Starting phenix.real_space_refine on Wed Mar 5 14:17:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vu8_32126/03_2025/7vu8_32126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vu8_32126/03_2025/7vu8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vu8_32126/03_2025/7vu8_32126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vu8_32126/03_2025/7vu8_32126.map" model { file = "/net/cci-nas-00/data/ceres_data/7vu8_32126/03_2025/7vu8_32126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vu8_32126/03_2025/7vu8_32126.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 1.99, per 1000 atoms: 1.39 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: 0.40 Conformation dependent library (CDL) restraints added in 168.8 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: 0.15 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: 0.29 Time building geometry restraints manager: 0.47 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.930 Find NCS groups from input model: 0.010 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:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.040 ------------------------------------------------------------------------------- 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= 0.636 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP B 202 HIS 0.003 0.001 HIS B 165 PHE 0.007 0.001 PHE B 83 TYR 0.007 0.001 TYR B 87 ARG 0.003 0.001 ARG B 68 *********************** 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 : 0.175 Fit side-chains REVERT: B 72 THR cc_start: 0.8243 (p) cc_final: 0.8016 (p) REVERT: B 86 TYR cc_start: 0.7721 (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: 0.7843 time to fit residues: 39.2682 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 : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.145697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.117225 restraints weight = 2368.036| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 4.71 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3077 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= 0.161 Angle : 0.574 5.390 1987 Z= 0.290 Chirality : 0.045 0.130 204 Planarity : 0.003 0.022 251 Dihedral : 17.896 139.020 220 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.30 % Allowed : 19.21 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.59), residues: 168 helix: -0.69 (0.57), residues: 70 sheet: -4.60 (0.92), residues: 19 loop : -2.53 (0.64), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 189 HIS 0.003 0.001 HIS B 165 PHE 0.012 0.001 PHE B 92 TYR 0.011 0.001 TYR B 156 ARG 0.002 0.000 ARG B 164 *********************** 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 37 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.161 Fit side-chains REVERT: B 86 TYR cc_start: 0.7790 (m-80) cc_final: 0.7154 (t80) outliers start: 8 outliers final: 2 residues processed: 33 average time/residue: 0.7067 time to fit residues: 23.9739 Evaluate side-chains 24 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 161 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 3 optimal weight: 0.0970 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.7382 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.144722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.115814 restraints weight = 2395.254| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 4.88 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1472 Z= 0.153 Angle : 0.539 8.488 1987 Z= 0.268 Chirality : 0.046 0.129 204 Planarity : 0.004 0.058 251 Dihedral : 17.865 147.646 220 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.65), residues: 168 helix: 0.29 (0.64), residues: 72 sheet: -4.35 (0.94), residues: 19 loop : -2.37 (0.66), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 202 HIS 0.003 0.001 HIS B 177 PHE 0.008 0.001 PHE B 92 TYR 0.007 0.001 TYR B 118 ARG 0.001 0.000 ARG B 93 *********************** 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 37 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 23 time to evaluate : 0.150 Fit side-chains REVERT: B 86 TYR cc_start: 0.7703 (m-80) cc_final: 0.7062 (t80) REVERT: B 150 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8512 (pp) outliers start: 14 outliers final: 9 residues processed: 32 average time/residue: 0.8289 time to fit residues: 27.1583 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 : 0.186 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 223 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6020 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.132673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.107174 restraints weight = 2499.771| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 4.55 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1472 Z= 0.106 Angle : 0.513 7.596 1987 Z= 0.243 Chirality : 0.043 0.128 204 Planarity : 0.004 0.049 251 Dihedral : 18.114 157.867 220 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.64 % Allowed : 23.84 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.63), residues: 168 helix: 0.58 (0.65), residues: 74 sheet: -3.82 (1.05), residues: 19 loop : -2.58 (0.58), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 131 HIS 0.001 0.000 HIS B 203 PHE 0.004 0.001 PHE B 92 TYR 0.005 0.001 TYR B 156 ARG 0.007 0.000 ARG B 141 *********************** 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 28 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.173 Fit side-chains