Starting phenix.real_space_refine on Mon Feb 10 19:51:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gh0_40027/02_2025/8gh0_40027.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gh0_40027/02_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_40027/02_2025/8gh0_40027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gh0_40027/02_2025/8gh0_40027.map" model { file = "/net/cci-nas-00/data/ceres_data/8gh0_40027/02_2025/8gh0_40027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gh0_40027/02_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-5592/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: 2.67, per 1000 atoms: 1.37 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: 0.62 Conformation dependent library (CDL) restraints added in 296.2 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: 0.15 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: 0.47 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: 1.770 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.990 ------------------------------------------------------------------------------- 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 : 0.214 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: 0.1044 time to fit residues: 5.3271 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 : 0.222 ------------------------------------------------------------------------------- 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 = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124433 restraints weight = 3996.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.127158 restraints weight = 2110.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.128894 restraints weight = 1311.168| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.221 Fit side-chains revert: symmetry clash REVERT: R 131 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.8412 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 36 average time/residue: 0.1104 time to fit residues: 4.9145 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 : 0.259 ------------------------------------------------------------------------------- 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: 2.9990 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.134960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122042 restraints weight = 4225.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124477 restraints weight = 2286.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126222 restraints weight = 1430.972| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2004 Z= 0.234 Angle : 0.575 5.373 2759 Z= 0.323 Chirality : 0.041 0.163 336 Planarity : 0.004 0.028 346 Dihedral : 5.229 18.465 307 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.78 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: 1.91 (0.53), residues: 277 helix: 1.88 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -0.77 (0.83), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 109 HIS 0.016 0.004 HIS R 296 PHE 0.010 0.001 PHE R 282 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 : 0.201 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.1247 time to fit residues: 4.8112 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 : 0.209 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.135562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122579 restraints weight = 4121.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125057 restraints weight = 2220.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126767 restraints weight = 1395.890| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2176 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= 0.201 Angle : 0.547 5.371 2759 Z= 0.307 Chirality : 0.041 0.164 336 Planarity : 0.003 0.027 346 Dihedral : 5.138 18.085 307 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.95 % Allowed : 18.42 % Favored : 77.63 % 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: 1.89 (0.52), residues: 277 helix: 1.91 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -0.95 (0.79), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 109 HIS 0.015 0.003 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 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 40 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 38 average time/residue: 0.1045 time to fit residues: 4.8558 Evaluate side-chains 36 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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: 0.7980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.135123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.122126 restraints weight = 4272.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124644 restraints weight = 2286.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126278 restraints weight = 1435.691| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2376 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= 0.213 Angle : 0.555 5.387 2759 Z= 0.310 Chirality : 0.041 0.169 336 Planarity : 0.003 0.027 346 Dihedral : 5.106 17.835 307 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 7.89 % Allowed : 19.08 % Favored : 73.03 % 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: 1.79 (0.52), residues: 277 helix: 1.86 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -1.11 (0.78), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 99 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 0.001 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 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 31 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 66 THR cc_start: 0.8805 (m) cc_final: 0.8600 (m) REVERT: R 272 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8814 (tp) outliers start: 12 outliers final: 8 residues processed: 38 average time/residue: 0.1155 time to fit residues: 5.3992 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 : 0.212 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 14 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.136747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.123581 restraints weight = 4095.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126078 restraints weight = 2180.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.127767 restraints weight = 1372.229| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2456 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= 0.179 Angle : 0.528 5.375 2759 Z= 0.295 Chirality : 0.040 0.170 336 Planarity : 0.003 0.026 346 Dihedral : 4.951 17.311 307 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 6.58 % Allowed : 23.03 % Favored : 70.39 % 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: 1.91 (0.52), residues: 277 helix: 1.89 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.92 (0.81), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 99 HIS 0.011 0.003 HIS R 296 PHE 0.012 0.001 PHE R 282 TYR 0.006 0.001 TYR R 199 ARG 0.001 0.000 ARG R 228 *********************** 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 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: R 66 THR cc_start: 0.8768 (m) cc_final: 0.8564 (m) REVERT: R 272 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8815 (tp) outliers start: 10 outliers final: 9 residues processed: 39 average time/residue: 0.1088 time to fit residues: 5.1885 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 : 0.227 ------------------------------------------------------------------------------- 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 74 SER 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 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: 0.7980 chunk 2 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.135044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.121645 restraints weight = 4179.