Starting phenix.real_space_refine on Wed Mar 5 15:11:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iyx_35832/03_2025/8iyx_35832.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iyx_35832/03_2025/8iyx_35832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iyx_35832/03_2025/8iyx_35832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iyx_35832/03_2025/8iyx_35832.map" model { file = "/net/cci-nas-00/data/ceres_data/8iyx_35832/03_2025/8iyx_35832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iyx_35832/03_2025/8iyx_35832.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 1489 2.51 5 N 344 2.21 5 O 353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2207 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 2165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2165 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 3, 'TRANS': 262} Chain breaks: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'S6R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.02, per 1000 atoms: 1.37 Number of scatterers: 2207 At special positions: 0 Unit cell: (59.5, 72.25, 58.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 20 16.00 O 353 8.00 N 344 7.00 C 1489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 204 " distance=2.04 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: 0.71 Conformation dependent library (CDL) restraints added in 280.4 milliseconds 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'C' and resid 51 through 83 removed outlier: 3.586A pdb=" N ILE C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 116 Proline residue: C 108 - end of helix Processing helix chain 'C' and resid 124 through 157 removed outlier: 3.683A pdb=" N SER C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 156 " --> pdb=" O ARG C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 195 removed outlier: 3.883A pdb=" N TRP C 179 " --> pdb=" O CYS C 175 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 190 " --> pdb=" O PHE C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 242 removed outlier: 3.637A pdb=" N TRP C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 279 removed outlier: 3.587A pdb=" N PHE C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE C 279 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.505A pdb=" N ARG C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 287 " --> pdb=" O HIS C 283 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 317 removed outlier: 3.714A pdb=" N GLU C 303 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 310 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 311 " --> pdb=" O LYS C 307 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 315 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 331 Proline residue: C 324 - end of helix removed outlier: 3.641A pdb=" N LEU C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 343 removed outlier: 3.694A pdb=" N ARG C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 489 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: 0.56 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 304 1.31 - 1.43: 653 1.43 - 1.56: 1270 1.56 - 1.68: 1 1.68 - 1.81: 32 Bond restraints: 2260 Sorted by residual: bond pdb=" C26 S6R C 401 " pdb=" N25 S6R C 401 " ideal model delta sigma weight residual 1.347 1.462 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C02 S6R C 401 " pdb=" N18 S6R C 401 " ideal model delta sigma weight residual 1.348 1.453 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CA SER C 141 " pdb=" CB SER C 141 " ideal model delta sigma weight residual 1.528 1.476 0.053 1.56e-02 4.11e+03 1.15e+01 bond pdb=" CA SER C 149 " pdb=" CB SER C 149 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.57e-02 4.06e+03 1.09e+01 bond pdb=" C19 S6R C 401 " pdb=" C23 S6R C 401 " ideal model delta sigma weight residual 1.538 1.475 0.063 2.00e-02 2.50e+03 9.91e+00 ... (remaining 2255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 2860 1.41 - 2.83: 127 2.83 - 4.24: 44 4.24 - 5.66: 21 5.66 - 7.07: 6 Bond angle restraints: 3058 Sorted by residual: angle pdb=" C LEU C 150 " pdb=" N ASP C 151 " pdb=" CA ASP C 151 " ideal model delta sigma weight residual 120.28 113.26 7.02 1.34e+00 5.57e-01 2.74e+01 angle pdb=" CA SER C 141 " pdb=" C SER C 141 " pdb=" O SER C 141 " ideal model delta sigma weight residual 120.55 116.25 4.30 1.06e+00 8.90e-01 1.64e+01 angle pdb=" N LEU C 150 " pdb=" CA LEU C 150 " pdb=" C LEU C 150 " ideal model delta sigma weight residual 111.11 106.36 4.75 1.20e+00 6.94e-01 1.57e+01 angle pdb=" N LEU C 145 " pdb=" CA LEU C 145 " pdb=" C LEU C 145 " ideal model delta sigma weight residual 112.23 107.64 4.59 1.26e+00 6.30e-01 1.33e+01 angle pdb=" CA TYR C 139 " pdb=" C TYR C 139 " pdb=" O TYR C 139 " ideal model delta sigma weight residual 120.42 116.63 3.79 1.06e+00 8.90e-01 1.28e+01 ... (remaining 3053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.98: 1153 15.98 - 31.97: 119 31.97 - 47.95: 39 47.95 - 63.93: 16 63.93 - 79.92: 2 Dihedral angle restraints: 1329 sinusoidal: 544 harmonic: 785 