Starting phenix.real_space_refine on Tue Mar 3 10:49:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vu8_32126/03_2026/7vu8_32126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vu8_32126/03_2026/7vu8_32126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vu8_32126/03_2026/7vu8_32126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vu8_32126/03_2026/7vu8_32126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vu8_32126/03_2026/7vu8_32126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vu8_32126/03_2026/7vu8_32126.map" } resolution = 3.0 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= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 5 5.16 5 C 914 2.51 5 N 251 2.21 5 O 262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1433 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1411 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'ACK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.38, per 1000 atoms: 0.27 Number of scatterers: 1433 At special positions: 0 Unit cell: (66.066, 54.054, 48.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 5 16.00 P 1 15.00 O 262 8.00 N 251 7.00 C 914 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: 0.12 Conformation dependent library (CDL) restraints added in 42.4 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 1 sheets defined 50.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.681A pdb=" N LEU B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 129 through 146 removed outlier: 4.028A pdb=" N LEU B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 138 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 removed outlier: 3.683A pdb=" N LYS B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 184 through 197 removed outlier: 4.061A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 227 removed outlier: 3.817A pdb=" N HIS B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.452A pdb=" N PHE B 64 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 118 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 41 hydrogen bonds defined for protein. 123 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: 0.10 Time building geometry restraints manager: 0.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 341 1.33 - 1.45: 326 1.45 - 1.57: 796 1.57 - 1.69: 2 1.69 - 1.81: 7 Bond restraints: 1472 Sorted by residual: bond pdb=" O3P ACK B 301 " pdb=" P ACK B 301 " ideal model delta sigma weight residual 1.588 1.480 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C PHE B 76 " pdb=" O PHE B 76 " ideal model delta sigma weight residual 1.235 1.288 -0.054 1.23e-02 6.61e+03 1.89e+01 bond pdb=" C THR B 77 " pdb=" O THR B 77 " ideal model delta sigma weight residual 1.236 1.284 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" N ILE B 89 " pdb=" CA ILE B 89 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.27e+01 bond pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.22e-02 6.72e+03 1.06e+01 ... (remaining 1467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 1814 2.12 - 4.24: 161 4.24 - 6.35: 8 6.35 - 8.47: 1 8.47 - 10.59: 3 Bond angle restraints: 1987 Sorted by residual: angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" C ASP B 198 " ideal model delta sigma weight residual 114.56 107.84 6.72 1.27e+00 6.20e-01 2.80e+01 angle pdb=" N TYR B 87 " pdb=" CA TYR B 87 " pdb=" C TYR B 87 " ideal model delta sigma weight residual 113.02 107.90 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" C LEU B 98 " pdb=" CA LEU B 98 " pdb=" CB LEU B 98 " ideal model delta sigma weight residual 117.23 112.07 5.16 1.36e+00 5.41e-01 1.44e+01 angle pdb=" CA VAL B 63 " pdb=" C VAL B 63 " pdb=" O VAL B 63 " ideal model delta sigma weight residual 121.49 117.79 3.70 1.01e+00 9.80e-01 1.34e+01 angle pdb=" N ASP B 95 " pdb=" CA ASP B 95 " pdb=" C ASP B 95 " ideal model delta sigma weight residual 114.39 109.10 5.29 1.45e+00 4.76e-01 1.33e+01 ... (remaining 1982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.13: 868 31.13 - 62.26: 25 62.26 - 93.39: 0 93.39 - 124.51: 2 124.51 - 155.64: 2 Dihedral angle restraints: 897 sinusoidal: 400 harmonic: 497 Sorted by residual: dihedral pdb=" C2' ACK B 301 " pdb=" O2' ACK B 301 " pdb=" P ACK B 301 " pdb=" O1P ACK B 301 " ideal model delta sinusoidal sigma weight residual 124.10 -80.26 -155.64 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C3' ACK B 301 " pdb=" O3' ACK B 301 " pdb=" P ACK B 301 " pdb=" O1P ACK B 301 " ideal model delta sinusoidal sigma weight residual 234.46 79.07 155.39 1 3.00e+01 1.11e-03 2.04e+01 dihedral pdb=" C3' ACK B 301 " pdb=" O3' ACK B 301 " pdb=" P ACK B 301 " pdb=" O3P ACK B 301 " ideal model