Starting phenix.real_space_refine on Fri Apr 5 12:41:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyx_35832/04_2024/8iyx_35832_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyx_35832/04_2024/8iyx_35832.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyx_35832/04_2024/8iyx_35832_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyx_35832/04_2024/8iyx_35832_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyx_35832/04_2024/8iyx_35832_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyx_35832/04_2024/8iyx_35832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyx_35832/04_2024/8iyx_35832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyx_35832/04_2024/8iyx_35832_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iyx_35832/04_2024/8iyx_35832_updated.pdb" } 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 Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C GLU 310": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 2.07, per 1000 atoms: 0.94 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 - 3.50 Amino acid : False - 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: 1.02 Conformation dependent library (CDL) restraints added in 359.9 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... running ksdssp... Secondary structure from input PDB file: 9 helices and 0 sheets defined 82.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'C' and resid 52 through 82 removed outlier: 3.586A pdb=" N ILE C 82 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 115 Proline residue: C 108 - end of helix Processing helix chain 'C' and resid 125 through 156 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 169 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 214 through 241 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 278 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) Processing helix chain 'C' and resid 280 through 293 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 299 through 330 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) removed outlier: 4.709A pdb=" N ASN C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N SER C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N CYS C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) Proline residue: C 324 - end of helix removed outlier: 3.641A pdb=" N LEU C 329 " --> pdb=" O VAL C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 152 hydrogen bonds defined for protein. 456 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: 0.60 Time building geometry restraints manager: 1.10 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=" 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=" C ILE C 140 " pdb=" O ILE C 140 " ideal model delta sigma weight residual 1.237 1.201 0.035 1.13e-02 7.83e+03 9.82e+00 bond pdb=" N ILE C 142 " pdb=" CA ILE C 142 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.00e+00 bond pdb=" N ILE C 143 " pdb=" CA ILE C 143 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.47e+00 ... (remaining 2255 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.70: 23 105.70 - 112.78: 1240 112.78 - 119.87: 744 119.87 - 126.95: 1028 126.95 - 134.03: 23 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=" C06 S6R C 401 " pdb=" C07 S6R C 401 " pdb=" O08 S6R C 401 " ideal model delta sigma weight residual 106.15 119.01 -12.86 3.00e+00 1.11e-01 1.84e+01 angle pdb=" C16 S6R C 401 " pdb=" C07 S6R C 401 " pdb=" O08 S6R C 401 " ideal model delta sigma weight residual 132.84 120.41 12.43 3.00e+00 1.11e-01 1.72e+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 ... (remaining 3053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 1193 22.05 - 44.11: 87 44.11 - 66.16: 19 66.16 - 88.21: 4 88.21 - 110.27: 1 Dihedral angle restraints: 1304 sinusoidal: 519 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=" C09 S6R C 401 " pdb=" C07 S6R C 401 " pdb=" O08 S6R C 401 " pdb=" C16 S6R C 401 " ideal model delta sinusoidal sigma weight residual 285.10 174.83 110.27 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 1301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.070: 362 1.070 - 2.139: 0 2.139 - 3.208: 0 3.208 - 4.278: 0 4.278 - 5.347: 1 Chirality restraints: 363 Sorted by residual: 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 -2.68 2.67 -5.35 2.00e-01 2.50e+01 7.15e+02 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 ... (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: 502 2.78 - 3.31: 2284 3.31 - 3.84: 3496 3.84 - 4.37: 3880 4.37 - 4.90: 6558 Nonbonded interactions: 16720 Sorted by model distance: nonbonded pdb=" O LEU C 192 " pdb=" N LYS C 196 " model vdw 2.252 2.520 nonbonded pdb=" OH TYR C 282 " pdb=" NH2 ARG C 286 " model vdw 2.263 2.520 nonbonded pdb=" O ALA C 99 " pdb=" ND2 ASN C 137 " model vdw 2.308 2.520 nonbonded pdb=" O ARG C 208 " pdb=" NE2 GLN C 293 " model vdw 2.348 2.520 nonbonded pdb=" OD1 ASN C 95 " pdb=" NE1 TRP C 179 " model vdw 2.353 2.520 ... (remaining 16715 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: 1.270 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: 3.500 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.510 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- 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 : 0.006 0.053 2260 Z= 0.359 Angle : 0.868 12.860 3058 Z= 0.511 Chirality : 0.285 5.347 363 Planarity : 0.004 0.031 353 Dihedral : 16.146 110.267 793 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 fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.257 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 83 average time/residue: 0.1818 time to fit residues: 17.0662 Evaluate side-chains 67 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2260 Z= 0.224 Angle : 1.065 26.499 3058 Z= 0.435 Chirality : 0.122 2.189 363 Planarity : 0.004 0.029 353 Dihedral : 13.412 109.400 306 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.90 % Allowed : 14.69 % 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: 2.02 (0.49), residues: 258 helix: 1.99 (0.32), residues: 217 sheet: None (None), residues: 0 loop : -2.35 (0.77), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 301 HIS 0.005 0.001 HIS C 206 PHE 0.016 0.001 PHE C 221 TYR 0.013 0.002 TYR C 327 ARG 0.002 0.000 ARG C 110 *********************** 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 83 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: C 207 TYR cc_start: 0.7661 (t80) cc_final: 0.7446 (t80) outliers start: 12 outliers final: 5 residues processed: 78 average time/residue: 0.1854 time to fit residues: 16.2776 Evaluate side-chains 67 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 156 ILE Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 6 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 11 optimal weight: 0.0980 chunk 15 optimal weight: 0.