Starting phenix.real_space_refine on Fri Aug 22 12:56:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tib_41283/08_2025/8tib_41283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tib_41283/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tib_41283/08_2025/8tib_41283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tib_41283/08_2025/8tib_41283.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tib_41283/08_2025/8tib_41283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tib_41283/08_2025/8tib_41283.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 0.69, per 1000 atoms: 0.26 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: 0.13 Conformation dependent library (CDL) restraints added in 70.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.11 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: 0.36 Time building geometry restraints manager: 0.18 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: 0.00 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.980 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.003 0.001 TYR C 103 PHE 0.006 0.001 PHE C 41 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 2679) covalent geometry : angle 0.62403 ( 3669) hydrogen bonds : bond 0.20848 ( 139) hydrogen bonds : angle 7.48844 ( 378) *********************** 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 : 0.093 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: 0.0314 time to fit residues: 1.1667 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 : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3169 r_free = 0.3169 target = 0.091323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.074738 restraints weight = 5472.851| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 2.23 r_work: 0.2811 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2679 Z= 0.117 Angle : 0.472 5.635 3669 Z= 0.256 Chirality : 0.041 0.184 525 Planarity : 0.002 0.012 450 Dihedral : 3.771 18.805 396 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.42 % Allowed : 29.59 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.44), residues: 387 helix: 1.81 (0.53), residues: 111 sheet: -2.02 (0.46), residues: 121 loop : -2.17 (0.46), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 103 PHE 0.009 0.001 PHE B 36 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 2679) covalent geometry : angle 0.47227 ( 3669) hydrogen bonds : bond 0.04574 ( 139) hydrogen bonds : angle 4.71774 ( 378) *********************** 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 34 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.099 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 33 average time/residue: 0.0280 time to fit residues: 1.4122 Evaluate side-chains 26 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.112 ------------------------------------------------------------------------------- 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 C residue 78 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3120 r_free = 0.3120 target = 0.088709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.071853 restraints weight = 5487.276| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.12 r_work: 0.2749 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2679 Z= 0.204 Angle : 0.540 5.747 3669 Z= 0.285 Chirality : 0.043 0.156 525 Planarity : 0.002 0.010 450 Dihedral : 4.086 20.973 396 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.44 % Allowed : 29.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.44), residues: 387 helix: 1.81 (0.53), residues: 112 sheet: -1.94 (0.47), residues: 119 loop : -2.14 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 103 PHE 0.013 0.002 PHE B 36 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 2679) covalent geometry : angle 0.53993 ( 3669) hydrogen bonds : bond 0.05323 ( 139) hydrogen bonds : angle 4.54795 ( 378) *********************** 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 34 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 18 time to evaluate : 0.083 Fit side-chains REVERT: C 44 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7819 (t80) outliers start: 16 outliers final: 11 residues processed: 33 average time/residue: 0.0269 time to fit residues: 1.3275 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 : 0.101 ------------------------------------------------------------------------------- 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 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 78 VAL 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 20 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.3070 r_free = 0.3070 target = 0.085721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.068454 restraints weight = 5504.875| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.29 r_work: 0.2683 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 2679 Z= 0.263 Angle : 0.585 6.165 3669 Z= 0.311 Chirality : 0.044 0.193 525 Planarity : 0.002 0.010 450 Dihedral : 4.461 23.102 396 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 8.50 % Allowed : 29.25 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.44), residues: 387 helix: 1.68 (0.53), residues: 112 sheet: -1.75 (0.49), residues: 112 loop : -2.24 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 103 PHE 0.015 0.002 PHE B 36 Details of bonding type rmsd covalent geometry : bond 0.00642 ( 2679) covalent geometry : angle 0.58550 ( 3669) hydrogen bonds : bond 0.05765 ( 139) hydrogen bonds : angle 4.57952 ( 378) *********************** 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 42 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 17 time to evaluate : 0.059 Fit side-chains REVERT: A 116 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8126 (tp-100) REVERT: C 44 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.7811 (t80) outliers start: 25 outliers final: 18 residues processed: 39 average time/residue: 0.0230 time to fit residues: 1.3097 Evaluate side-chains 36 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 17 time to evaluate : 0.120 ------------------------------------------------------------------------------- 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 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 135 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 71 ASN 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 19 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3057 r_free = 0.3057 target = 0.084957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.067586 restraints weight = 5419.068| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.28 r_work: 0.2662 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 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 : 0.008 0.041 2679 Z= 0.310 Angle : 0.631 6.621 3669 Z= 0.333 Chirality : 0.046 0.214 525 Planarity : 0.002 0.012 450 Dihedral : 4.703 23.880 396 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.20 % Favored : 93.54 % Rotamer: Outliers : 9.52 % Allowed : 27.