Starting phenix.real_space_refine on Fri Aug 22 12:53:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t2e_25611/08_2025/7t2e_25611.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2e_25611/08_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_25611/08_2025/7t2e_25611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2e_25611/08_2025/7t2e_25611.map" model { file = "/net/cci-nas-00/data/ceres_data/7t2e_25611/08_2025/7t2e_25611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2e_25611/08_2025/7t2e_25611.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 0.85, per 1000 atoms: 0.36 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: 0.19 Conformation dependent library (CDL) restraints added in 131.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.07 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: 0.20 Time building geometry restraints manager: 0.29 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: 0.00 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.600 Find NCS groups from input model: 0.020 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:5.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.080 ------------------------------------------------------------------------------- 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= 0.128 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (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 ARG 0.001 0.000 ARG A 155 TYR 0.009 0.001 TYR A 108 PHE 0.012 0.002 PHE B 120 TRP 0.005 0.001 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2450) covalent geometry : angle 0.53950 ( 3342) hydrogen bonds : bond 0.14774 ( 78) hydrogen bonds : angle 5.69209 ( 204) *********************** 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 : 0.055 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.5112 time to fit residues: 19.2348 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 : 0.054 ------------------------------------------------------------------------------- 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 27 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.111544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.089882 restraints weight = 2954.747| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.14 r_work: 0.2912 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.0518 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= 0.133 Angle : 0.509 4.238 3342 Z= 0.268 Chirality : 0.046 0.147 364 Planarity : 0.004 0.029 434 Dihedral : 5.391 45.178 339 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 21.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.47), residues: 308 helix: 2.39 (1.10), residues: 28 sheet: -0.05 (0.40), residues: 158 loop : 0.51 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 148 TYR 0.007 0.001 TYR A 108 PHE 0.013 0.002 PHE A 120 TRP 0.007 0.001 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 2450) covalent geometry : angle 0.50900 ( 3342) hydrogen bonds : bond 0.03630 ( 78) hydrogen bonds : angle 5.11492 ( 204) *********************** 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 55 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.053 Fit side-chains REVERT: A 31 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8264 (mm) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 0.3519 time to fit residues: 18.3485 Evaluate side-chains 49 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.054 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.3253 r_free = 0.3253 target = 0.110656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.088976 restraints weight = 2994.965| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.15 r_work: 0.2845 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2450 Z= 0.157 Angle : 0.533 4.266 3342 Z= 0.280 Chirality : 0.047 0.150 364 Planarity : 0.004 0.031 434 Dihedral : 4.409 17.051 334 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.36 % Allowed : 21.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.47), residues: 308 helix: 2.22 (1.06), residues: 28 sheet: -0.10 (0.40), residues: 158 loop : 0.47 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.007 0.001 TYR A 108 PHE 0.015 0.003 PHE A 120 TRP 0.008 0.001 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 2450) covalent geometry : angle 0.53329 ( 3342) hydrogen bonds : bond 0.03808 ( 78) hydrogen bonds : angle 5.12817 ( 204) *********************** 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 51 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.077 Fit side-chains REVERT: A 31 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8336 (mm) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.7333 time to fit residues: 35.8427 Evaluate side-chains 50 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.114 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain A residue 109 LYS 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 24 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3274 r_free = 0.3274 target = 0.112218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.090502 restraints weight = 2963.243| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.15 r_work: 0.2879 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2450 Z= 0.108 Angle : 0.478 4.166 3342 Z= 0.250 Chirality : 0.045 0.142 364 Planarity : 0.003 0.027 434 Dihedral : 4.081 15.501 334 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.15 % Allowed : 21.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.47), residues: 308 helix: 2.33 (1.03), residues: 28 sheet: -0.07 (0.40), residues: 158 loop : 0.58 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.007 0.001 TYR A 108 PHE 0.011 0.002 PHE A 120 TRP 0.006 0.001 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 2450) covalent geometry : angle 0.47758 ( 3342) hydrogen bonds : bond 0.03144 ( 78) hydrogen bonds : angle 4.93058 ( 204) *********************** 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 55 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.111 Fit side-chains REVERT: A 31 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8327 (mm) outliers start: 8 outliers final: 7 residues processed: 50 average time/residue: 0.5949 time to fit residues: 30.3592 Evaluate side-chains 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.139 ------------------------------------------------------------------------------- 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 66 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 4 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.110135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.088600 restraints weight = 2951.942| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.13 r_work: 0.2894 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.004 0.022 2450 Z= 0.171 Angle : 0.541 4.339 3342 Z= 0.284 Chirality : 0.047 0.151 364 Planarity : 0.004 0.031 434 Dihedral : 4.400 17.359 334 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.15 % Allowed : 21.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.47), residues: 308 helix: 2.11 (1.04), residues: 28 sheet: -0.10 (0.40), residues: 158 loop : 0.48 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.007 0.001 TYR A 108 PHE 0.015 0.003 PHE A 120 TRP 0.009 0.001 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 2450) covalent geometry : angle 0.54058 ( 3342) hydrogen bonds : bond 0.03823 ( 78) hydrogen bonds : angle 5.12787 ( 204) *********************** 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 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.097 Fit side-chains REVERT: A 31 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8334 (mm) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.6425 time to fit residues: 27.5125 Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.059 ------------------------------------------------------------------------------- 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 66 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.109947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.088484 restraints weight = 2962.633| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.13 r_work: 0.2891 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0950 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= 0.175 Angle : 0.544 4.469 3342 Z= 0.285 Chirality : 0.047 0.150 364 Planarity : 0.004 0.033 434 Dihedral : 4.432 17.558 334 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.15 % Allowed : 21.