delta sinusoidal sigma weight residual 105.56 -157.87 -96.57 1 3.00e+01 1.11e-03 1.19e+01 ... (remaining 894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 124 0.047 - 0.094: 51 0.094 - 0.141: 18 0.141 - 0.188: 5 0.188 - 0.236: 6 Chirality restraints: 204 Sorted by residual: chirality pdb=" CA LYS B 100 " pdb=" N LYS B 100 " pdb=" C LYS B 100 " pdb=" CB LYS B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE B 104 " pdb=" CA ILE B 104 " pdb=" CG1 ILE B 104 " pdb=" CG2 ILE B 104 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE B 151 " pdb=" N ILE B 151 " pdb=" C ILE B 151 " pdb=" CB ILE B 151 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 201 not shown) Planarity restraints: 251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 70 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PRO B 70 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO B 70 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 71 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 71 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ASP B 71 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP B 71 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B 72 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 86 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C TYR B 86 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR B 86 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR B 87 " -0.011 2.00e-02 2.50e+03 ... (remaining 248 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 407 2.83 - 3.34: 1290 3.34 - 3.86: 2123 3.86 - 4.38: 2502 4.38 - 4.90: 3971 Nonbonded interactions: 10293 Sorted by model distance: nonbonded pdb=" OD1 ASP B 182 " pdb=" N GLY B 183 " model vdw 2.308 3.120 nonbonded pdb=" OE2 GLU B 138 " pdb=" NH2 ARG B 141 " model vdw 2.308 3.120 nonbonded pdb=" CD2 LEU B 98 " pdb=" N ARG B 99 " model vdw 2.426 3.540 nonbonded pdb=" NE ARG B 164 " pdb=" O GLY B 197 " model vdw 2.428 3.120 nonbonded pdb=" O ALA B 219 " pdb=" OG SER B 223 " model vdw 2.436 3.040 ... (remaining 10288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.500 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: 0.010 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 2.430 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 : 0.009 0.108 1472 Z= 0.674 Angle : 1.189 10.589 1987 Z= 0.809 Chirality : 0.069 0.236 204 Planarity : 0.005 0.033 251 Dihedral : 16.690 155.641 577 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.64 % Allowed : 7.95 % Favored : 87.42 % 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 are not related in a simple way. whole: -5.27 (0.46), residues: 168 helix: -3.13 (0.41), residues: 66 sheet: -5.55 (0.71), residues: 19 loop : -3.25 (0.52), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 68 TYR 0.007 0.001 TYR B 87 PHE 0.007 0.001 PHE B 83 TRP 0.006 0.001 TRP B 202 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00945 ( 1472) covalent geometry : angle 1.18944 ( 1987) hydrogen bonds : bond 0.32582 ( 41) hydrogen bonds : angle 10.34552 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.056 Fit side-chains REVERT: B 72 THR cc_start: 0.8244 (p) cc_final: 0.8016 (p) REVERT: B 86 TYR cc_start: 0.7722 (m-80) cc_final: 0.7138 (t80) REVERT: B 119 VAL cc_start: 0.8934 (t) cc_final: 0.8672 (m) outliers start: 7 outliers final: 0 residues processed: 49 average time/residue: 0.3959 time to fit residues: 19.7837 Evaluate side-chains 24 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.143435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.114954 restraints weight = 2404.209| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.76 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1472 Z= 0.130 Angle : 0.589 5.261 1987 Z= 0.300 Chirality : 0.046 0.129 204 Planarity : 0.004 0.023 251 Dihedral : 17.904 139.387 220 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 7.28 % Allowed : 18.54 % Favored : 74.17 % 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 are not related in a simple way. whole: -3.18 (0.58), residues: 168 helix: -0.85 (0.57), residues: 70 sheet: -4.78 (0.87), residues: 19 loop : -2.57 (0.62), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.009 0.001 TYR B 156 PHE 0.012 0.001 PHE B 92 TRP 0.010 0.001 TRP B 189 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 1472) covalent geometry : angle 0.58867 ( 1987) hydrogen bonds : bond 0.03564 ( 41) hydrogen bonds : angle 5.05502 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.054 Fit side-chains REVERT: B 86 TYR cc_start: 0.7784 (m-80) cc_final: 0.7162 (t80) outliers start: 11 outliers final: 5 residues processed: 32 average time/residue: 