Starting phenix.real_space_refine on Mon Feb 10 20:42:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t2e_25611/02_2025/7t2e_25611.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2e_25611/02_2025/7t2e_25611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t2e_25611/02_2025/7t2e_25611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2e_25611/02_2025/7t2e_25611.map" model { file = "/net/cci-nas-00/data/ceres_data/7t2e_25611/02_2025/7t2e_25611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2e_25611/02_2025/7t2e_25611.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1500 2.51 5 N 404 2.21 5 O 480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2390 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1195 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "B" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1195 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Time building chain proxies: 2.14, per 1000 atoms: 0.90 Number of scatterers: 2390 At special positions: 0 Unit cell: (61.6, 77, 108.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 480 8.00 N 404 7.00 C 1500 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: 0.54 Conformation dependent library (CDL) restraints added in 295.5 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 12.8% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 151 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 removed outlier: 5.634A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS A 142 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 127 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 140 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS A 129 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR A 138 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 131 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N VAL A 136 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 81 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A 45 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR A 83 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 6.681A pdb=" N THR A 51 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 75 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLU A 53 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.506A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS B 142 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 127 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 140 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS B 129 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 138 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 131 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N VAL B 136 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER B 81 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 45 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 83 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.665A pdb=" N THR B 51 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS B 75 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU B 53 " --> pdb=" O GLY B 73 " (cutoff:3.500A) 78 hydrogen bonds defined for protein. 204 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: 0.44 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 788 1.34 - 1.46: 564 1.46 - 1.58: 1086 1.58 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2450 Sorted by residual: bond pdb=" CA GLY A 22 " pdb=" C GLY A 22 " ideal model delta sigma weight residual 1.519 1.512 0.007 8.90e-03 1.26e+04 5.52e-01 bond pdb=" CA ASP A 25 " pdb=" CB ASP A 25 " ideal model delta sigma weight residual 1.528 1.518 0.009 1.50e-02 4.44e+03 3.86e-01 bond pdb=" CG PRO A 113 " pdb=" CD PRO A 113 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.65e-01 bond pdb=" CB LYS A 109 " pdb=" CG LYS A 109 " ideal model delta sigma weight residual 1.520 1.505 0.015 3.00e-02 1.11e+03 2.50e-01 bond pdb=" CA LYS A 21 " pdb=" C LYS A 21 " ideal model delta sigma weight residual 1.523 1.530 -0.008 1.61e-02 3.86e+03 2.33e-01 ... (remaining 2445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 3066 0.84 - 1.68: 219 1.68 - 2.52: 27 2.52 - 3.36: 23 3.36 - 4.20: 7 Bond angle restraints: 3342 Sorted by residual: angle pdb=" C VAL B 34 " pdb=" N ASP B 35 " pdb=" CA ASP B 35 " ideal model delta sigma weight residual 122.74 125.43 -2.69 1.44e+00 4.82e-01 3.50e+00 angle pdb=" C GLY A 147 " pdb=" N ARG A 148 " pdb=" CA ARG A 148 " ideal model delta sigma weight residual 121.61 124.16 -2.55 1.39e+00 5.18e-01 3.36e+00 angle pdb=" N PHE A 82 " pdb=" CA PHE A 82 " pdb=" C PHE A 82 " ideal model delta sigma weight residual 109.14 111.70 -2.56 1.49e+00 4.50e-01 2.95e+00 angle pdb=" CA TRP B 99 " pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 113.60 116.59 -2.99 1.90e+00 2.77e-01 2.48e+00 angle pdb=" N GLY B 122 " pdb=" CA GLY B 122 " pdb=" C GLY B 122 " ideal model delta sigma weight residual 110.55 113.11 -2.56 1.64e+00 3.72e-01 2.43e+00 ... (remaining 3337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1252 16.87 - 33.73: 130 33.73 - 50.59: 48 50.59 - 67.46: 9 67.46 - 84.32: 1 Dihedral angle restraints: 1440 sinusoidal: 556 harmonic: 884 Sorted by residual: dihedral pdb=" CA ASP A 79 " pdb=" CB ASP A 79 " pdb=" CG ASP A 79 " pdb=" OD1 ASP A 79 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA LYS A 109 " pdb=" C LYS A 109 " pdb=" N ILE A 110 " pdb=" CA ILE A 110 " ideal model delta harmonic sigma weight residual 180.00 164.47 15.53 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" CB GLU B 135 " pdb=" CG GLU B 135 " pdb=" CD GLU B 135 " pdb=" OE1 GLU B 135 " ideal model delta sinusoidal sigma weight residual 0.00 -84.32 84.32 1 3.00e+01 1.11e-03 9.61e+00 ... (remaining 1437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 209 0.028 - 0.057: 95 0.057 - 0.085: 23 0.085 - 0.113: 29 0.113 - 0.141: 8 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE B 127 " pdb=" N ILE B 127 " pdb=" C ILE B 127 " pdb=" CB ILE