REVERT: B 86 TYR cc_start: 0.7669 (m-80) cc_final: 0.7055 (t80) REVERT: B 150 ILE cc_start: 0.8991 (pt) cc_final: 0.8650 (pp) REVERT: B 162 ASP cc_start: 0.8820 (m-30) cc_final: 0.8566 (m-30) outliers start: 7 outliers final: 4 residues processed: 26 average time/residue: 0.7432 time to fit residues: 19.9176 Evaluate side-chains 25 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 223 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 11 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.143695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.115560 restraints weight = 2387.031| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.83 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1472 Z= 0.138 Angle : 0.500 6.150 1987 Z= 0.246 Chirality : 0.044 0.131 204 Planarity : 0.004 0.044 251 Dihedral : 18.147 158.239 220 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 8.61 % Allowed : 19.87 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.65), residues: 168 helix: 1.01 (0.66), residues: 74 sheet: -3.88 (1.01), residues: 19 loop : -2.63 (0.58), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 131 HIS 0.002 0.001 HIS B 177 PHE 0.007 0.001 PHE B 76 TYR 0.006 0.001 TYR B 118 ARG 0.007 0.001 ARG B 141 *********************** 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 36 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 23 time to evaluate : 0.167 Fit side-chains REVERT: B 86 TYR cc_start: 0.7660 (m-80) cc_final: 0.6955 (t80) REVERT: B 130 LYS cc_start: 0.2364 (pttt) cc_final: 0.1810 (mttp) REVERT: B 150 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8526 (pp) REVERT: B 162 ASP cc_start: 0.8859 (m-30) cc_final: 0.8613 (m-30) outliers start: 13 outliers final: 7 residues processed: 32 average time/residue: 0.8511 time to fit residues: 27.9212 Evaluate side-chains 26 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 18 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 3 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 4 optimal weight: 0.0670 chunk 2 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.140587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.113685 restraints weight = 2434.354| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 4.76 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4393 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= 0.207 Angle : 0.561 5.830 1987 Z= 0.281 Chirality : 0.045 0.131 204 Planarity : 0.004 0.043 251 Dihedral : 18.175 157.612 220 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 9.93 % Allowed : 18.54 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.64), residues: 168 helix: 0.99 (0.65), residues: 73 sheet: -4.07 (0.95), residues: 19 loop : -2.44 (0.59), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 131 HIS 0.003 0.001 HIS B 177 PHE 0.007 0.001 PHE B 76 TYR 0.008 0.001 TYR B 118 ARG 0.005 0.001 ARG B 141 *********************** 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 35 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 0.179 Fit side-chains REVERT: B 86 TYR cc_start: 0.7675 (m-80) cc_final: 0.6965 (t80) REVERT: B 130 LYS cc_start: 0.2214 (pttt) cc_final: 0.1522 (mttp) REVERT: B 150 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8538 (pp) REVERT: B 226 SER cc_start: 0.4663 (t) cc_final: 0.4103 (m) outliers start: 15 outliers final: 10 residues processed: 31 average time/residue: 0.6139 time to fit residues: 19.6870 Evaluate side-chains 30 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 19 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 223 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.143876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.116060 restraints weight = 2506.603| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.95 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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= 0.117 Angle : 0.509 5.434 1987 Z= 0.243 Chirality : 0.043 0.135 204 Planarity : 0.004 0.040 251 Dihedral : 18.433 165.283 220 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.97 % Allowed : 23.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.63), residues: 168 helix: 0.68 (0.62), residues: 80 sheet: -3.53 (1.03), residues: 19 loop : -2.56 (0.57), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 131 HIS 0.001 0.000 HIS B 177 PHE 0.004 0.001 PHE B 67 TYR 0.005 0.001 TYR B 156 ARG 0.004 0.000 ARG B 141 *********************** 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 28 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.177 Fit side-chains REVERT: B 86 TYR cc_start: 0.7611 (m-80) cc_final: 0.6888 (t80) REVERT: B 130 LYS cc_start: 0.2136 (pttt) cc_final: 0.1339 (mttp) REVERT: B 134 MET cc_start: 0.7446 (ptm) cc_final: 0.7197 (ptp) REVERT: B 150 ILE cc_start: 0.8941 (pt) cc_final: 0.8565 (pp) REVERT: B 162 ASP cc_start: 0.8733 (m-30) cc_final: 0.8503 (m-30) REVERT: B 226 SER cc_start: 0.4334 (t) cc_final: 0.3814 (m) outliers start: 6 outliers final: 6 residues processed: 28 average time/residue: 0.6986 time to fit residues: 20.1897 Evaluate side-chains 25 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 CYS 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 12 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3826 r_free = 0.3826 target = 0.131099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.106111 restraints weight = 2530.570| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 4.65 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 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 0.018 1472 Z= 0.113 Angle : 0.495 5.416 1987 Z= 0.241 Chirality : 0.043 0.129 204 Planarity : 0.005 0.071 251 Dihedral : 18.321 163.212 220 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 : 27.