Sorted by residual: dihedral pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " pdb=" SG CYS C 204 " pdb=" CB CYS C 204 " ideal model delta sinusoidal sigma weight residual -86.00 -138.93 52.93 1 1.00e+01 1.00e-02 3.81e+01 dihedral pdb=" C TYR C 139 " pdb=" N TYR C 139 " pdb=" CA TYR C 139 " pdb=" CB TYR C 139 " ideal model delta harmonic sigma weight residual -122.60 -132.66 10.06 0 2.50e+00 1.60e-01 1.62e+01 dihedral pdb=" CA ILE C 82 " pdb=" C ILE C 82 " pdb=" N HIS C 83 " pdb=" CA HIS C 83 " ideal model delta harmonic sigma weight residual 180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 1326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 324 0.069 - 0.138: 34 0.138 - 0.206: 2 0.206 - 0.275: 2 0.275 - 0.344: 1 Chirality restraints: 363 Sorted by residual: chirality pdb=" CA TYR C 139 " pdb=" N TYR C 139 " pdb=" C TYR C 139 " pdb=" CB TYR C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ILE C 140 " pdb=" N ILE C 140 " pdb=" C ILE C 140 " pdb=" CB ILE C 140 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C19 S6R C 401 " pdb=" C20 S6R C 401 " pdb=" C23 S6R C 401 " pdb=" C42 S6R C 401 " both_signs ideal model delta sigma weight residual False 2.88 2.67 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 360 not shown) Planarity restraints: 353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 146 " -0.011 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C GLY C 146 " 0.040 2.00e-02 2.50e+03 pdb=" O GLY C 146 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE C 147 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 205 " -0.012 2.00e-02 2.50e+03 1.36e-02 3.26e+00 pdb=" CG PHE C 205 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 205 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 205 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 205 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 205 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 205 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 152 " 0.009 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C ARG C 152 " -0.029 2.00e-02 2.50e+03 pdb=" O ARG C 152 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR C 153 " 0.010 2.00e-02 2.50e+03 ... (remaining 350 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 501 2.78 - 3.31: 2279 3.31 - 3.84: 3484 3.84 - 4.37: 3862 4.37 - 4.90: 6550 Nonbonded interactions: 16676 Sorted by model distance: nonbonded pdb=" O LEU C 192 " pdb=" N LYS C 196 " model vdw 2.252 3.120 nonbonded pdb=" OH TYR C 282 " pdb=" NH2 ARG C 286 " model vdw 2.263 3.120 nonbonded pdb=" O ALA C 99 " pdb=" ND2 ASN C 137 " model vdw 2.308 3.120 nonbonded pdb=" O ARG C 208 " pdb=" NE2 GLN C 293 " model vdw 2.348 3.120 nonbonded pdb=" OD1 ASN C 95 " pdb=" NE1 TRP C 179 " model vdw 2.353 3.120 ... (remaining 16671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.180 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 : 0.007 0.115 2260 Z= 0.420 Angle : 0.857 7.071 3058 Z= 0.509 Chirality : 0.050 0.344 363 Planarity : 0.004 0.031 353 Dihedral : 15.492 79.918 818 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.49 % Favored : 96.12 % Rotamer: Outliers : 4.08 % Allowed : 1.63 % Favored : 94.29 % 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: 0.98 (0.50), residues: 258 helix: 1.32 (0.34), residues: 207 sheet: None (None), residues: 0 loop : -2.10 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 228 HIS 0.002 0.001 HIS C 206 PHE 0.032 0.002 PHE C 205 TYR 0.021 0.002 TYR C 139 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.251 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 83 average time/residue: 0.1845 time to fit residues: 17.3631 Evaluate side-chains 67 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 264 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.161887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.130582 restraints weight = 3517.630| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.66 r_work: 0.3593 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2260 Z= 0.219 Angle : 0.676 7.341 3058 Z= 0.349 Chirality : 0.041 0.113 363 Planarity : 0.005 0.042 353 Dihedral : 9.256 57.069 331 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.49 % Allowed : 15.10 % Favored : 80.41 % 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: 2.20 (0.50), residues: 258 helix: 1.98 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -1.94 (0.86), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 228 HIS 0.003 0.001 HIS C 206 PHE 0.014 0.001 PHE C 221 TYR 0.014 0.002 TYR C 327 ARG 0.002 0.001 ARG C 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.279 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 3 residues processed: 76 average time/residue: 0.2044 time to fit residues: 17.6716 Evaluate side-chains 66 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 18 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.153368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119915 restraints weight = 3481.456| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.65 