 0.001 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.244 Fit side-chains REVERT: A 41 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: B 75 ASP cc_start: 0.8401 (t0) cc_final: 0.7862 (t0) REVERT: B 84 GLN cc_start: 0.8682 (tp-100) cc_final: 0.8259 (tp40) REVERT: B 85 MET cc_start: 0.8338 (mtt) cc_final: 0.8124 (mtt) outliers start: 15 outliers final: 5 residues processed: 50 average time/residue: 0.9781 time to fit residues: 50.2029 Evaluate side-chains 44 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.0370 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- 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 = 0.3055 r_free = 0.3055 target = 0.060191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.039763 restraints weight = 6472.968| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 3.17 r_work: 0.2387 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2279 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2226 Z= 0.232 Angle : 0.514 5.852 3019 Z= 0.272 Chirality : 0.042 0.141 349 Planarity : 0.003 0.025 383 Dihedral : 5.238 51.277 346 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.49 % Allowed : 28.14 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.50), residues: 284 helix: 1.33 (0.75), residues: 51 sheet: 0.50 (0.54), residues: 77 loop : -0.42 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.008 0.001 TYR B 82 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.262 Fit side-chains REVERT: A 41 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8619 (tm-30) REVERT: B 40 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8740 (ttp-170) REVERT: B 48 GLU cc_start: 0.9173 (pt0) cc_final: 0.8951 (pt0) REVERT: B 75 ASP cc_start: 0.8390 (t0) cc_final: 0.7856 (t0) REVERT: B 84 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8328 (tp40) REVERT: B 85 MET cc_start: 0.8403 (mtt) cc_final: 0.8128 (mtt) REVERT: B 89 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8230 (mtpp) REVERT: B 103 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7473 (mmp80) outliers start: 15 outliers final: 6 residues processed: 49 average time/residue: 1.1945 time to fit residues: 59.8150 Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3059 r_free = 0.3059 target = 0.060441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.039961 restraints weight = 6511.768| |-----------------------------------------------------------------------------| r_work (start): 0.2508 rms_B_bonded: 3.17 r_work: 0.2394 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2287 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2226 Z= 0.221 Angle : 0.532 6.999 3019 Z= 0.276 Chirality : 0.043 0.140 349 Planarity : 0.003 0.026 383 Dihedral : 5.188 50.915 346 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.76 % Allowed : 28.57 % Favored : 66.67 % 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: 0.34 (0.50), residues: 284 helix: 1.57 (0.75), residues: 51 sheet: 0.67 (0.55), residues: 77 loop : -0.42 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.006 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.231 Fit side-chains REVERT: A 41 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8626 (tm-30) REVERT: B 40 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8798 (ttp-170) REVERT: B 48 GLU cc_start: 0.9124 (pt0) cc_final: 0.8829 (pt0) REVERT: B 75 ASP cc_start: 0.8450 (t0) cc_final: 0.7864 (t70) REVERT: B 84 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8360 (tp40) REVERT: B 85 MET cc_start: 0.8523 (mtt) cc_final: 0.8264 (mtt) REVERT: B 103 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7462 (mmp80) REVERT: B 121 LYS cc_start: 0.8876 (mppt) cc_final: 0.8543 (pmmt) outliers start: 11 outliers final: 6 residues processed: 45 average time/residue: 1.2064 time to fit residues: 55.4774 Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 = 0.3034 r_free = 0.3034 target = 0.059483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.038833 restraints weight = 6492.176| |-----------------------------------------------------------------------------| r_work (start): 0.2473 rms_B_bonded: 3.18 r_work: 0.2358 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2249 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2226 Z= 0.311 Angle : 0.556 6.129 3019 Z= 0.294 Chirality : 0.044 0.136 349 Planarity : 0.003 0.027 383 Dihedral : 5.399 50.475 346 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.76 % Allowed : 29.87 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.50), residues: 284 helix: 1.46 (0.74), residues: 51 sheet: 0.69 (0.56), residues: 77 loop : -0.50 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.006 0.001 PHE B 102 TYR 0.008 0.001 TYR B 118 ARG 0.003 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.253 Fit side-chains REVERT: A 41 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8607 (tm-30) REVERT: B 75 ASP cc_start: 0.8448 (t0) cc_final: 0.7859 (t70) REVERT: B 85 MET cc_start: 0.8497 (mtt) cc_final: 0.8269 (mtt) REVERT: B 103 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7398 (mmp80) REVERT: B 121 LYS cc_start: 0.8816 (mppt) cc_final: 0.8548 (pmmt) outliers start: 11 outliers final: 6 residues processed: 47 average time/residue: 1.1771 time to fit residues: 56.6114 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 17 optimal weight: 0.0570 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- 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 = 0.3043 r_free = 0.3043 target = 0.059846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.039258 restraints weight = 6480.418| |-----------------------------------------------------------------------------| r_work (start): 0.2486 rms_B_bonded: 3.18 r_work: 0.2370 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2261 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2226 Z= 0.255 Angle : 0.557 7.178 3019 Z= 0.287 Chirality : 0.043 0.142 349 Planarity : 0.003 0.029 383 Dihedral : 5.304 50.648 346 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.33 % Allowed : 31.60 % Favored : 64.07 % 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: 0.42 (0.50), residues: 284 helix: 1.59 (0.75), residues: 51 sheet: 0.81 (0.57), residues: 77 loop : -0.42 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.250 Fit side-chains REVERT: A 41 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8609 (tm-30) REVERT: B 40 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8792 (ttp-170) REVERT: B 75 ASP cc_start: 0.8451 (t0) cc_final: 0.7852 (t70) REVERT: B 84 GLN cc_start: 0.8737 (tp-100) cc_final: 0.8339 (tp40) REVERT: B 103 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7403 (mmp80) REVERT: B 121 LYS cc_start: 0.8881 (mppt) cc_final: 0.8664 (pmmt) outliers start: 10 outliers final: 6 residues processed: 45 average time/residue: 1.2884 time to fit residues: 59.1615 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 11 optimal weight: 4.9990 chunk 9 optimal weight: 0.0570 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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 = 0.3051 r_free = 0.3051 target = 0.060115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.039513 restraints weight = 6648.186| |-----------------------------------------------------------------------------| r_work (start): 0.2498 rms_B_bonded: 3.24 r_work: 0.2383 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2226 Z= 0.215 Angle : 0.528 6.028 3019 Z= 0.278 Chirality : 0.042 0.140 349 Planarity : 0.003 0.030 383 Dihedral : 5.198 50.614 346 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.76 % Allowed : 29.44 % Favored : 65.80 % 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: 0.49 (0.51), residues: 284 helix: 1.71 (0.76), residues: 51 sheet: 0.77 (0.57), residues: 77 loop : -0.34 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 82 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.224 Fit side-chains REVERT: A 41 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8637 (tm-30) REVERT: B 40 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8833 (ttp-170) REVERT: B 41 GLN cc_start: 0.8525 (tp-100) cc_final: 0.7846 (tp40) REVERT: B 75 ASP cc_start: 0.8419 (t0) cc_final: 0.7826 (t70) REVERT: B 84 GLN cc_start: 0.8819 (tp-100) cc_final: 0.8417 (mm-40) REVERT: B 85 MET cc_start: 0.8242 (mtt) cc_final: 0.7731 (mtt) REVERT: B 103 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7458 (mmp80) outliers start: 11 outliers final: 7 residues processed: 44 average time/residue: 1.2059 time to fit residues: 54.2310 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.3980 chunk 4 optimal weight: 0.4980 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 = 0.3097 r_free = 0.3097 target = 0.062083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.041636 restraints weight = 6438.097| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 3.21 r_work: 0.2451 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2342 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 2226 Z= 0.147 Angle : 0.536 8.480 3019 Z= 0.270 Chirality : 0.041 0.137 349 Planarity : 0.003 0.032 383 Dihedral : 4.933 50.627 346 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.46 % Allowed : 31.60 % Favored : 64.94 % 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: 0.72 (0.52), residues: 284 helix: 1.95 (0.77), residues: 51 sheet: 0.82 (0.55), residues: 82 loop : -0.19 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.006 0.001 TYR B 96 ARG 0.001 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.246 Fit side-chains REVERT: A 41 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8040 (tt0) REVERT: B 40 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8822 (ttp-170) REVERT: B 41 GLN cc_start: 0.8536 (tp-100) cc_final: 0.7841 (tp40) REVERT: B 75 ASP cc_start: 0.8467 (t0) cc_final: 0.7888 (t70) REVERT: B 84 GLN cc_start: 0.8873 (tp-100) cc_final: 0.8453 (mm-40) REVERT: B 85 MET cc_start: 0.8316 (mtt) cc_final: 0.7874 (mtt) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 1.1107 time to fit residues: 50.0889 Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 overall best weight: 1.2740 ------------------------------------------------------------------------------- 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 = 0.3082 r_free = 0.3082 target = 0.061379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.040894 restraints weight = 6408.716| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 3.18 r_work: 0.2429 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2319 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2226 Z= 0.175 Angle : 0.555 6.198 3019 Z= 0.290 Chirality : 0.042 0.134 349 Planarity : 0.003 0.032 383 Dihedral : 4.997 50.266 346 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.90 % Allowed : 29.87 % Favored : 66.23 % 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: 0.76 (0.51), residues: 284 helix: 1.96 (0.77), residues: 51 sheet: 0.86 (0.55), residues: 82 loop : -0.16 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.000 0.000 HIS A 54 PHE 0.004 0.001 PHE B 102 TYR 0.006 0.001 TYR B 118 ARG 0.001 0.000 ARG B 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.294 Fit side-chains REVERT: A 41 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8069 (tt0) REVERT: B 40 ARG cc_start: 0.9175 (OUTLIER) cc_final: 0.8870 (ttp-170) REVERT: B 48 GLU cc_start: 0.9157 (pt0) cc_final: 0.8459 (pp20) REVERT: B 75 ASP cc_start: 0.8415 (t0) cc_final: 0.7785 (t70) REVERT: B 84 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8443 (mm-40) REVERT: B 85 MET cc_start: 0.8276 (mtt) cc_final: 0.7823 (mtt) outliers start: 9 outliers final: 7 residues processed: 45 average time/residue: 1.0785 time to fit residues: 49.7715 Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 40 ARG Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 4 optimal weight: 0.1980 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.061167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.040420 restraints weight = 6446.182| |-----------------------------------------------------------------------------| r_work (start): 0.2524 rms_B_bonded: 3.19 r_work: 0.2413 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2304 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2226 Z= 0.192 Angle : 0.584 8.372 3019 Z= 0.298 Chirality : 0.043 0.175 349 Planarity : 0.003 0.032 383 Dihedral : 5.067 50.266 346 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.90 % Allowed : 30.74 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.51), residues: 284 helix: 1.87 (0.77), residues: 51 sheet: 0.79 (0.55), residues: 82 loop : -0.13 (0.53), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 118 ARG 0.001 0.000 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2506.46 seconds wall clock time: 43 minutes 30.03 seconds (2610.03 seconds total)