Starting phenix.real_space_refine on Mon Feb 10 21:11:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tib_41283/02_2025/8tib_41283.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tib_41283/02_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_41283/02_2025/8tib_41283.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tib_41283/02_2025/8tib_41283.map" model { file = "/net/cci-nas-00/data/ceres_data/8tib_41283/02_2025/8tib_41283.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tib_41283/02_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-5592/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: 2.44, per 1000 atoms: 0.91 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: 0.68 Conformation dependent library (CDL) restraints added in 345.2 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: 0.34 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: 0.57 Time building geometry restraints manager: 0.77 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: 1.320 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.770 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.880 ------------------------------------------------------------------------------- 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= 0.225 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 *********************** 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 : 0.279 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: 0.0861 time to fit residues: 3.2390 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 : 0.298 ------------------------------------------------------------------------------- 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 = 0.088838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.071883 restraints weight = 5483.822| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.19 r_work: 0.2750 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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= 0.285 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 *********************** 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 : 0.264 Fit side-chains REVERT: C 44 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7731 (t80) outliers start: 15 outliers final: 8 residues processed: 33 average time/residue: 0.0740 time to fit residues: 3.5413 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 : 0.271 ------------------------------------------------------------------------------- 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: 0.9980 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3195 r_free = 0.3195 target = 0.093058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.076554 restraints weight = 5251.513| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.21 r_work: 0.2838 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1332 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= 0.124 Angle : 0.426 4.780 3669 Z= 0.234 Chirality : 0.040 0.134 525 Planarity : 0.002 0.009 450 Dihedral : 3.711 18.675 396 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.74 % Allowed : 31.63 % 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: -1.30 (0.44), residues: 387 helix: 2.06 (0.53), residues: 111 sheet: -1.90 (0.46), residues: 119 loop : -2.15 (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 *********************** 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 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.302 Fit side-chains REVERT: A 116 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8129 (tp-100) REVERT: C 103 TYR cc_start: 0.8671 (m-80) cc_final: 0.8456 (m-80) outliers start: 11 outliers final: 7 residues processed: 31 average time/residue: 0.0749 time to fit residues: 3.4272 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 : 0.283 ------------------------------------------------------------------------------- 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 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.092499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.076020 restraints weight = 5366.973| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.13 r_work: 0.2830 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2679 Z= 0.152 Angle : 0.437 6.617 3669 Z= 0.233 Chirality : 0.040 0.130 525 Planarity : 0.002 0.010 450 Dihedral : 3.680 18.918 396 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 6.80 % Allowed : 28.91 % Favored : 64.29 % 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: -1.17 (0.44), residues: 387 helix: 2.20 (0.53), residues: 111 sheet: -1.77 (0.47), residues: 119 loop : -2.16 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 36 TYR 0.003 0.001 TYR A 103 *********************** 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 39 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 19 time to evaluate : 0.270 Fit side-chains REVERT: C 44 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7581 (t80) outliers start: 20 outliers final: 13 residues processed: 37 average time/residue: 0.0699 time to fit residues: 3.7954 Evaluate side-chains 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.092462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.075662 restraints weight = 5318.275| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.33 r_work: 0.2820 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2679 Z= 0.132 Angle : 0.423 5.113 3669 Z= 0.229 Chirality : 0.040 0.128 525 Planarity : 0.002 0.011 450 Dihedral : 3.603 18.475 396 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.44 % Allowed : 29.59 % Favored : 64.97 % 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: -1.06 (0.44), residues: 387 helix: 2.34 (0.53), residues: 111 sheet: -1.71 (0.47), residues: 119 loop : -2.13 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE B 36 TYR 0.003 0.001 TYR A 103 *********************** 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 35 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 0.280 Fit side-chains REVERT: C 44 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7638 (t80) outliers start: 16 outliers final: 12 residues processed: 34 average time/residue: 0.0763 time to fit residues: 3.7895 Evaluate side-chains 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.0960 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.092612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.076123 restraints weight = 5403.956| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.14 r_work: 0.2832 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1612 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= 0.153 Angle : 0.420 4.952 3669 Z= 0.227 Chirality : 0.040 0.126 525 Planarity : 0.002 0.013 450 Dihedral : 3.603 18.428 396 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.65 % Favored : 95.09 % Rotamer: Outliers : 7.14 % Allowed : 28.57 % Favored : 64.29 % 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: 2.38 (0.52), residues: 111 sheet: -1.67 (0.47), residues: 119 loop : -2.10 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 36 TYR 0.006 0.001 TYR C 103 *********************** 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 40 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 19 time to evaluate : 0.300 Fit side-chains REVERT: C 44 PHE cc_start: 0.8150 (OUTLIER) cc_final: 0.7631 (t80) outliers