Starting phenix.real_space_refine on Wed Mar 5 14:42:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh0_40027/03_2025/8gh0_40027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh0_40027/03_2025/8gh0_40027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gh0_40027/03_2025/8gh0_40027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh0_40027/03_2025/8gh0_40027.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh0_40027/03_2025/8gh0_40027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh0_40027/03_2025/8gh0_40027.cif" } resolution = 4.0 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= 0.000 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 1287 2.51 5 N 326 2.21 5 O 332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1954 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1939 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 420 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 153 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.32, per 1000 atoms: 1.19 Number of scatterers: 1954 At special positions: 0 Unit cell: (55.5328, 85.0346, 65.0775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 332 8.00 N 326 7.00 C 1287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.04 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 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: 0.59 Conformation dependent library (CDL) restraints added in 278.3 milliseconds 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 87.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'R' and resid 37 through 61 removed outlier: 3.699A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 4.021A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix removed outlier: 3.588A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.637A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.728A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.905A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE R 154 " --> pdb=" O ALA R 150 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL R 160 " --> pdb=" O MET R 156 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 181 through 186 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.693A pdb=" N ALA R 200 " --> pdb=" O ASN R 196 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.992A pdb=" N PHE R 217 " --> pdb=" O VAL R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 299 removed outlier: 4.225A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.515A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 161 hydrogen bonds defined for protein. 480 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: 0.38 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 596 1.34 - 1.46: 518 1.46 - 1.58: 878 1.58 - 1.71: 0 1.71 - 1.83: 12 Bond restraints: 2004 Sorted by residual: bond pdb=" CA HIS R 296 " pdb=" C HIS R 296 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.27e-02 6.20e+03 9.02e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.452 -0.055 2.00e-02 2.50e+03 7.54e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.443 -0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.570 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C HIS R 296 " pdb=" N VAL R 297 " ideal model delta sigma weight residual 1.335 1.306 0.028 1.26e-02 6.30e+03 5.07e+00 ... (remaining 1999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 2562 1.10 - 2.20: 151 2.20 - 3.30: 32 3.30 - 4.40: 6 4.40 - 5.50: 8 Bond angle restraints: 2759 Sorted by residual: angle pdb=" N THR R 189 " pdb=" CA THR R 189 " pdb=" C THR R 189 " ideal model delta sigma weight residual 111.28 113.69 -2.41 1.09e+00 8.42e-01 4.89e+00 angle pdb=" CA CYS R 191 " pdb=" CB CYS R 191 " pdb=" SG CYS R 191 " ideal model delta sigma weight residual 114.40 119.24 -4.84 2.30e+00 1.89e-01 4.43e+00 angle pdb=" N ASN R 322 " pdb=" CA ASN R 322 " pdb=" C ASN R 322 " ideal model delta sigma weight residual 112.75 115.56 -2.81 1.36e+00 5.41e-01 4.28e+00 angle pdb=" CA TRP R 109 " pdb=" CB TRP R 109 " pdb=" CG TRP R 109 " ideal model delta sigma weight residual 113.60 117.46 -3.86 1.90e+00 2.77e-01 4.12e+00 angle pdb=" C VAL R 295 " pdb=" N HIS R 296 " pdb=" CA HIS R 296 " ideal model delta sigma weight residual 120.44 117.81 2.63 1.30e+00 5.92e-01 4.10e+00 ... (remaining 2754 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 1043 16.85 - 33.70: 77 33.70 - 50.54: 15 50.54 - 67.39: 2 67.39 - 84.24: 2 Dihedral angle restraints: 1139 sinusoidal: 314 harmonic: 825 Sorted by residual: dihedral pdb=" CA ALA R 59 " pdb=" C ALA R 59 " pdb=" N LYS R 60 " pdb=" CA LYS R 60 " ideal model delta harmonic sigma weight residual -180.00 -161.04 -18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA TRP R 99 " pdb=" C TRP R 99 " pdb=" N THR R 100 " pdb=" CA THR R 100 " ideal model delta harmonic sigma weight residual 180.00 161.56 18.44 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU R 302 " pdb=" C LEU R 302 " pdb=" N ILE R 303 " pdb=" CA ILE R 303 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 1136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 214 0.033 - 0.067: 93 0.067 - 0.100: 18 0.100 - 0.133: 9 0.133 - 0.167: 2 Chirality restraints: 336 Sorted by residual: chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.57 -0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA HIS R 296 " pdb=" N HIS R 296 " pdb=" C HIS R 296 " pdb=" CB HIS R 296 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CB VAL R 218 " pdb=" CA VAL R 218 " pdb=" CG1 VAL R 218 " pdb=" CG2 VAL R 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.51 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 333 not shown) Planarity restraints: 346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 155 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C LEU R 155 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU R 155 " -0.010 2.00e-02 2.50e+03 pdb=" N MET R 156 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 277 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ILE R 277 " 0.026 2.00e-02 2.50e+03 pdb=" O ILE R 277 " -0.010 2.00e-02 2.50e+03 pdb=" N ILE R 278 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 99 " 0.008 2.00e-02 2.50e+03 7.37e-03 1.36e+00 pdb=" CG TRP R 99 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP R 99 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 99 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 99 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 99 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP R 99 " -0.000 2.00e-02 2.50e+03 ... (remaining 343 