Starting phenix.real_space_refine on Sun Mar 10 15:10:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tib_41283/03_2024/8tib_41283.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tib_41283/03_2024/8tib_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tib_41283/03_2024/8tib_41283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tib_41283/03_2024/8tib_41283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tib_41283/03_2024/8tib_41283.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tib_41283/03_2024/8tib_41283.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.73, per 1000 atoms: 0.65 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 - 3.50 Amino acid : False - 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: 1.00 Conformation dependent library (CDL) restraints added in 499.3 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: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 13 through 46 Processing helix chain 'A' and resid 111 through 117 Processing helix chain 'B' and resid 17 through 46 removed outlier: 3.542A pdb=" N LEU B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 28 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 118 removed outlier: 4.237A pdb=" N LEU B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 46 removed outlier: 3.591A pdb=" N THR C 18 " --> pdb=" O SER C 14 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 20 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 119 removed outlier: 3.621A pdb=" N VAL C 119 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 82 removed outlier: 6.663A pdb=" N GLN A 128 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA A 81 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR A 126 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 137 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 56 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N THR A 142 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU A 58 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 64 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.930A pdb=" N THR B 49 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 72 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.149A pdb=" N ALA B 56 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR B 142 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 58 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY B 80 " --> pdb=" O GLN B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 67 Processing sheet with id=AA6, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 59 Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 67 139 hydrogen bonds defined for protein. 378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 1.10 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: 106.35 - 110.13: 490 110.13 - 113.92: 1263 113.92 - 117.71: 449 117.71 - 121.50: 779 121.50 - 125.29: 688 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 2.440 nonbonded pdb=" O SER B 106 " pdb=" OG SER B 106 " model vdw 2.335 2.440 nonbonded pdb=" O THR B 122 " pdb=" OG1 THR B 122 " model vdw 2.339 2.440 nonbonded pdb=" O SER C 112 " pdb=" NE2 GLN C 116 " model vdw 2.392 2.520 nonbonded pdb=" OD1 ASN C 131 " pdb=" NE2 GLN C 133 " model vdw 2.392 2.520 ... (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 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: 1.490 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: 6.340 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.390 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.290 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: 0.0869 time to fit residues: 3.2447 Evaluate side-chains 24 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 6.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2679 Z= 0.213 Angle : 0.481 5.645 3669 Z= 0.257 Chirality : 0.041 0.179 525 Planarity : 0.002 0.012 450 Dihedral : 3.819 19.476 396 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.10 % Allowed : 29.93 % 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: -1.51 (0.44), residues: 387 helix: 1.79 (0.53), residues: 111 sheet: -2.02 (0.47), residues: 119 loop : -2.20 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE B 36 TYR 0.002 0.001 TYR C 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 34 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 19 time to evaluate : 0.295 Fit side-chains REVERT: C 44 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7359 (t80) outliers start: 15 outliers final: 8 residues processed: 33 average time/residue: 0.0712 time to fit residues: 3.4877 Evaluate side-chains 27 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 18 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 19 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 26 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2679 Z= 0.160 Angle : 0.432 4.958 3669 Z= 0.234 Chirality : 0.040 0.135 525 Planarity : 0.002 0.009 450 Dihedral : 3.682 19.117 396 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 4.42 % Allowed : 30.95 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.44), residues: 387 helix: 2.10 (0.53), residues: 111 sheet: -1.94 (0.47), residues: 119 loop : -2.16 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE B 36 TYR 0.002 0.001 TYR C 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 33 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 20 time to evaluate : 0.292 Fit side-chains REVERT: C 44 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7356 (t80) outliers start: 13 outliers final: 9 residues processed: 32 average time/residue: 0.0719 time to fit residues: 3.4177 Evaluate side-chains 28 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 18 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2679 Z= 0.175 Angle : 0.443 6.315 3669 Z= 0.239 Chirality : 0.040 0.127 525 Planarity : 0.002 0.014 450 Dihedral : 3.707 19.485 396 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 7.14 % Allowed : 29.25 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.45), residues: 387 helix: 2.21 (0.53), residues: 111 sheet: -1.87 (0.47), residues: 119 loop : -2.18 (0.45), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE B 36 TYR 0.002 0.001 TYR C 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 41 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 20 time to evaluate : 0.288 Fit side-chains REVERT: C 44 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7336 (t80) outliers start: 21 outliers final: 15 residues processed: 39 average time/residue: 0.0680 time to fit residues: 3.8877 Evaluate side-chains 34 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 18 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 122 THR 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 15 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2679 Z= 0.301 Angle : 0.500 5.693 3669 Z= 0.266 Chirality : 0.042 0.159 525 Planarity : 0.002 0.012 450 Dihedral : 4.016 21.200 396 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.20 % Favored : 93.54 % Rotamer: Outliers : 8.16 % Allowed : 29.93 % 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 (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: -1.24 (0.45), residues: 387 helix: 2.01 (0.53), residues: 112 sheet: -1.79 (0.48), residues: 119 loop : -2.12 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE B 36 TYR 0.003 0.001 TYR C 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 40 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 16 time to evaluate : 0.269 Fit side-chains REVERT: C 44 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7545 (t80) REVERT: C 77 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7925 (pt0) outliers start: 24 outliers final: 15 residues processed: 39 average time/residue: 0.0711 time to fit residues: 4.1200 Evaluate side-chains 33 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 16 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 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 122 THR 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 77 GLN 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: 6.