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.44), residues: 387 helix: 1.49 (0.53), residues: 112 sheet: -1.74 (0.50), residues: 112 loop : -2.17 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 103 PHE 0.017 0.002 PHE B 36 Details of bonding type rmsd covalent geometry : bond 0.00759 ( 2679) covalent geometry : angle 0.63100 ( 3669) hydrogen bonds : bond 0.06032 ( 139) hydrogen bonds : angle 4.70166 ( 378) *********************** 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 43 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 15 time to evaluate : 0.078 Fit side-chains REVERT: C 44 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7883 (t80) REVERT: C 133 GLN cc_start: 0.8937 (pp30) cc_final: 0.8113 (pp30) outliers start: 28 outliers final: 20 residues processed: 40 average time/residue: 0.0283 time to fit residues: 1.6969 Evaluate side-chains 35 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 14 time to evaluate : 0.094 ------------------------------------------------------------------------------- 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 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 51 THR 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 51 THR Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 78 VAL 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 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** C 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.073975 restraints weight = 5344.970| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.30 r_work: 0.2793 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2679 Z= 0.098 Angle : 0.446 5.285 3669 Z= 0.244 Chirality : 0.040 0.130 525 Planarity : 0.002 0.017 450 Dihedral : 4.014 20.957 396 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.91 % Favored : 94.83 % Rotamer: Outliers : 4.76 % Allowed : 32.99 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.44), residues: 387 helix: 2.05 (0.53), residues: 111 sheet: -1.61 (0.50), residues: 112 loop : -2.13 (0.43), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR B 103 PHE 0.007 0.001 PHE C 41 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 2679) covalent geometry : angle 0.44637 ( 3669) hydrogen bonds : bond 0.03863 ( 139) hydrogen bonds : angle 3.99882 ( 378) *********************** 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 33 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 0.104 Fit side-chains REVERT: C 44 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7610 (t80) REVERT: C 133 GLN cc_start: 0.8823 (pp30) cc_final: 0.8097 (pp30) outliers start: 14 outliers final: 9 residues processed: 31 average time/residue: 0.0315 time to fit residues: 1.4353 Evaluate side-chains 28 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL 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 78 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 94 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3113 r_free = 0.3113 target = 0.088333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.071262 restraints weight = 5290.350| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.29 r_work: 0.2736 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2679 Z= 0.161 Angle : 0.485 5.526 3669 Z= 0.262 Chirality : 0.041 0.145 525 Planarity : 0.002 0.013 450 Dihedral : 4.074 21.740 396 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.43 % Favored : 94.32 % Rotamer: Outliers : 6.12 % Allowed : 31.63 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.44), residues: 387 helix: 1.97 (0.53), residues: 112 sheet: -1.55 (0.49), residues: 112 loop : -2.07 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 103 PHE 0.011 0.001 PHE B 36 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 2679) covalent geometry : angle 0.48455 ( 3669) hydrogen bonds : bond 0.04677 ( 139) hydrogen bonds : angle 4.13595 ( 378) *********************** 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 35 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 17 time to evaluate : 0.099 Fit side-chains REVERT: B 116 GLN cc_start: 0.9275 (mm-40) cc_final: 0.9025 (pt0) REVERT: C 44 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7696 (t80) REVERT: C 133 GLN cc_start: 0.8882 (pp30) cc_final: 0.8351 (pp30) outliers start: 18 outliers final: 14 residues processed: 33 average time/residue: 0.0249 time to fit residues: 1.2624 Evaluate side-chains 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 17 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL 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 51 THR Chi-restraints excluded: chain B residue 64 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 94 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 24 optimal weight: 0.0040 chunk 19 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.2196 ------------------------------------------------------------------------------- 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 = 0.3141 r_free = 0.3141 target = 0.089931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.072959 restraints weight = 5434.744| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.34 r_work: 0.2767 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2679 Z= 0.116 Angle : 0.448 6.438 3669 Z= 0.242 Chirality : 0.040 0.127 525 Planarity : 0.002 0.014 450 Dihedral : 3.921 20.734 396 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.65 % Favored : 95.09 % Rotamer: Outliers : 4.42 % Allowed : 33.67 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.44), residues: 387 helix: 2.17 (0.53), residues: 111 sheet: -1.68 (0.47), residues: 119 loop : -1.97 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 103 PHE 0.008 0.001 PHE B 36 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2679) covalent geometry : angle 0.44758 ( 3669) hydrogen bonds : bond 0.04066 ( 139) hydrogen bonds : angle 3.87569 ( 378) *********************** 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 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 17 time to evaluate : 0.078 Fit side-chains REVERT: B 116 GLN cc_start: 0.9386 (mm-40) cc_final: 0.9171 (pt0) REVERT: C 44 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7655 (t80) REVERT: C 133 GLN cc_start: 0.8835 (pp30) cc_final: 0.8304 (pp30) outliers start: 13 outliers final: 12 residues processed: 28 average time/residue: 0.0264 time to fit residues: 1.1247 Evaluate side-chains 30 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 17 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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 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 94 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3132 r_free = 0.3132 target = 0.089361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.072293 restraints weight = 5470.324| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.36 r_work: 0.2750 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1751 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= 0.138 Angle : 0.465 6.439 3669 Z= 0.252 Chirality : 0.040 0.129 525 Planarity : 0.002 0.015 450 Dihedral : 3.915 20.907 396 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.43 % Favored : 94.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.44), residues: 387 helix: 2.17 (0.52), residues: 111 sheet: -1.64 (0.47), residues: 119 loop : -1.94 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 103 PHE 0.009 0.001 PHE B 36 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2679) covalent geometry : angle 0.46467 ( 3669) hydrogen bonds : bond 0.04338 ( 139) hydrogen bonds : angle 3.90951 ( 378) *********************** 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 33 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 16 time to evaluate : 0.084 Fit side-chains REVERT: B 116 GLN cc_start: 0.9416 (mm-40) cc_final: 0.9199 (pt0) REVERT: C 44 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7676 (t80) REVERT: C 133 GLN cc_start: 0.8871 (pp30) cc_final: 0.8347 (pp30) outliers start: 17 outliers final: 16 residues processed: 32 average time/residue: 0.0261 time to fit residues: 1.2333 Evaluate side-chains 33 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 16 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 94 VAL 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 51 THR 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 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 0 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3106 r_free = 0.3106 target = 0.087833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.071129 restraints weight = 5560.885| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 2.23 r_work: 0.2728 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2679 Z= 0.180 Angle : 0.499 6.616 3669 Z= 0.268 Chirality : 0.041 0.156 525 Planarity : 0.002 0.017 450 Dihedral : 4.095 21.748 396 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.17 % Favored : 94.57 % Rotamer: Outliers : 6.12 % Allowed : 32.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.44), residues: 387 helix: 2.00 (0.52), residues: 112 sheet: -1.63 (0.48), residues: 119 loop : -1.91 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 103 PHE 0.011 0.001 PHE B 36 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 2679) covalent geometry : angle 0.49933 ( 3669) hydrogen bonds : bond 0.04910 ( 139) hydrogen bonds : angle 4.08992 ( 378) ********************** 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 35 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 17 time to evaluate : 0.103 Fit side-chains REVERT: B 116 GLN cc_start: 0.9403 (mm-40) cc_final: 0.9201 (pt0) REVERT: C 44 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7729 (t80) REVERT: C 133 GLN cc_start: 0.8898 (pp30) cc_final: 0.8370 (pp30) outliers start: 18 outliers final: 17 residues processed: 34 average time/residue: 0.0299 time to fit residues: 1.5273 Evaluate side-chains 35 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 17 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 94 VAL 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 51 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 64 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 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 34 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.090821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.073980 restraints weight = 5365.963| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.31 r_work: 0.2792 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2679 Z= 0.106 Angle : 0.437 6.221 3669 Z= 0.241 Chirality : 0.039 0.127 525 Planarity : 0.002 0.018 450 Dihedral : 3.799 20.085 396 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.91 % Favored : 94.83 % Rotamer: Outliers : 6.12 % Allowed : 32.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.90 (0.44), residues: 387 helix: 2.29 (0.52), residues: 111 sheet: -1.60 (0.47), residues: 119 loop : -1.90 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 103 PHE 0.007 0.001 PHE C 41 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 2679) covalent geometry : angle 0.43688 ( 3669) hydrogen bonds : bond 0.03804 ( 139) hydrogen bonds : angle 3.73303 ( 378) =============================================================================== Job complete usr+sys time: 754.51 seconds wall clock time: 13 minutes 34.81 seconds (814.81 seconds total)