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 760 2.88 - 3.38: 2097 3.38 - 3.89: 3039 3.89 - 4.39: 2998 4.39 - 4.90: 5005 Nonbonded interactions: 13899 Sorted by model distance: nonbonded pdb=" OD1 ASP R 130 " pdb=" N ARG R 131 " model vdw 2.374 3.120 nonbonded pdb=" O ASN R 318 " pdb=" OD1 ASN R 318 " model vdw 2.516 3.040 nonbonded pdb=" O ILE R 58 " pdb=" NE2 GLN R 65 " model vdw 2.556 3.120 nonbonded pdb=" O HIS R 296 " pdb=" O GLN R 299 " model vdw 2.558 3.040 nonbonded pdb=" O ILE R 127 " pdb=" OD1 ASP R 130 " model vdw 2.579 3.040 ... (remaining 13894 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 group one per residue 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.750 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.004 0.055 2004 Z= 0.283 Angle : 0.651 5.502 2759 Z= 0.375 Chirality : 0.041 0.167 336 Planarity : 0.004 0.027 346 Dihedral : 13.375 84.238 595 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.51), residues: 277 helix: 1.34 (0.38), residues: 202 sheet: None (None), residues: 0 loop : -1.47 (0.62), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP R 99 HIS 0.004 0.002 HIS R 178 PHE 0.016 0.002 PHE R 108 TYR 0.007 0.001 TYR R 132 ARG 0.008 0.001 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.200 Fit side-chains REVERT: R 190 CYS cc_start: 0.6395 (t) cc_final: 0.5772 (t) REVERT: R 215 MET cc_start: 0.7844 (mmm) cc_final: 0.7401 (mtt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1024 time to fit residues: 5.2092 Evaluate side-chains 27 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.0870 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.138470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124434 restraints weight = 3996.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127064 restraints weight = 2110.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.128965 restraints weight = 1321.662| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2004 Z= 0.188 Angle : 0.566 5.264 2759 Z= 0.319 Chirality : 0.041 0.147 336 Planarity : 0.004 0.027 346 Dihedral : 5.262 18.661 307 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.32 % Allowed : 17.76 % Favored : 80.92 % 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: 2.01 (0.53), residues: 277 helix: 1.92 (0.37), residues: 212 sheet: None (None), residues: 0 loop : -0.60 (0.87), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 158 HIS 0.014 0.003 HIS R 296 PHE 0.009 0.001 PHE R 108 TYR 0.013 0.001 TYR R 141 ARG 0.002 0.001 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: R 131 ARG cc_start: 0.8636 (mmm-85) cc_final: 0.8409 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.0920 time to fit residues: 4.0697 Evaluate side-chains 31 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120806 restraints weight = 4250.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123248 restraints weight = 2295.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124753 restraints weight = 1439.557| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2004 Z= 0.257 Angle : 0.593 5.365 2759 Z= 0.335 Chirality : 0.042 0.175 336 Planarity : 0.004 0.029 346 Dihedral : 5.314 18.684 307 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 4.61 % Allowed : 15.79 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.52), residues: 277 helix: 1.83 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -0.84 (0.83), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 109 HIS 0.016 0.004 HIS R 296 PHE 0.011 0.001 PHE R 290 TYR 0.009 0.001 TYR R 141 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: R 66 THR cc_start: 0.8833 (m) cc_final: 0.8599 (m) outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.1516 time to fit residues: 5.9734 Evaluate side-chains 32 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121576 restraints weight = 4142.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124027 restraints weight = 2216.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125731 restraints weight = 1391.618| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2004 Z= 0.209 Angle : 0.552 5.373 2759 Z= 0.310 Chirality : 0.041 0.163 336 Planarity : 0.003 0.027 346 Dihedral : 5.198 18.455 307 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.61 % Allowed : 18.42 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.52), residues: 277 helix: 1.82 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.17 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 109 HIS 0.014 0.003 HIS R 296 PHE 0.010 0.001 PHE R 282 TYR 0.008 0.001 TYR R 141 ARG 0.001 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 THR cc_start: 0.8771 (m) cc_final: 0.8547 (m) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.1158 time to fit residues: 5.5009 Evaluate side-chains 37 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122663 restraints weight = 4260.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.125208 restraints weight = 2269.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126929 restraints weight = 1420.921| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2004 Z= 0.187 Angle : 0.536 5.368 2759 Z= 0.300 Chirality : 0.040 0.166 336 Planarity : 0.003 0.026 346 Dihedral : 5.065 17.944 307 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 7.24 % Allowed : 20.39 % Favored : 72.37 % 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: 1.83 (0.52), residues: 277 helix: 1.87 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.05 (0.79), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 99 HIS 0.012 0.003 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.001 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 THR cc_start: 0.8719 (m) cc_final: 0.8499 (m) REVERT: R 272 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8809 (tp) outliers start: 11 outliers final: 8 residues processed: 39 average time/residue: 0.1232 time to fit residues: 5.8636 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 13 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 11 optimal weight: 0.0050 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 269 HIS R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.125950 restraints weight = 4072.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.128518 restraints weight = 2181.