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.47), residues: 308 helix: 2.04 (1.04), residues: 28 sheet: -0.14 (0.40), residues: 158 loop : 0.45 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.007 0.001 TYR A 108 PHE 0.015 0.003 PHE A 120 TRP 0.009 0.001 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 2450) covalent geometry : angle 0.54352 ( 3342) hydrogen bonds : bond 0.03860 ( 78) hydrogen bonds : angle 5.14789 ( 204) *********************** 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 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.099 Fit side-chains REVERT: A 31 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8350 (mm) outliers start: 8 outliers final: 6 residues processed: 42 average time/residue: 0.6260 time to fit residues: 26.8341 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 : 0.070 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.111377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.089861 restraints weight = 2967.704| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.14 r_work: 0.2857 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0918 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= 0.119 Angle : 0.487 4.204 3342 Z= 0.255 Chirality : 0.045 0.144 364 Planarity : 0.003 0.030 434 Dihedral : 4.136 16.094 334 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.15 % Allowed : 21.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.47), residues: 308 helix: 2.21 (1.02), residues: 28 sheet: -0.10 (0.40), residues: 158 loop : 0.55 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.007 0.001 TYR A 108 PHE 0.012 0.002 PHE A 120 TRP 0.006 0.001 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2450) covalent geometry : angle 0.48739 ( 3342) hydrogen bonds : bond 0.03246 ( 78) hydrogen bonds : angle 4.98068 ( 204) *********************** 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 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.072 Fit side-chains REVERT: A 31 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8350 (mm) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 0.6396 time to fit residues: 26.7350 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 : 0.100 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.111009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.089486 restraints weight = 2985.036| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.14 r_work: 0.2905 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2450 Z= 0.131 Angle : 0.497 4.215 3342 Z= 0.261 Chirality : 0.046 0.146 364 Planarity : 0.003 0.030 434 Dihedral : 4.184 16.602 334 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 21.65 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.47), residues: 308 helix: 2.24 (1.03), residues: 28 sheet: -0.12 (0.40), residues: 158 loop : 0.53 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 155 TYR 0.007 0.001 TYR A 108 PHE 0.013 0.002 PHE A 120 TRP 0.007 0.001 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 2450) covalent geometry : angle 0.49722 ( 3342) hydrogen bonds : bond 0.03373 ( 78) hydrogen bonds : angle 4.99714 ( 204) *********************** 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 : 0.088 Fit side-chains REVERT: A 31 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8335 (mm) outliers start: 7 outliers final: 6 residues processed: 41 average time/residue: 0.6094 time to fit residues: 25.4827 Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.096 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.112314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.090677 restraints weight = 3034.906| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.17 r_work: 0.2922 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2450 Z= 0.102 Angle : 0.465 4.130 3342 Z= 0.243 Chirality : 0.045 0.142 364 Planarity : 0.003 0.028 434 Dihedral : 3.958 15.073 334 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.15 % Allowed : 21.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.47), residues: 308 helix: 2.42 (1.02), residues: 28 sheet: -0.10 (0.40), residues: 158 loop : 0.64 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 155 TYR 0.007 0.001 TYR A 108 PHE 0.010 0.002 PHE B 120 TRP 0.005 0.001 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 2450) covalent geometry : angle 0.46491 ( 3342) hydrogen bonds : bond 0.02990 ( 78) hydrogen bonds : angle 4.85193 ( 204) *********************** 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 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.115 Fit side-chains REVERT: A 31 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8328 (mm) REVERT: A 104 ASP cc_start: 0.7586 (m-30) cc_final: 0.7224 (m-30) outliers start: 8 outliers final: 5 residues processed: 44 average time/residue: 0.6190 time to fit residues: 27.7917 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 : 0.091 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.109694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.088246 restraints weight = 3016.076| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.15 r_work: 0.2885 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2450 Z= 0.192 Angle : 0.562 4.755 3342 Z= 0.294 Chirality : 0.048 0.151 364 Planarity : 0.004 0.032 434 Dihedral : 4.455 17.673 334 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.36 % Allowed : 22.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.47), residues: 308 helix: 2.08 (1.03), residues: 28 sheet: -0.17 (0.40), residues: 158 loop : 0.40 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 155 TYR 0.008 0.001 TYR A 108 PHE 0.017 0.003 PHE A 120 TRP 0.010 0.002 TRP B 18 Details of bonding type rmsd covalent geometry : bond 0.00485 ( 2450) covalent geometry : angle 0.56196 ( 3342) hydrogen bonds : bond 0.03967 ( 78) hydrogen bonds : angle 5.16995 ( 204) ********************** 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 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.097 Fit side-chains REVERT: A 31 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8361 (mm) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.7319 time to fit residues: 29.8064 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 : 0.116 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.0870 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.112684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.091108 restraints weight = 3005.185| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.16 r_work: 0.2876 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0993 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= 0.091 Angle : 0.459 4.049 3342 Z= 0.239 Chirality : 0.044 0.142 364 Planarity : 0.003 0.029 434 Dihedral : 3.898 14.542 334 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.36 % Allowed : 22.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.47), residues: 308 helix: 2.47 (1.02), residues: 28 sheet: -0.10 (0.40), residues: 158 loop : 0.62 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 139 TYR 0.006 0.001 TYR A 108 PHE 0.010 0.002 PHE B 82 TRP 0.004 0.001 TRP B 36 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 2450) covalent geometry : angle 0.45887 ( 3342) hydrogen bonds : bond 0.02850 ( 78) hydrogen bonds : angle 4.82775 ( 204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1182.91 seconds wall clock time: 20 minutes 54.04 seconds (1254.04 seconds total)