Starting phenix.real_space_refine on Sat Apr 26 17:03:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tib_41283/04_2025/8tib_41283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tib_41283/04_2025/8tib_41283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tib_41283/04_2025/8tib_41283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tib_41283/04_2025/8tib_41283.map" model { file = "/net/cci-nas-00/data/ceres_data/8tib_41283/04_2025/8tib_41283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tib_41283/04_2025/8tib_41283.cif" } resolution = 3.47 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.031 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: 3 Type Number sf(0) Gaussians C 1677 2.51 5 N 438 2.21 5 O 552 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-5669/modules/chem_data/mon_lib" Total number of atoms: 2667 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 889 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "B" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 889 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Chain: "C" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 889 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Time building chain proxies: 2.78, per 1000 atoms: 1.04 Number of scatterers: 2667 At special positions: 0 Unit cell: (69.12, 58.32, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 552 8.00 N 438 7.00 C 1677 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: 0.73 Conformation dependent library (CDL) restraints added in 356.4 milliseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 678 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 8 sheets defined 29.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 13 through 46 Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'B' and resid 17 through 46 removed outlier: 3.542A pdb=" N LEU B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 4.237A pdb=" N LEU B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 46 removed outlier: 3.591A pdb=" N THR C 18 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.621A pdb=" N VAL C 119 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 82 removed outlier: 6.663A pdb=" N GLN A 128 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA A 81 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR A 126 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 137 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 56 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A 142 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU A 58 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 64 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.930A pdb=" N THR B 49 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 72 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.149A pdb=" N ALA B 56 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 142 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 58 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 80 " --> pdb=" O GLN B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 67 Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 59 Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 67 139 hydrogen bonds defined for protein. 378 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: 0.65 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 438 1.27 - 1.34: 432 1.34 - 1.41: 93 1.41 - 1.48: 504 1.48 - 1.55: 1212 Bond restraints: 2679 Sorted by residual: bond pdb=" C THR C 95 " pdb=" O THR C 95 " ideal model delta sigma weight residual 1.236 1.202 0.033 1.31e-02 5.83e+03 6.48e+00 bond pdb=" C ILE C 96 " pdb=" O ILE C 96 " ideal model delta sigma weight residual 1.236 1.215 0.021 1.19e-02 7.06e+03 3.21e+00 bond pdb=" C ALA C 98 " pdb=" O ALA C 98 " ideal model delta sigma weight residual 1.234 1.212 0.022 1.23e-02 6.61e+03 3.12e+00 bond pdb=" C SER C 97 " pdb=" O SER C 97 " ideal model delta sigma weight residual 1.234 1.216 0.019 1.19e-02 7.06e+03 2.43e+00 bond pdb=" CA ALA C 98 " pdb=" CB ALA C 98 " ideal model delta sigma weight residual 1.531 1.506 0.025 1.65e-02 3.67e+03 2.36e+00 ... (remaining 2674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 3654 3.06 - 6.12: 12 6.12 - 9.19: 1 9.19 - 12.25: 1 12.25 - 15.31: 1 Bond angle restraints: 3669 Sorted by residual: angle pdb=" N VAL C 94 " pdb=" CA VAL C 94 " pdb=" C VAL C 94 " ideal model delta sigma weight residual 106.21 121.52 -15.31 1.07e+00 8.73e-01 2.05e+02 angle pdb=" C VAL C 94 " pdb=" CA VAL C 94 " pdb=" CB VAL C 94 " ideal model delta sigma weight residual 113.22 106.35 6.87 1.12e+00 7.97e-01 3.77e+01 angle pdb=" N ILE C 96 " pdb=" CA ILE C 96 " pdb=" C ILE C 96 " ideal model delta sigma weight residual 109.34 119.99 -10.65 2.08e+00 2.31e-01 2.62e+01 angle pdb=" N VAL C 94 " pdb=" CA VAL C 94 " pdb=" CB VAL C 94 " ideal model delta sigma weight residual 112.28 108.17 4.11 1.00e+00 1.00e+00 1.69e+01 angle pdb=" CA VAL C 94 " pdb=" C VAL C 94 " pdb=" N THR C 95 " ideal model delta sigma weight residual 115.25 118.90 -3.65 9.50e-01 1.11e+00 1.48e+01 ... (remaining 3664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 1340 17.86 - 35.72: 161 35.72 - 53.57: 23 53.57 - 71.43: 8 71.43 - 89.29: 4 Dihedral angle restraints: 1536 sinusoidal: 465 harmonic: 1071 Sorted by residual: dihedral pdb=" CA GLY C 46 " pdb=" C GLY C 46 " pdb=" N GLN C 47 " pdb=" CA GLN C 47 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" C THR C 95 " pdb=" N THR C 95 " pdb=" CA THR C 95 " pdb=" CB THR C 95 " ideal model delta harmonic