0.3272 time to fit residues: 10.7073 Evaluate side-chains 28 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 218 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.141552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.113053 restraints weight = 2464.532| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 4.91 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 1472 Z= 0.137 Angle : 0.577 8.699 1987 Z= 0.292 Chirality : 0.047 0.131 204 Planarity : 0.005 0.059 251 Dihedral : 17.910 146.706 220 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 9.27 % Allowed : 18.54 % Favored : 72.19 % 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 are not related in a simple way. whole: -2.34 (0.64), residues: 168 helix: 0.25 (0.64), residues: 71 sheet: -4.61 (0.90), residues: 19 loop : -2.48 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.009 0.001 TYR B 118 PHE 0.009 0.001 PHE B 76 TRP 0.007 0.001 TRP B 202 HIS 0.003 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 1472) covalent geometry : angle 0.57749 ( 1987) hydrogen bonds : bond 0.03349 ( 41) hydrogen bonds : angle 4.76137 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 24 time to evaluate : 0.056 Fit side-chains REVERT: B 86 TYR cc_start: 0.7717 (m-80) cc_final: 0.7024 (t80) outliers start: 14 outliers final: 8 residues processed: 35 average time/residue: 0.3718 time to fit residues: 13.3122 Evaluate side-chains 28 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.141393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.113582 restraints weight = 2472.817| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 4.82 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1472 Z= 0.114 Angle : 0.577 7.999 1987 Z= 0.278 Chirality : 0.045 0.131 204 Planarity : 0.004 0.049 251 Dihedral : 18.080 154.380 220 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.96 % Allowed : 23.18 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.65), residues: 168 helix: 0.50 (0.65), residues: 73 sheet: -4.32 (0.95), residues: 19 loop : -2.38 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.006 0.001 TYR B 118 PHE 0.006 0.001 PHE B 67 TRP 0.006 0.001 TRP B 202 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 1472) covalent geometry : angle 0.57651 ( 1987) hydrogen bonds : bond 0.02892 ( 41) hydrogen bonds : angle 4.28429 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.034 Fit side-chains REVERT: B 86 TYR cc_start: 0.7713 (m-80) cc_final: 0.6997 (t80) REVERT: B 130 LYS cc_start: 0.2210 (pttt) cc_final: 0.1520 (mttp) REVERT: B 150 ILE cc_start: 0.8948 (pt) cc_final: 0.8546 (pp) REVERT: B 226 SER cc_start: 0.4562 (t) cc_final: 0.4013 (m) outliers start: 9 outliers final: 7 residues processed: 30 average time/residue: 0.2702 time to fit residues: 8.3340 Evaluate side-chains 27 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 20 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 0.0870 chunk 11 optimal weight: 0.0020 chunk 3 optimal weight: 8.9990 overall best weight: 0.5970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.146111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.118455 restraints weight = 2322.856| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 4.70 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 1472 Z= 0.080 Angle : 0.516 7.116 1987 Z= 0.248 Chirality : 0.043 0.131 204 Planarity : 0.003 0.042 251 Dihedral : 18.356 163.216 220 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.64 % Allowed : 23.18 % Favored : 72.19 % 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 are not related in a simple way. whole: -2.16 (0.62), residues: 168 helix: 0.20 (0.61), residues: 80 sheet: -3.81 (1.06), residues: 19 loop : -2.71 (0.56), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.006 0.000 TYR B 156 PHE 0.003 0.001 PHE B 67 TRP 0.004 0.001 TRP B 131 HIS 0.002 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 1472) covalent geometry : angle 0.51595 ( 1987) hydrogen bonds : bond 0.02312 ( 41) hydrogen bonds : angle 4.20388 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.060 Fit side-chains REVERT: B 86 TYR cc_start: 0.7681 (m-80) cc_final: 0.6985 (t80) REVERT: B 130 LYS cc_start: 0.2259 (pttt) cc_final: 0.1592 (mttp) REVERT: B 150 ILE cc_start: 0.8902 (pt) cc_final: 0.8525 (pp) REVERT: B 162 ASP cc_start: 0.8787 (m-30) cc_final: 0.8561 (m-30) REVERT: B 226 SER cc_start: 0.4390 (t) cc_final: 0.3857 (m) outliers start: 7 outliers final: 2 residues processed: 29 average time/residue: 0.3043 time to fit residues: 9.0635 Evaluate side-chains 23 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 161 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 