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.63), residues: 168 helix: 0.83 (0.63), residues: 80 sheet: -3.33 (1.03), residues: 19 loop : -2.44 (0.57), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 202 HIS 0.001 0.001 HIS B 177 PHE 0.003 0.001 PHE B 67 TYR 0.007 0.001 TYR B 81 ARG 0.004 0.000 ARG B 141 *********************** 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 24 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.178 Fit side-chains REVERT: B 86 TYR cc_start: 0.7604 (m-80) cc_final: 0.6901 (t80) REVERT: B 130 LYS cc_start: 0.2703 (pttt) cc_final: 0.1917 (mttp) REVERT: B 134 MET cc_start: 0.7397 (ptm) cc_final: 0.7141 (ptp) REVERT: B 150 ILE cc_start: 0.8980 (pt) cc_final: 0.8604 (pp) REVERT: B 162 ASP cc_start: 0.8696 (m-30) cc_final: 0.8486 (m-30) REVERT: B 226 SER cc_start: 0.4695 (t) cc_final: 0.4147 (m) outliers start: 4 outliers final: 3 residues processed: 24 average time/residue: 0.7633 time to fit residues: 18.8785 Evaluate side-chains 23 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 199 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.143898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.116752 restraints weight = 2354.163| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 4.76 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1472 Z= 0.130 Angle : 0.494 5.375 1987 Z= 0.241 Chirality : 0.044 0.128 204 Planarity : 0.005 0.068 251 Dihedral : 18.281 162.025 220 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.65 % Allowed : 27.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.64), residues: 168 helix: 1.34 (0.65), residues: 74 sheet: -3.26 (1.04), residues: 19 loop : -2.44 (0.57), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 202 HIS 0.002 0.001 HIS B 177 PHE 0.006 0.001 PHE B 76 TYR 0.005 0.001 TYR B 118 ARG 0.004 0.000 ARG B 141 *********************** 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 24 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.177 Fit side-chains REVERT: B 86 TYR cc_start: 0.7647 (m-80) cc_final: 0.6854 (t80) REVERT: B 130 LYS cc_start: 0.2281 (pttt) cc_final: 0.1867 (mttp) REVERT: B 150 ILE cc_start: 0.8841 (pt) cc_final: 0.8407 (pp) REVERT: B 162 ASP cc_start: 0.8665 (m-30) cc_final: 0.8425 (m-30) REVERT: B 209 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8070 (mp0) REVERT: B 226 SER cc_start: 0.4486 (t) cc_final: 0.3962 (m) outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.6479 time to fit residues: 16.1321 Evaluate side-chains 23 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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 3 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.4020 r_free = 0.4020 target = 0.142683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.115014 restraints weight = 2427.824| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.86 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1472 Z= 0.153 Angle : 0.508 5.433 1987 Z= 0.250 Chirality : 0.044 0.127 204 Planarity : 0.005 0.071 251 Dihedral : 18.276 161.331 220 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.31 % Allowed : 26.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.64), residues: 168 helix: 1.27 (0.64), residues: 74 sheet: -3.30 (1.02), residues: 19 loop : -2.33 (0.61), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 202 HIS 0.002 0.001 HIS B 177 PHE 0.006 0.001 PHE B 76 TYR 0.006 0.001 TYR B 118 ARG 0.004 0.000 ARG B 141 ********************** 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: 5 poor density : 21 time to evaluate : 0.186 Fit side-chains REVERT: B 86 TYR cc_start: 0.7638 (m-80) cc_final: 0.6839 (t80) REVERT: B 130 LYS cc_start: 0.2371 (pttt) cc_final: 0.1797 (mttp) REVERT: B 150 ILE cc_start: 0.8877 (pt) cc_final: 0.8458 (pp) REVERT: B 162 ASP cc_start: 0.8647 (m-30) cc_final: 0.8402 (m-30) REVERT: B 209 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8075 (mp0) REVERT: B 226 SER cc_start: 0.4597 (t) cc_final: 0.4094 (m) outliers start: 5 outliers final: 4 residues processed: 26 average time/residue: 0.7766 time to fit residues: 20.8859 Evaluate side-chains 23 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 19 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 4 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.141808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114320 restraints weight = 2399.629| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 4.82 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1472 Z= 0.193 Angle : 0.554 5.816 1987 Z= 0.276 Chirality : 0.045 0.131 204 Planarity : 0.005 0.069 251 Dihedral : 18.304 161.142 220 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.97 % Allowed : 27.81 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.64), residues: 168 helix: 1.23 (0.63), residues: 74 sheet: -3.39 (1.00), residues: 19 loop : -2.34 (0.62), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 202 HIS 0.003 0.001 HIS B 177 PHE 0.007 0.001 PHE B 76 TYR 0.010 0.001 TYR B 126 ARG 0.004 0.000 ARG B 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1281.91 seconds wall clock time: 22 minutes 42.59 seconds (1362.59 seconds total)