r_work: 0.3344 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2260 Z= 0.204 Angle : 0.640 8.918 3058 Z= 0.326 Chirality : 0.040 0.111 363 Planarity : 0.004 0.038 353 Dihedral : 7.036 47.767 323 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.04 % Allowed : 18.78 % Favored : 79.18 % 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: 2.56 (0.49), residues: 258 helix: 2.26 (0.32), residues: 222 sheet: None (None), residues: 0 loop : -2.07 (0.86), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS C 206 PHE 0.014 0.001 PHE C 221 TYR 0.011 0.001 TYR C 238 ARG 0.004 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: C 195 LYS cc_start: 0.4588 (mmtt) cc_final: 0.3910 (mptt) outliers start: 5 outliers final: 4 residues processed: 69 average time/residue: 0.1670 time to fit residues: 13.2671 Evaluate side-chains 64 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 343 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.153622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119853 restraints weight = 3464.269| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.60 r_work: 0.3339 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2260 Z= 0.204 Angle : 0.622 8.018 3058 Z= 0.313 Chirality : 0.040 0.140 363 Planarity : 0.004 0.040 353 Dihedral : 6.548 42.916 323 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.86 % Allowed : 20.00 % Favored : 77.14 % 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: 2.75 (0.50), residues: 258 helix: 2.41 (0.32), residues: 223 sheet: None (None), residues: 0 loop : -2.29 (0.88), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 120 HIS 0.003 0.001 HIS C 206 PHE 0.010 0.001 PHE C 205 TYR 0.009 0.001 TYR C 207 ARG 0.004 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.238 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 65 average time/residue: 0.1551 time to fit residues: 11.6394 Evaluate side-chains 59 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 337 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.153475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119394 restraints weight = 3553.028| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.61 r_work: 0.3340 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2260 Z= 0.198 Angle : 0.603 6.378 3058 Z= 0.306 Chirality : 0.039 0.112 363 Planarity : 0.004 0.041 353 Dihedral : 6.265 39.326 323 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.86 % Allowed : 20.82 % Favored : 76.33 % 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: 2.76 (0.50), residues: 258 helix: 2.45 (0.32), residues: 222 sheet: None (None), residues: 0 loop : -2.45 (0.84), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS C 206 PHE 0.008 0.001 PHE C 134 TYR 0.007 0.001 TYR C 139 ARG 0.003 0.001 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.251 Fit side-chains REVERT: C 173 TYR cc_start: 0.7696 (m-10) cc_final: 0.7343 (m-80) outliers start: 7 outliers final: 4 residues processed: 62 average time/residue: 0.1418 time to fit residues: 10.3970 Evaluate side-chains 59 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 343 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.120133 restraints weight = 3534.085| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.67 r_work: 0.3342 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2260 Z= 0.188 Angle : 0.644 11.901 3058 Z= 0.309 Chirality : 0.038 0.112 363 Planarity : 0.004 0.042 353 Dihedral : 6.056 37.019 323 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.04 % Allowed : 22.45 % Favored : 75.51 % 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: 2.96 (0.50), residues: 258 helix: 2.62 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.67 (0.81), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS C 206 PHE 0.010 0.001 PHE C 205 TYR 0.008 0.001 TYR C 238 ARG 0.003 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.257 Fit side-chains REVERT: C 83 HIS cc_start: 0.6881 (m90) cc_final: 0.6678 (m-70) REVERT: C 195 LYS cc_start: 0.4380 (mptt) cc_final: 0.3155 (tppt) outliers start: 5 outliers final: 4 residues processed: 57 average time/residue: 0.1527 time to fit residues: 10.2334 Evaluate side-chains 58 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 343 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.154750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119971 restraints weight = 3653.666| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.76 r_work: 0.3358 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2260 Z= 0.180 Angle : 0.607 6.878 3058 Z= 0.299 Chirality : 0.038 0.113 363 Planarity : 0.004 0.043 353 Dihedral : 6.025 35.554 323 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.45 % Allowed : 23.67 % Favored : 73.88 % 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: 2.98 (0.50), residues: 258 helix: 2.64 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.67 (0.81), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 120 HIS 0.002 0.001 HIS C 206 PHE 0.008 0.001 PHE C 205 TYR 0.020 0.001 TYR C 238 ARG 