11 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.138700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.111629 restraints weight = 2461.703| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 4.84 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1472 Z= 0.172 Angle : 0.597 6.749 1987 Z= 0.299 Chirality : 0.047 0.133 204 Planarity : 0.006 0.068 251 Dihedral : 18.156 155.077 220 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 7.95 % Allowed : 21.85 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.64), residues: 168 helix: 0.93 (0.65), residues: 72 sheet: -4.27 (0.92), residues: 19 loop : -2.49 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.010 0.002 TYR B 118 PHE 0.010 0.001 PHE B 76 TRP 0.008 0.001 TRP B 202 HIS 0.004 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 1472) covalent geometry : angle 0.59664 ( 1987) hydrogen bonds : bond 0.03297 ( 41) hydrogen bonds : angle 4.42993 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 22 time to evaluate : 0.062 Fit side-chains REVERT: B 71 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7773 (t0) REVERT: B 75 GLN cc_start: 0.8091 (tp-100) cc_final: 0.7869 (tp-100) REVERT: B 86 TYR cc_start: 0.7640 (m-80) cc_final: 0.6900 (t80) REVERT: B 130 LYS cc_start: 0.2268 (pttt) cc_final: 0.1560 (mttp) REVERT: B 226 SER cc_start: 0.4588 (t) cc_final: 0.4038 (m) outliers start: 12 outliers final: 9 residues processed: 31 average time/residue: 0.3365 time to fit residues: 10.7286 Evaluate side-chains 30 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 2 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.143642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.116066 restraints weight = 2408.251| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.84 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1472 Z= 0.076 Angle : 0.515 5.944 1987 Z= 0.244 Chirality : 0.043 0.128 204 Planarity : 0.004 0.060 251 Dihedral : 18.475 165.265 220 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.97 % Allowed : 25.17 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.63), residues: 168 helix: 0.57 (0.62), residues: 80 sheet: -3.71 (1.01), residues: 19 loop : -2.66 (0.57), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 149 TYR 0.006 0.001 TYR B 156 PHE 0.004 0.001 PHE B 67 TRP 0.005 0.001 TRP B 202 HIS 0.002 0.001 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00169 ( 1472) covalent geometry : angle 0.51526 ( 1987) hydrogen bonds : bond 0.02192 ( 41) hydrogen bonds : angle 3.81223 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.059 Fit side-chains REVERT: B 86 TYR cc_start: 0.7585 (m-80) cc_final: 0.6840 (t80) REVERT: B 130 LYS cc_start: 0.2304 (pttt) cc_final: 0.1598 (mttp) REVERT: B 150 ILE cc_start: 0.8937 (pt) cc_final: 0.8552 (pp) REVERT: B 162 ASP cc_start: 0.8835 (m-30) cc_final: 0.8621 (m-30) REVERT: B 226 SER cc_start: 0.4395 (t) cc_final: 0.3894 (m) outliers start: 6 outliers final: 5 residues processed: 26 average time/residue: 0.3472 time to fit residues: 9.2546 Evaluate side-chains 23 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.142014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.114618 restraints weight = 2387.862| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.81 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1472 Z= 0.113 Angle : 0.538 5.429 1987 Z= 0.264 Chirality : 0.044 0.131 204 Planarity : 0.005 0.067 251 Dihedral : 18.314 161.520 220 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.96 % Allowed : 23.18 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.64), residues: 168 helix: 1.08 (0.65), residues: 74 sheet: -3.78 (0.99), residues: 19 loop : -2.61 (0.56), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.007 0.001 TYR B 118 PHE 0.007 0.001 PHE B 76 TRP 0.006 0.001 TRP B 202 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 1472) covalent geometry : angle 0.53786 ( 1987) hydrogen bonds : bond 0.02595 ( 41) hydrogen bonds : angle 3.94993 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.036 Fit side-chains REVERT: B 86 TYR cc_start: 0.7633 (m-80) cc_final: 0.6844 (t80) REVERT: B 130 LYS cc_start: 0.2307 (pttt) cc_final: 0.1600 (mttp) REVERT: B 150 ILE cc_start: 0.8946 (pt) cc_final: 0.8544 (pp) REVERT: B 162 ASP cc_start: 0.8854 (m-30) cc_final: 0.8643 (m-30) REVERT: B 209 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8123 (mp0) REVERT: B 226 SER cc_start: 0.4623 (t) cc_final: 0.4098 (m) outliers start: 9 outliers final: 7 residues processed: 28 average time/residue: 0.3035 time to fit residues: 8.7301 Evaluate side-chains 26 