B 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA VAL B 3 " pdb=" N VAL B 3 " pdb=" C VAL B 3 " pdb=" CB VAL B 3 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 361 not shown) Planarity restraints: 434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 112 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 113 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 8 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO A 9 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 8 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.04e-01 pdb=" N PRO B 9 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " 0.012 5.00e-02 4.00e+02 ... (remaining 431 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 419 2.77 - 3.30: 1887 3.30 - 3.84: 3607 3.84 - 4.37: 3992 4.37 - 4.90: 7404 Nonbonded interactions: 17309 Sorted by model distance: nonbonded pdb=" OH TYR B 108 " pdb=" OD1 ASN B 145 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 108 " pdb=" OD1 ASN A 145 " model vdw 2.307 3.040 nonbonded pdb=" O THR A 157 " pdb=" OG1 THR A 157 " model vdw 2.489 3.040 nonbonded pdb=" O SER A 156 " pdb=" OG1 THR A 157 " model vdw 2.498 3.040 nonbonded pdb=" O PRO B 30 " pdb=" NZ LYS B 109 " model vdw 2.538 3.120 ... (remaining 17304 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' } 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: 0.660 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: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.690 Find NCS groups from input model: 0.080 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 0.017 2450 Z= 0.178 Angle : 0.540 4.198 3342 Z= 0.297 Chirality : 0.045 0.141 364 Planarity : 0.004 0.032 434 Dihedral : 16.112 84.321 876 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.18 % Allowed : 22.83 % Favored : 75.98 % 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: 0.14 (0.45), residues: 308 helix: 1.97 (1.05), residues: 28 sheet: -0.11 (0.39), residues: 158 loop : 0.17 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 18 PHE 0.012 0.002 PHE B 120 TYR 0.009 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.255 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 1.4662 time to fit residues: 55.3968 Evaluate side-chains 38 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.088111 restraints weight = 2935.163| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.12 r_work: 0.2886 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2450 Z= 0.327 Angle : 0.585 4.936 3342 Z= 0.308 Chirality : 0.048 0.156 364 Planarity : 0.004 0.036 434 Dihedral : 5.817 48.169 339 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.54 % Allowed : 20.87 % Favored : 75.59 % 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: 0.21 (0.47), residues: 308 helix: 2.06 (1.10), residues: 28 sheet: -0.14 (0.40), residues: 158 loop : 0.31 (0.52), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 18 PHE 0.017 0.003 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.234 Fit side-chains REVERT: A 31 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8343 (mm) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 1.5115 time to fit residues: 60.0548 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.088623 restraints weight = 2939.078| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.12 r_work: 0.2895 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2450 Z= 0.282 Angle : 0.550 4.413 3342 Z= 0.289 Chirality : 0.047 0.151 364 Planarity : 0.004 0.035 434 Dihedral : 5.249 47.252 336 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 22.05 % Favored : 75.20 % 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: 0.23 (0.47), residues: 308 helix: 2.08 (1.08), residues: 28 sheet: -0.15 (0.40), residues: 158 loop : 0.36 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 PHE 0.016 0.003 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.268 Fit side-chains REVERT: A 31 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8349 (mm) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 1.3791 time to fit residues: 59.1319 Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.087313 restraints weight = 2945.171| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.11 r_work: 0.2871 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 2450 Z= 0.392 Angle : 0.612 5.500 3342 Z= 0.322 Chirality : 0.050 0.157 364 Planarity : 0.005 0.040 434 Dihedral : 5.527 48.614 336 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 22.44 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.47), residues: 308 helix: 1.82 (1.07), residues: 28 sheet: -0.22 (0.40), residues: 158 loop : 0.17 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 18 PHE 0.019 0.003 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.004 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.309 Fit side-chains REVERT: A 31 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8371 (mm) outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 1.6027 time to fit residues: 60.4578 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.089979 restraints weight = 3004.229| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.15 r_work: 0.2896 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.0759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2450 Z= 0.161 Angle : 0.479 4.330 3342 Z= 0.252 Chirality : 0.045 0.144 364 Planarity : 0.003 0.033 434 Dihedral : 4.838 44.266 336 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.36 % Allowed : 23.23 % Favored : 74.41 % 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: 0.28 (0.47), residues: 308 helix: 2.26 (1.05), residues: 28 sheet: -0.14 (0.40), residues: 158 loop : 0.40 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 18 PHE 0.011 0.002 PHE A 120 TYR 0.006 0.001 TYR A 108 ARG 0.001 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.269 Fit side-chains REVERT: A 31 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8328 (mm) outliers start: 6 outliers final: 