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124239 restraints weight = 2270.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.125893 restraints weight = 1431.285| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2576 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= 0.203 Angle : 0.541 5.425 2759 Z= 0.304 Chirality : 0.041 0.170 336 Planarity : 0.003 0.026 346 Dihedral : 4.961 17.364 307 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 7.24 % Allowed : 26.32 % 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: 1.79 (0.52), residues: 277 helix: 1.85 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.13 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 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 43 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.223 Fit side-chains REVERT: R 66 THR cc_start: 0.8748 (m) cc_final: 0.8537 (m) outliers start: 11 outliers final: 10 residues processed: 39 average time/residue: 0.1140 time to fit residues: 5.4120 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 : 0.226 ------------------------------------------------------------------------------- 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 74 SER 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: 0.7980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 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 = 0.3599 r_free = 0.3599 target = 0.134863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121588 restraints weight = 4165.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.124155 restraints weight = 2290.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125816 restraints weight = 1442.331| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2737 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= 0.199 Angle : 0.563 6.890 2759 Z= 0.316 Chirality : 0.041 0.171 336 Planarity : 0.003 0.026 346 Dihedral : 4.979 19.136 307 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 5.92 % Allowed : 26.97 % 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: 1.83 (0.52), residues: 277 helix: 1.86 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -1.06 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.202 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 39 average time/residue: 0.1132 time to fit residues: 5.3704 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 : 0.240 ------------------------------------------------------------------------------- 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 74 SER 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 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: 0.7980 chunk 1 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.136199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.122657 restraints weight = 4187.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125204 restraints weight = 2295.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126965 restraints weight = 1460.505| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2004 Z= 0.185 Angle : 0.549 6.177 2759 Z= 0.309 Chirality : 0.041 0.172 336 Planarity : 0.003 0.026 346 Dihedral : 4.893 19.073 307 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 1.89 (0.52), residues: 277 helix: 1.90 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.98 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 109 HIS 0.010 0.003 HIS R 296 PHE 0.011 0.001 PHE R 282 TYR 0.006 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 44 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.243 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 40 average time/residue: 0.1170 time to fit residues: 5.7057 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 56 THR Chi-restraints excluded: chain R residue 74 SER 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 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: 0.9980 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.0170 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.135943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122496 restraints weight = 4050.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124917 restraints weight = 2214.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.126694 restraints weight = 1422.046| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2004 Z= 0.185 Angle : 0.549 5.625 2759 Z= 0.309 Chirality : 0.040 0.171 336 Planarity : 0.003 0.026 346 Dihedral : 4.825 19.028 307 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 7.24 % Allowed : 28.29 % Favored : 64.47 % 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: 1.92 (0.52), residues: 277 helix: 1.90 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -0.91 (0.78), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.009 0.003 HIS R 296 PHE 0.012 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 42 residues out of total 248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.219 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 39 average time/residue: 0.1106 time to fit residues: 5.2768 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 : 0.222 ------------------------------------------------------------------------------- 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 74 SER 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 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 18 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.0270 chunk 6 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.136572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.123082 restraints weight = 4048.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.125529 restraints weight = 2251.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127189 restraints weight = 1439.703| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2004 Z= 0.180 Angle : 0.540 5.386 2759 Z= 0.303 Chirality : 0.040 0.171 336 Planarity : 0.003 0.026 346 Dihedral : 4.747 18.759 307 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 7.89 % Allowed : 28.29 % Favored : 63.82 % 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 (0.52), residues: 277 helix: 1.94 (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 0.015 0.002 TRP R 109 HIS 0.009 0.002 HIS R 296 PHE 0.012 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: 1005.56 seconds wall clock time: 18 minutes 57.43 seconds (1137.43 seconds total)