sigma weight residual -122.00 -130.26 8.26 0 2.50e+00 1.60e-01 1.09e+01 dihedral pdb=" CA GLN C 100 " pdb=" CB GLN C 100 " pdb=" CG GLN C 100 " pdb=" CD GLN C 100 " ideal model delta sinusoidal sigma weight residual -60.00 -119.53 59.53 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 465 0.070 - 0.140: 56 0.140 - 0.210: 2 0.210 - 0.280: 0 0.280 - 0.350: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA THR C 95 " pdb=" N THR C 95 " pdb=" C THR C 95 " pdb=" CB THR C 95 " both_signs ideal model delta sigma weight residual False 2.53 2.18 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA ILE C 96 " pdb=" N ILE C 96 " pdb=" C ILE C 96 " pdb=" CB ILE C 96 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA VAL C 94 " pdb=" N VAL C 94 " pdb=" C VAL C 94 " pdb=" CB VAL C 94 " both_signs ideal model delta sigma weight residual False 2.44 2.28 0.16 2.00e-01 2.50e+01 6.52e-01 ... (remaining 522 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 84 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.22e+00 pdb=" C ASN C 84 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN C 84 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY C 85 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 93 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C GLN C 93 " 0.028 2.00e-02 2.50e+03 pdb=" O GLN C 93 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 94 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 96 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C ILE C 96 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE C 96 " 0.007 2.00e-02 2.50e+03 pdb=" N SER C 97 " 0.006 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1015 2.84 - 3.36: 2398 3.36 - 3.87: 4028 3.87 - 4.39: 4156 4.39 - 4.90: 7835 Nonbonded interactions: 19432 Sorted by model distance: nonbonded pdb=" O THR B 72 " pdb=" OG1 THR B 72 " model vdw 2.328 3.040 nonbonded pdb=" O SER B 106 " pdb=" OG SER B 106 " model vdw 2.335 3.040 nonbonded pdb=" O THR B 122 " pdb=" OG1 THR B 122 " model vdw 2.339 3.040 nonbonded pdb=" O SER C 112 " pdb=" NE2 GLN C 116 " model vdw 2.392 3.120 nonbonded pdb=" OD1 ASN C 131 " pdb=" NE2 GLN C 133 " model vdw 2.392 3.120 ... (remaining 19427 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.420 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 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 : 0.003 0.040 2679 Z= 0.177 Angle : 0.624 15.312 3669 Z= 0.428 Chirality : 0.046 0.350 525 Planarity : 0.002 0.021 450 Dihedral : 16.691 89.291 858 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.34 % Allowed : 32.31 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.45), residues: 387 helix: 1.73 (0.54), residues: 109 sheet: -2.11 (0.47), residues: 119 loop : -2.18 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 41 TYR 0.003 0.001 TYR C 103 Details of bonding type rmsd hydrogen bonds : bond 0.20848 ( 139) hydrogen bonds : angle 7.48844 ( 378) covalent geometry : bond 0.00337 ( 2679) covalent geometry : angle 0.62403 ( 3669) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.296 Fit side-chains REVERT: A 115 LEU cc_start: 0.8811 (tp) cc_final: 0.8589 (tp) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.0901 time to fit residues: 3.3477 Evaluate side-chains 24 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.3125 r_free = 0.3125 target = 0.088845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.071909 restraints weight = 5483.560| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.19 r_work: 0.2749 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2679 Z= 0.183 Angle : 0.528 5.794 3669 Z= 0.282 Chirality : 0.043 0.199 525 Planarity : 0.002 0.013 450 Dihedral : 4.015 20.339 396 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.10 % Allowed : 30.27 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.44), residues: 387 helix: 1.61 (0.52), residues: 112 sheet: -1.99 (0.47), residues: 119 loop : -2.19 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE B 36 TYR 0.003 0.001 TYR A 103 Details of bonding type rmsd hydrogen bonds : bond 0.05276 ( 139) hydrogen bonds : angle 4.88079 ( 378) covalent geometry : bond 0.00433 ( 2679) covalent geometry : angle 0.52759 ( 3669) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 0.255 Fit side-chains REVERT: C 44 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7732 (t80) outliers start: 15 outliers final: 8 residues processed: 33 average time/residue: 0.0672 time to fit residues: 3.2976 Evaluate side-chains 27 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 18 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.076327 restraints weight = 5249.809| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.11 r_work: 0.2839 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2679 Z= 0.095 Angle : 0.429 4.852 3669 Z= 0.235 Chirality : 0.040 0.132 525 Planarity : 0.002 0.009 450 Dihedral : 3.724 18.814 396 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.08 % Allowed : 31.29 % Favored : 64.63 % 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: -1.31 (0.44), residues: 387 helix: 2.03 (0.53), residues: 111 sheet: -1.91 (0.46), residues: 119 loop : -2.14 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 36 TYR 0.004 0.001 TYR A 103 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 139) hydrogen bonds : angle 4.16201 ( 378) covalent geometry : bond 0.00200 ( 2679) covalent geometry : angle 0.42878 ( 3669) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 21 time to evaluate : 0.298 Fit side-chains