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.143485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115993 restraints weight = 2332.675| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 4.74 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 1472 Z= 0.092 Angle : 0.536 5.432 1987 Z= 0.266 Chirality : 0.044 0.129 204 Planarity : 0.005 0.064 251 Dihedral : 18.446 164.878 220 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.30 % Allowed : 24.50 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.63), residues: 168 helix: 0.64 (0.62), residues: 80 sheet: -3.57 (1.00), residues: 19 loop : -2.54 (0.58), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.005 0.001 TYR B 156 PHE 0.004 0.001 PHE B 67 TRP 0.004 0.001 TRP B 222 HIS 0.001 0.000 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 1472) covalent geometry : angle 0.53589 ( 1987) hydrogen bonds : bond 0.02435 ( 41) hydrogen bonds : angle 4.18452 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.057 Fit side-chains REVERT: B 86 TYR cc_start: 0.7580 (m-80) cc_final: 0.6836 (t80) REVERT: B 130 LYS cc_start: 0.2213 (pttt) cc_final: 0.1379 (mttp) REVERT: B 134 MET cc_start: 0.7381 (ptm) cc_final: 0.7135 (ptp) REVERT: B 150 ILE cc_start: 0.8947 (pt) cc_final: 0.8562 (pp) REVERT: B 162 ASP cc_start: 0.8757 (m-30) cc_final: 0.8530 (m-30) REVERT: B 209 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8095 (mp0) REVERT: B 226 SER cc_start: 0.4567 (t) cc_final: 0.4052 (m) outliers start: 8 outliers final: 8 residues processed: 23 average time/residue: 0.2911 time to fit residues: 6.9173 Evaluate side-chains 25 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 17 time to evaluate : 0.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 223 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 13 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.145817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.117954 restraints weight = 2298.216| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 4.70 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 1472 Z= 0.119 Angle : 0.549 5.207 1987 Z= 0.276 Chirality : 0.045 0.130 204 Planarity : 0.005 0.071 251 Dihedral : 18.323 161.656 220 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.64 % Allowed : 25.17 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.63), residues: 168 helix: 1.08 (0.64), residues: 74 sheet: -3.65 (0.98), residues: 19 loop : -2.51 (0.58), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.007 0.001 TYR B 118 PHE 0.007 0.001 PHE B 76 TRP 0.005 0.001 TRP B 202 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 1472) covalent geometry : angle 0.54896 ( 1987) hydrogen bonds : bond 0.02748 ( 41) hydrogen bonds : angle 4.32394 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.037 Fit side-chains REVERT: B 86 TYR cc_start: 0.7591 (m-80) cc_final: 0.6808 (t80) REVERT: B 130 LYS cc_start: 0.2226 (pttt) cc_final: 0.1412 (mttp) REVERT: B 134 MET cc_start: 0.7474 (ptm) cc_final: 0.7226 (ptp) REVERT: B 150 ILE cc_start: 0.8917 (pt) cc_final: 0.8507 (pp) REVERT: B 162 ASP cc_start: 0.8810 (m-30) cc_final: 0.8574 (m-30) REVERT: B 209 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8125 (mp0) REVERT: B 226 SER cc_start: 0.4781 (t) cc_final: 0.4274 (m) outliers start: 7 outliers final: 8 residues processed: 25 average time/residue: 0.2830 time to fit residues: 7.2578 Evaluate side-chains 27 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 19 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.0980 overall best weight: 0.4960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.145883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.118057 restraints weight = 2326.703| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.79 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 1472 Z= 0.080 Angle : 0.514 5.255 1987 Z= 0.254 Chirality : 0.043 0.126 204 Planarity : 0.005 0.068 251 Dihedral : 18.548 167.537 220 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.65 % Allowed : 27.81 % Favored : 69.54 % 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 are not related in a simple way. whole: -1.43 (0.64), residues: 168 helix: 0.85 (0.63), residues: 80 sheet: -3.32 (1.02), residues: 19 loop : -2.45 (0.59), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.006 0.001 TYR B 156 PHE 0.003 0.001 PHE B 67 TRP 0.004 0.001 TRP B 222 HIS 0.001 0.000 HIS B 203 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 1472) covalent geometry : angle 0.51400 ( 1987) hydrogen bonds : bond 0.01997 ( 41) hydrogen bonds : angle 4.01772 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 641.67 seconds wall clock time: 12 minutes 19.50 seconds (739.50 seconds total)