start: 21 outliers final: 16 residues processed: 38 average time/residue: 0.0701 time to fit residues: 3.8972 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 : 0.290 ------------------------------------------------------------------------------- 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 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: 6.9990 chunk 37 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 38 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.0270 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.077751 restraints weight = 5448.478| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.28 r_work: 0.2869 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2679 Z= 0.102 Angle : 0.405 5.030 3669 Z= 0.223 Chirality : 0.039 0.127 525 Planarity : 0.002 0.015 450 Dihedral : 3.433 17.360 396 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.65 % Favored : 95.09 % Rotamer: Outliers : 5.10 % Allowed : 30.95 % Favored : 63.95 % 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: -0.86 (0.44), residues: 387 helix: 2.48 (0.52), residues: 112 sheet: -1.55 (0.47), residues: 117 loop : -2.06 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE B 36 TYR 0.006 0.001 TYR C 103 *********************** 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 38 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 23 time to evaluate : 0.274 Fit side-chains REVERT: C 44 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7562 (t80) outliers start: 15 outliers final: 13 residues processed: 36 average time/residue: 0.0738 time to fit residues: 3.8690 Evaluate side-chains 32 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 62 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 68 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 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: 2.9990 chunk 24 optimal weight: 0.6980 chunk 17 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.090393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.073799 restraints weight = 5355.331| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.07 r_work: 0.2783 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1770 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= 0.251 Angle : 0.500 6.985 3669 Z= 0.267 Chirality : 0.042 0.197 525 Planarity : 0.002 0.016 450 Dihedral : 3.838 19.785 396 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.91 % Favored : 94.83 % Rotamer: Outliers : 6.46 % Allowed : 30.95 % 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: -0.94 (0.44), residues: 387 helix: 2.27 (0.52), residues: 112 sheet: -1.38 (0.48), residues: 112 loop : -2.18 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE B 36 TYR 0.003 0.001 TYR C 103 *********************** 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 35 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 16 time to evaluate : 0.275 Fit side-chains REVERT: C 44 PHE cc_start: 0.8271 (OUTLIER) cc_final: 0.7729 (t80) outliers start: 19 outliers final: 17 residues processed: 34 average time/residue: 0.0706 time to fit residues: 3.5253 Evaluate side-chains 34 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 16 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 105 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 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 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: 8.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 = 0.3133 r_free = 0.3133 target = 0.089172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.072131 restraints weight = 5442.896| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.18 r_work: 0.2749 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1701 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= 0.292 Angle : 0.514 6.068 3669 Z= 0.277 Chirality : 0.042 0.165 525 Planarity : 0.002 0.016 450 Dihedral : 4.036 21.212 396 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.17 % Favored : 94.57 % Rotamer: Outliers : 6.80 % Allowed : 30.27 % 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: -0.96 (0.44), residues: 387 helix: 2.11 (0.52), residues: 112 sheet: -1.33 (0.49), residues: 112 loop : -2.11 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE B 36 TYR 0.008 0.001 TYR C 103 *********************** 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 38 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 18 time to evaluate : 0.313 Fit side-chains REVERT: C 44 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7755 (t80) REVERT: C 133 GLN cc_start: 0.8866 (pp30) cc_final: 0.8073 (pp30) outliers start: 20 outliers final: 17 residues processed: 36 average time/residue: 0.0757 time to fit residues: 4.0615 Evaluate side-chains 36 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 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 105 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 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 = 0.3146 r_free = 0.3146 target = 0.090176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.073265 restraints weight = 5408.747| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.21 r_work: 0.2773 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1832 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= 0.211 Angle : 0.467 5.314 3669 Z= 0.253 Chirality : 0.041 0.148 525 Planarity : 0.002 0.018 450 Dihedral : 3.878 20.424 396 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.17 % Favored : 94.57 % Rotamer: Outliers : 6.12 % Allowed : 30.27 % 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: -0.87 (0.44), residues: 387 helix: 2.15 (0.51), residues: 113 sheet: -1.32 (0.49), residues: 112 loop : -2.02 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE B 36 TYR 0.004 0.001 TYR C 103 ********************** 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 36 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 18 time to evaluate : 0.268 Fit side-chains REVERT: C 44 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7647 (t80) REVERT: C 133 GLN cc_start: 0.8839 (pp30) cc_final: 0.8041 (pp30) outliers start: 18 outliers final: 16 residues processed: 34 average time/residue: 0.0784 time to fit residues: 3.8932 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 105 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 17 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3190 r_free = 0.3190 target = 0.092869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.076617 restraints weight = 5333.110| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.12 r_work: 0.2838 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2679 Z= 0.138 Angle : 0.435 5.202 3669 Z= 0.240 Chirality : 0.040 0.136 525 Planarity : 0.002 0.019 450 Dihedral : 3.652 19.015 396 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.17 % Favored : 94.57 % Rotamer: Outliers : 5.10 % Allowed : 31.63 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.44), residues: 387 helix: 2.38 (0.52), residues: 112 sheet: -1.29 (0.49), residues: 112 loop : -2.00 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.005 0.001 PHE B 36 TYR 0.007 0.001 TYR C 103 =============================================================================== Job complete usr+sys time: 1579.70 seconds wall clock time: 28 minutes 42.68 seconds (1722.68 seconds total)