0.003 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: C 195 LYS cc_start: 0.4286 (mptt) cc_final: 0.3102 (tppt) REVERT: C 214 LYS cc_start: 0.7832 (mttt) cc_final: 0.7027 (pttm) REVERT: C 269 PHE cc_start: 0.7553 (m-10) cc_final: 0.7195 (m-10) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.1473 time to fit residues: 10.4838 Evaluate side-chains 61 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 136 MET Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 343 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.154315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119723 restraints weight = 3657.408| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.67 r_work: 0.3329 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2260 Z= 0.198 Angle : 0.627 7.037 3058 Z= 0.304 Chirality : 0.039 0.130 363 Planarity : 0.004 0.043 353 Dihedral : 5.887 33.126 323 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.45 % Allowed : 23.27 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.51), residues: 258 helix: 2.73 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.68 (0.80), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS C 83 PHE 0.009 0.001 PHE C 205 TYR 0.016 0.001 TYR C 238 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.232 Fit side-chains REVERT: C 83 HIS cc_start: 0.6868 (m90) cc_final: 0.6656 (m-70) REVERT: C 195 LYS cc_start: 0.4500 (mptt) cc_final: 0.3334 (tppt) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.1430 time to fit residues: 10.0943 Evaluate side-chains 58 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.155573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122178 restraints weight = 3674.622| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.68 r_work: 0.3339 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2260 Z= 0.200 Angle : 0.665 13.994 3058 Z= 0.315 Chirality : 0.039 0.144 363 Planarity : 0.004 0.042 353 Dihedral : 5.891 36.823 323 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.45 % Allowed : 24.08 % Favored : 73.47 % 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: 2.87 (0.51), residues: 258 helix: 2.57 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.71 (0.79), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.002 0.000 HIS C 114 PHE 0.009 0.001 PHE C 205 TYR 0.014 0.001 TYR C 238 ARG 0.002 0.000 ARG C 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.281 Fit side-chains REVERT: C 173 TYR cc_start: 0.7433 (m-10) cc_final: 0.7218 (m-10) REVERT: C 195 LYS cc_start: 0.4648 (mptt) cc_final: 0.3433 (tppt) outliers start: 6 outliers final: 5 residues processed: 59 average time/residue: 0.1518 time to fit residues: 10.5504 Evaluate side-chains 58 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 297 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.155899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122263 restraints weight = 3623.701| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.69 r_work: 0.3369 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2260 Z= 0.171 Angle : 0.603 8.082 3058 Z= 0.293 Chirality : 0.038 0.136 363 Planarity : 0.004 0.042 353 Dihedral : 5.864 39.052 323 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.45 % Allowed : 23.27 % Favored : 74.29 % 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: 2.97 (0.51), residues: 258 helix: 2.66 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -2.90 (0.76), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 120 HIS 0.004 0.001 HIS C 83 PHE 0.008 0.001 PHE C 205 TYR 0.013 0.001 TYR C 238 ARG 0.002 0.000 ARG C 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 516 Ramachandran restraints generated. 258 Oldfield, 0 Emsley, 258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.194 Fit side-chains REVERT: C 195 LYS cc_start: 0.4525 (mptt) cc_final: 0.3453 (tppt) REVERT: C 214 LYS cc_start: 0.7656 (mttt) cc_final: 0.6915 (pttm) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.1455 time to fit residues: 10.1850 Evaluate side-chains 57 residues out of total 245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 1.9990 chunk 20 optimal weight: 0.1980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110967 restraints weight = 3656.194| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.94 r_work: 0.3252 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2260 Z= 0.241 Angle : 0.694 15.145 3058 Z= 0.329 Chirality : 0.039 0.112 363 Planarity : 0.004 0.041 353 Dihedral : 5.931 38.630 323 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.63 % Allowed : 24.49 % Favored : 73.88 % 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: 2.71 (0.50), residues: 258 helix: 2.50 (0.33), residues: 222 sheet: None (None), residues: 0 loop : -3.12 (0.71), residues: 36 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 120 HIS 0.003 0.001 HIS C 114 PHE 0.012 0.001 PHE C 205 TYR 0.011 0.001 TYR C 238 ARG 0.002 0.000 ARG C 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1482.66 seconds wall clock time: 26 minutes 13.21 seconds (1573.21 seconds total)