REVERT: A 116 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8116 (tp-100) REVERT: C 44 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7504 (t80) REVERT: C 103 TYR cc_start: 0.8653 (m-80) cc_final: 0.8441 (m-80) outliers start: 12 outliers final: 7 residues processed: 32 average time/residue: 0.0778 time to fit residues: 3.6718 Evaluate side-chains 27 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.089822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.073043 restraints weight = 5421.019| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.15 r_work: 0.2776 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 2679 Z= 0.153 Angle : 0.480 6.299 3669 Z= 0.255 Chirality : 0.041 0.138 525 Planarity : 0.002 0.010 450 Dihedral : 3.904 20.091 396 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 7.82 % Allowed : 28.57 % Favored : 63.61 % 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: -1.26 (0.44), residues: 387 helix: 2.01 (0.53), residues: 112 sheet: -1.82 (0.47), residues: 119 loop : -2.13 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE B 36 TYR 0.004 0.001 TYR A 103 Details of bonding type rmsd hydrogen bonds : bond 0.04596 ( 139) hydrogen bonds : angle 4.07744 ( 378) covalent geometry : bond 0.00357 ( 2679) covalent geometry : angle 0.47997 ( 3669) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 20 time to evaluate : 0.287 Fit side-chains REVERT: C 44 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7644 (t80) outliers start: 23 outliers final: 16 residues processed: 41 average time/residue: 0.0705 time to fit residues: 4.1933 Evaluate side-chains 36 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 19 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 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 = 0.3188 r_free = 0.3188 target = 0.092591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.075874 restraints weight = 5319.482| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.33 r_work: 0.2828 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2679 Z= 0.086 Angle : 0.419 5.037 3669 Z= 0.228 Chirality : 0.039 0.129 525 Planarity : 0.002 0.011 450 Dihedral : 3.631 18.294 396 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.76 % Allowed : 30.61 % Favored : 64.63 % 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: -1.05 (0.45), residues: 387 helix: 2.29 (0.53), residues: 111 sheet: -1.64 (0.48), residues: 117 loop : -2.14 (0.46), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 36 TYR 0.003 0.001 TYR A 103 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 139) hydrogen bonds : angle 3.72454 ( 378) covalent geometry : bond 0.00176 ( 2679) covalent geometry : angle 0.41880 ( 3669) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 22 time to evaluate : 0.295 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 35 average time/residue: 0.0749 time to fit residues: 3.8164 Evaluate side-chains 31 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 94 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.092138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.075583 restraints weight = 5409.710| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.15 r_work: 0.2820 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2679 Z= 0.113 Angle : 0.430 4.985 3669 Z= 0.233 Chirality : 0.040 0.128 525 Planarity : 0.002 0.014 450 Dihedral : 3.656 18.903 396 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.65 % Favored : 95.09 % Rotamer: Outliers : 7.14 % Allowed : 29.93 % Favored : 62.93 % 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: -1.01 (0.44), residues: 387 helix: 2.31 (0.53), residues: 111 sheet: -1.60 (0.48), residues: 117 loop : -2.12 (0.45), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 36 TYR 0.006 0.001 TYR C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 139) hydrogen bonds : angle 3.74312 ( 378) covalent geometry : bond 0.00257 ( 2679) covalent geometry : angle 0.42967 ( 3669) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 18 time to evaluate : 0.268 Fit side-chains REVERT: C 44 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7635 (t80) outliers start: 21 outliers final: 16 residues processed: 37 average time/residue: 0.0672 time to fit residues: 3.6569 Evaluate side-chains 35 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 18 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.088705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.071791 restraints weight = 5617.426| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.14 r_work: 0.2740 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2679 Z= 0.209 Angle : 0.532 6.126 3669 Z= 0.284 Chirality : 0.043 0.175 525 Planarity : 0.002 0.016 450 Dihedral : 4.099 21.242 396 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.68 % Favored : 94.06 % Rotamer: Outliers : 7.82 % Allowed : 30.61 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.44), residues: 387 helix: 2.01 (0.53), residues: 112 sheet: -1.51 (0.49), residues: 112 loop : -2.17 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE B 36 TYR 0.007 0.001 TYR C 103 Details of bonding type rmsd hydrogen bonds : bond 0.05257 ( 139) hydrogen bonds : angle 4.24151 ( 378) covalent geometry : bond 0.00500 ( 2679) covalent geometry : angle 0.53223 ( 3669) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 17 time to evaluate : 0.372 Fit side-chains REVERT: A 117 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8252 (t0) REVERT: C 44 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7730 (t80) outliers start: 23 outliers final: 18 residues processed: 38 average time/residue: 0.0687 time to fit residues: 3.8234 Evaluate side-chains 36 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 16 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 0.0020 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.092820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.076489 restraints weight = 5332.617| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.13 r_work: 0.2833 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2679 Z= 0.091 Angle : 0.423 4.980 3669 Z= 0.231 Chirality : 0.039 0.128 525 Planarity : 0.002 0.014 450 Dihedral : 3.688 19.186 396 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.39 % Favored : 95.35 % Rotamer: Outliers : 5.78 % Allowed : 32.65 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.44), residues: 387 helix: 2.27 (0.52), residues: 111 sheet: -1.44 (0.48), residues: 112 loop : -2.14 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE C 41 TYR 0.006 0.001 TYR C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 139) hydrogen bonds : angle 3.65593 ( 378) covalent geometry : bond 0.00183 ( 2679) covalent geometry : angle 0.42280 ( 3669) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 19 time to evaluate : 0.286 Fit side-chains REVERT: C 44 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7482 (t80) REVERT: C 133 GLN cc_start: 0.8784 (pp30) cc_final: 0.8001 (pp30) outliers start: 17 outliers final: 13 residues processed: 33 average time/residue: 0.0744 time to fit residues: 3.5895 Evaluate side-chains 33 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.092122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.075786 restraints weight = 5412.389| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.14 r_work: 0.2821 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2679 Z= 0.102 Angle : 0.429 5.072 3669 Z= 0.236 Chirality : 0.040 0.127 525 Planarity : 0.002 0.016 450 Dihedral : 3.642 19.104 396 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.91 % Favored : 94.83 % Rotamer: Outliers : 4.42 % Allowed : 34.01 % Favored : 61.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.44), residues: 387 helix: 2.33 (0.52), residues: 111 sheet: -1.40 (0.49), residues: 112 loop : -2.10 (0.45), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE B 36 TYR 0.006 0.001 TYR C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 139) hydrogen bonds : angle 3.64621 ( 378) covalent geometry : bond 0.00221 ( 2679) covalent geometry : angle 0.42895 ( 3669) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 0.275 Fit side-chains REVERT: C 44 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7598 (t80) REVERT: C 133 GLN cc_start: 0.8807 (pp30) cc_final: 0.8281 (pp30) outliers start: 13 outliers final: 11 residues processed: 30 average time/residue: 0.0715 time to fit residues: 3.2022 Evaluate side-chains 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 = 0.3151 r_free = 0.3151 target = 0.090731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.074168 restraints weight = 5438.226| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.14 r_work: 0.2791 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2679 Z= 0.132 Angle : 0.445 5.157 3669 Z= 0.242 Chirality : 0.040 0.126 525 Planarity : 0.002 0.017 450 Dihedral : 3.737 19.577 396 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.91 % Favored : 94.83 % Rotamer: Outliers : 4.08 % Allowed : 33.33 % Favored : 62.59 % 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: -0.90 (0.44), residues: 387 helix: 2.33 (0.52), residues: 111 sheet: -1.42 (0.49), residues: 112 loop : -2.09 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE B 36 TYR 0.004 0.001 TYR C 103 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 139) hydrogen bonds : angle 3.71381 ( 378) covalent geometry : bond 0.00302 ( 2679) covalent geometry : angle 0.44487 ( 3669) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.286 Fit side-chains REVERT: C 44 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7635 (t80) REVERT: C 133 GLN cc_start: 0.8824 (pp30) cc_final: 0.8291 (pp30) outliers start: 12 outliers final: 11 residues processed: 28 average time/residue: 0.0732 time to fit residues: 3.0726 Evaluate side-chains 29 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 17 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 94 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.076543 restraints weight = 5329.986| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.10 r_work: 0.2839 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2679 Z= 0.095 Angle : 0.419 4.948 3669 Z= 0.232 Chirality : 0.039 0.127 525 Planarity : 0.002 0.018 450 Dihedral : 3.583 18.633 396 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.91 % Favored : 94.83 % Rotamer: Outliers : 5.10 % Allowed : 32.31 % Favored : 62.59 % 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: -0.80 (0.44), residues: 387 helix: 2.47 (0.52), residues: 111 sheet: -1.36 (0.49), residues: 110 loop : -2.07 (0.45), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 36 TYR 0.006 0.001 TYR C 103 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 139) hydrogen bonds : angle 3.55721 ( 378) covalent geometry : bond 0.00201 ( 2679) covalent geometry : angle 0.41921 ( 3669) =============================================================================== Job complete usr+sys time: 1687.28 seconds wall clock time: 29 minutes 40.97 seconds (1780.97 seconds total)