3 residues processed: 44 average time/residue: 1.3878 time to fit residues: 62.3558 Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 109 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.092263 restraints weight = 2937.046| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.13 r_work: 0.2947 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2450 Z= 0.123 Angle : 0.438 4.139 3342 Z= 0.228 Chirality : 0.044 0.142 364 Planarity : 0.003 0.027 434 Dihedral : 3.759 13.619 334 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.57 % Allowed : 23.62 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.48), residues: 308 helix: 2.53 (1.03), residues: 28 sheet: -0.06 (0.40), residues: 158 loop : 0.60 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 123 PHE 0.009 0.002 PHE B 82 TYR 0.006 0.001 TYR A 108 ARG 0.001 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.282 Fit side-chains REVERT: A 31 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8338 (mm) outliers start: 4 outliers final: 1 residues processed: 48 average time/residue: 1.2044 time to fit residues: 59.1882 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.090078 restraints weight = 2985.645| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.14 r_work: 0.2898 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2450 Z= 0.192 Angle : 0.488 4.301 3342 Z= 0.253 Chirality : 0.045 0.145 364 Planarity : 0.003 0.029 434 Dihedral : 4.006 13.451 334 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.57 % Allowed : 24.02 % Favored : 74.41 % 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: 0.44 (0.47), residues: 308 helix: 2.28 (1.02), residues: 28 sheet: -0.06 (0.40), residues: 158 loop : 0.57 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 PHE 0.012 0.002 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.284 Fit side-chains REVERT: A 31 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8329 (mm) outliers start: 4 outliers final: 3 residues processed: 39 average time/residue: 1.3360 time to fit residues: 53.2757 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.109355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.087851 restraints weight = 3063.283| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.17 r_work: 0.2823 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2450 Z= 0.337 Angle : 0.572 4.980 3342 Z= 0.298 Chirality : 0.048 0.154 364 Planarity : 0.004 0.035 434 Dihedral : 4.493 15.139 334 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 22.83 % Favored : 74.41 % 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: 0.24 (0.47), residues: 308 helix: 1.96 (1.01), residues: 28 sheet: -0.13 (0.40), residues: 158 loop : 0.39 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 18 PHE 0.017 0.003 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.003 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.283 Fit side-chains REVERT: A 31 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8379 (mm) outliers start: 7 outliers final: 4 residues processed: 41 average time/residue: 1.3290 time to fit residues: 55.7588 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.088106 restraints weight = 2986.503| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.13 r_work: 0.2886 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 2450 Z= 0.307 Angle : 0.557 4.508 3342 Z= 0.291 Chirality : 0.048 0.152 364 Planarity : 0.004 0.038 434 Dihedral : 4.493 14.911 334 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.36 % Allowed : 23.23 % Favored : 74.41 % 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: 0.15 (0.47), residues: 308 helix: 1.96 (1.03), residues: 28 sheet: -0.15 (0.40), residues: 158 loop : 0.25 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 18 PHE 0.016 0.003 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.236 Fit side-chains REVERT: A 31 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8360 (mm) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 1.2935 time to fit residues: 52.9129 Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.090606 restraints weight = 2948.289| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.14 r_work: 0.2870 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2450 Z= 0.145 Angle : 0.464 4.256 3342 Z= 0.242 Chirality : 0.045 0.142 364 Planarity : 0.003 0.033 434 Dihedral : 3.979 12.571 334 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.18 % Allowed : 24.41 % Favored : 74.41 % 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: 0.40 (0.48), residues: 308 helix: 2.33 (1.02), residues: 28 sheet: -0.06 (0.40), residues: 158 loop : 0.48 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 18 PHE 0.010 0.002 PHE B 82 TYR 0.006 0.001 TYR A 108 ARG 0.001 0.000 ARG A 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.262 Fit side-chains REVERT: A 104 ASP cc_start: 0.7611 (m-30) cc_final: 0.7346 (m-30) outliers start: 3 outliers final: 2 residues processed: 40 average time/residue: 1.3004 time to fit residues: 53.1973 Evaluate side-chains 42 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 57 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.091702 restraints weight = 3011.411| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.15 r_work: 0.2895 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2450 Z= 0.128 Angle : 0.450 4.131 3342 Z= 0.232 Chirality : 0.044 0.142 364 Planarity : 0.003 0.031 434 Dihedral : 3.729 11.786 334 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.79 % Allowed : 24.80 % Favored : 74.41 % 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: 0.56 (0.48), residues: 308 helix: 2.57 (1.01), residues: 28 sheet: -0.02 (0.40), residues: 158 loop : 0.65 (0.56), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 123 PHE 0.009 0.002 PHE B 82 TYR 0.006 0.001 TYR A 108 ARG 0.001 0.000 ARG A 139 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2292.57 seconds wall clock time: 40 minutes 59.22 seconds (2459.22 seconds total)