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130241 restraints weight = 1365.286| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2004 Z= 0.155 Angle : 0.509 5.338 2759 Z= 0.284 Chirality : 0.040 0.169 336 Planarity : 0.003 0.025 346 Dihedral : 4.843 16.900 307 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.61 % Allowed : 24.34 % Favored : 71.05 % 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: 2.05 (0.52), residues: 277 helix: 1.97 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -0.72 (0.82), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 99 HIS 0.008 0.002 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 141 ARG 0.001 0.000 ARG R 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: R 66 THR cc_start: 0.8627 (m) cc_final: 0.8411 (m) REVERT: R 272 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8767 (tp) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.1141 time to fit residues: 5.5615 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 272 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123356 restraints weight = 4074.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126027 restraints weight = 2183.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127840 restraints weight = 1363.881| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2004 Z= 0.192 Angle : 0.519 5.410 2759 Z= 0.292 Chirality : 0.040 0.167 336 Planarity : 0.003 0.028 346 Dihedral : 4.826 16.924 307 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 6.58 % Allowed : 26.97 % Favored : 66.45 % 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: 1.93 (0.52), residues: 277 helix: 1.93 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.00 (0.80), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 109 HIS 0.011 0.003 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.204 Fit side-chains REVERT: R 66 THR cc_start: 0.8650 (m) cc_final: 0.8427 (m) outliers start: 10 outliers final: 9 residues processed: 36 average time/residue: 0.1301 time to fit residues: 5.6900 Evaluate side-chains 38 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 29 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121821 restraints weight = 4139.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124360 restraints weight = 2234.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126032 restraints weight = 1400.704| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2004 Z= 0.213 Angle : 0.560 6.595 2759 Z= 0.316 Chirality : 0.041 0.165 336 Planarity : 0.003 0.028 346 Dihedral : 4.952 18.874 307 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 7.89 % Allowed : 24.34 % Favored : 67.76 % 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: 1.87 (0.52), residues: 277 helix: 1.89 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.03 (0.77), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.012 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.224 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 38 average time/residue: 0.1157 time to fit residues: 5.3269 Evaluate side-chains 39 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 28 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 139 PHE Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121691 restraints weight = 4199.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124215 restraints weight = 2235.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.126032 restraints weight = 1398.492| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2004 Z= 0.198 Angle : 0.551 5.921 2759 Z= 0.311 Chirality : 0.041 0.165 336 Planarity : 0.003 0.029 346 Dihedral : 4.934 19.104 307 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 8.55 % Allowed : 24.34 % Favored : 67.11 % 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: 1.90 (0.52), residues: 277 helix: 1.90 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.00 (0.77), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.011 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.007 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.208 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 37 average time/residue: 0.1157 time to fit residues: 5.2447 Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 139 PHE Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.0060 chunk 11 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 296 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.137319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124030 restraints weight = 3981.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126625 restraints weight = 2143.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128350 restraints weight = 1336.017| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2004 Z= 0.161 Angle : 0.526 5.395 2759 Z= 0.298 Chirality : 0.041 0.167 336 Planarity : 0.003 0.028 346 Dihedral : 4.786 18.597 307 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 6.58 % Allowed : 27.63 % Favored : 65.79 % 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: 2.02 (0.52), residues: 277 helix: 1.98 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.92 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.010 0.003 HIS R 296 PHE 0.010 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 554 Ramachandran restraints generated. 277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.223 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 37 average time/residue: 0.1145 time to fit residues: 5.1486 Evaluate side-chains 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 99 TRP Chi-restraints excluded: chain R residue 104 PHE Chi-restraints excluded: chain R residue 120 SER Chi-restraints excluded: chain R residue 133 PHE Chi-restraints excluded: chain R residue 139 PHE Chi-restraints excluded: chain R residue 158 TRP Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3624 r_free = 0.3624 target = 0.137092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124167 restraints weight = 3994.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.126658 restraints weight = 2167.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.128453 restraints weight = 1359.718| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2004 Z= 0.187 Angle : 0.531 5.387 2759 Z= 0.298 Chirality : 0.040 0.166 336 Planarity : 0.003 0.028 346 Dihedral : 4.681 18.653 307 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 5.92 % Allowed : 28.95 % Favored : 65.13 % 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: 1.97 (0.51), residues: 277 helix: 1.95 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.97 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 109 HIS 0.004 0.001 HIS R 178 PHE 0.011 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.002 0.000 ARG R 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1053.64 seconds wall clock time: 19 minutes 11.24 seconds (1151.24 seconds total)