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2679 Z= 0.224 Angle : 0.466 5.361 3669 Z= 0.251 Chirality : 0.040 0.135 525 Planarity : 0.002 0.016 450 Dihedral : 3.914 21.026 396 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.94 % Favored : 93.80 % Rotamer: Outliers : 7.14 % Allowed : 31.97 % Favored : 60.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.45), residues: 387 helix: 2.08 (0.53), residues: 112 sheet: -1.75 (0.48), residues: 119 loop : -2.10 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE B 36 TYR 0.003 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 39 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 18 time to evaluate : 0.282 Fit side-chains REVERT: C 44 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7483 (t80) REVERT: C 77 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7900 (pt0) outliers start: 21 outliers final: 17 residues processed: 36 average time/residue: 0.0718 time to fit residues: 3.7995 Evaluate side-chains 37 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 18 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR 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 40 LEU 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 122 THR 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 77 GLN 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 21 optimal weight: 0.0870 chunk 31 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2679 Z= 0.198 Angle : 0.445 5.141 3669 Z= 0.242 Chirality : 0.040 0.125 525 Planarity : 0.002 0.015 450 Dihedral : 3.806 20.389 396 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.94 % Favored : 93.80 % Rotamer: Outliers : 8.16 % Allowed : 31.63 % Favored : 60.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.45), residues: 387 helix: 2.16 (0.53), residues: 112 sheet: -1.73 (0.48), residues: 119 loop : -2.08 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE B 36 TYR 0.003 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 42 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 18 time to evaluate : 0.259 Fit side-chains REVERT: C 44 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7406 (t80) REVERT: C 77 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7877 (pt0) outliers start: 24 outliers final: 22 residues processed: 39 average time/residue: 0.0680 time to fit residues: 3.8900 Evaluate side-chains 42 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 18 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 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 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 122 THR 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 49 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 77 GLN 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 3 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1514 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= 0.188 Angle : 0.439 5.159 3669 Z= 0.240 Chirality : 0.040 0.126 525 Planarity : 0.002 0.016 450 Dihedral : 3.782 20.347 396 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.94 % Favored : 93.80 % Rotamer: Outliers : 9.52 % Allowed : 30.95 % Favored : 59.52 % 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: -1.08 (0.45), residues: 387 helix: 2.25 (0.53), residues: 111 sheet: -1.70 (0.48), residues: 119 loop : -2.09 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE B 36 TYR 0.002 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 46 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 18 time to evaluate : 0.269 Fit side-chains REVERT: C 44 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7393 (t80) REVERT: C 77 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7871 (pt0) outliers start: 28 outliers final: 24 residues processed: 43 average time/residue: 0.0691 time to fit residues: 4.3518 Evaluate side-chains 44 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 18 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 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 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 122 THR 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 49 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 77 GLN 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 33 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1636 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= 0.306 Angle : 0.502 5.609 3669 Z= 0.270 Chirality : 0.041 0.162 525 Planarity : 0.002 0.017 450 Dihedral : 4.044 21.681 396 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.20 % Favored : 93.54 % Rotamer: Outliers : 9.18 % Allowed : 30.95 % Favored : 59.86 % 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: -1.15 (0.44), residues: 387 helix: 2.01 (0.52), residues: 112 sheet: -1.68 (0.48), residues: 119 loop : -2.06 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE B 36 TYR 0.002 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 45 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 18 time to evaluate : 0.297 Fit side-chains REVERT: B 14 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8793 (p) REVERT: C 44 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7480 (t80) REVERT: C 77 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.8004 (pt0) outliers start: 27 outliers final: 22 residues processed: 42 average time/residue: 0.0706 time to fit residues: 4.3648 Evaluate side-chains 42 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 17 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 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 14 SER Chi-restraints excluded: chain B residue 51 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 122 THR 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 49 THR Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 77 GLN 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 23 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1647 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= 0.115 Angle : 0.407 4.743 3669 Z= 0.226 Chirality : 0.038 0.123 525 Planarity : 0.002 0.017 450 Dihedral : 3.628 19.423 396 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.94 % Favored : 93.80 % Rotamer: Outliers : 6.12 % Allowed : 34.01 % Favored : 59.86 % 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: -0.99 (0.45), residues: 387 helix: 2.36 (0.52), residues: 111 sheet: -1.64 (0.48), residues: 119 loop : -2.07 (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 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 fitting. rotamer outliers: 18 poor density : 18 time to evaluate : 0.313 Fit side-chains REVERT: C 44 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7334 (t80) REVERT: C 77 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7883 (pt0) outliers start: 18 outliers final: 14 residues processed: 33 average time/residue: 0.0725 time to fit residues: 3.5369 Evaluate side-chains 34 residues out of total 294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 18 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 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 77 GLN 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 3 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3207 r_free = 0.3207 target = 0.093903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.077415 restraints weight = 5380.582| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.19 r_work: 0.2851 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2679 Z= 0.124 Angle : 0.406 4.623 3669 Z= 0.225 Chirality : 0.039 0.123 525 Planarity : 0.002 0.019 450 Dihedral : 3.482 18.599 396 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.68 % Favored : 94.06 % Rotamer: Outliers : 4.76 % Allowed : 35.37 % Favored : 59.86 % 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: -0.89 (0.45), residues: 387 helix: 2.46 (0.52), residues: 111 sheet: -1.56 (0.48), residues: 119 loop : -2.06 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.001 PHE B 36 TYR 0.006 0.001 TYR C 103 =============================================================================== Job complete usr+sys time: 982.08 seconds wall clock time: 18 minutes 23.70 seconds (1103.70 seconds total)