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3107 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= 0.198 Angle : 1.035 25.975 3058 Z= 0.417 Chirality : 0.120 2.154 363 Planarity : 0.003 0.033 353 Dihedral : 11.790 99.464 298 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.63 % Allowed : 18.78 % Favored : 79.59 % 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: 2.63 (0.49), residues: 258 helix: 2.45 (0.32), residues: 216 sheet: None (None), residues: 0 loop : -2.29 (0.81), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 120 HIS 0.001 0.001 HIS C 206 PHE 0.011 0.001 PHE C 205 TYR 0.009 0.001 TYR C 77 ARG 0.004 0.000 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 68 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.229 Fit side-chains REVERT: C 195 LYS cc_start: 0.4281 (mmtt) cc_final: 0.3739 (mptt) REVERT: C 286 ARG cc_start: 0.8618 (tpp80) cc_final: 0.7800 (tpp80) outliers start: 4 outliers final: 3 residues processed: 66 average time/residue: 0.1421 time to fit residues: 10.9223 Evaluate side-chains 60 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 343 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2260 Z= 0.203 Angle : 1.029 25.412 3058 Z= 0.408 Chirality : 0.119 2.141 363 Planarity : 0.003 0.034 353 Dihedral : 11.126 89.113 298 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.27 % Allowed : 19.59 % 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: 2.98 (0.50), residues: 258 helix: 2.68 (0.32), residues: 218 sheet: None (None), residues: 0 loop : -2.38 (0.84), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.005 0.001 HIS C 206 PHE 0.012 0.001 PHE C 205 TYR 0.008 0.001 TYR C 238 ARG 0.003 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 fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: C 236 LEU cc_start: 0.9117 (mp) cc_final: 0.8887 (mp) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.1538 time to fit residues: 11.2902 Evaluate side-chains 62 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.269 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain C residue 308 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3828 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= 0.200 Angle : 1.011 25.099 3058 Z= 0.401 Chirality : 0.119 2.146 363 Planarity : 0.003 0.035 353 Dihedral : 10.478 73.998 298 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.67 % Allowed : 20.41 % Favored : 75.92 % 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: 3.13 (0.51), residues: 258 helix: 2.84 (0.33), residues: 216 sheet: None (None), residues: 0 loop : -2.44 (0.81), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 120 HIS 0.004 0.001 HIS C 206 PHE 0.008 0.001 PHE C 134 TYR 0.010 0.001 TYR C 139 ARG 0.002 0.000 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 69 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.271 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 64 average time/residue: 0.1666 time to fit residues: 12.2836 Evaluate side-chains 62 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 202 THR Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 11 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2260 Z= 0.198 Angle : 1.063 24.869 3058 Z= 0.421 Chirality : 0.119 2.144 363 Planarity : 0.003 0.036 353 Dihedral : 9.953 71.084 298 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.27 % Allowed : 21.22 % 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: 3.04 (0.51), residues: 258 helix: 2.82 (0.33), residues: 216 sheet: None (None), residues: 0 loop : -2.72 (0.78), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 301 HIS 0.001 0.001 HIS C 114 PHE 0.008 0.001 PHE C 205 TYR 0.014 0.001 TYR C 238 ARG 0.002 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 64 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 195 LYS cc_start: 0.4049 (mptt) cc_final: 0.3605 (mptt) outliers start: 8 outliers final: 7 residues processed: 60 average time/residue: 0.1675 time to fit residues: 11.6553 Evaluate side-chains 61 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 308 THR Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 341 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 4 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2260 Z= 0.174 Angle : 1.018 24.652 3058 Z= 0.403 Chirality : 0.119 2.145 363 Planarity : 0.003 0.036 353 Dihedral : 9.439 72.586 298 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.04 % Allowed : 24.90 % Favored : 73.06 % 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: 3.15 (0.51), residues: 258 helix: 2.90 (0.33), residues: 216 sheet: None (None), residues: 0 loop : -2.75 (0.77), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 301 HIS 0.001 0.000 HIS C 206 PHE 0.007 0.001 PHE C 134 TYR 0.008 0.001 TYR C 238 ARG 0.002 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 61 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: C 195 LYS cc_start: 0.3928 (mptt) cc_final: 0.3467 (mptt) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.1559 time to fit residues: 10.8698 Evaluate side-chains 56 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 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 339 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 chunk 18 optimal weight: 0.0470 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 11 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4451 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= 0.172 Angle : 1.053 24.487 3058 Z= 0.417 Chirality : 0.119 2.144 363 Planarity : 0.003 0.037 353 Dihedral : 9.208 73.632 298 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.04 % Allowed : 25.31 % Favored : 72.65 % 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: 3.10 (0.52), residues: 258 helix: 2.93 (0.34), residues: 214 sheet: None (None), residues: 0 loop : -2.86 (0.74), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 301 HIS 0.001 0.000 HIS C 206 PHE 0.007 0.001 PHE C 134 TYR 0.020 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 fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: C 195 LYS cc_start: 0.3930 (mptt) cc_final: 0.3015 (tppt) outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 0.1672 time to fit residues: 11.6221 Evaluate side-chains 59 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4528 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= 0.223 Angle : 1.087 24.511 3058 Z= 0.427 Chirality : 0.119 2.139 363 Planarity : 0.003 0.035 353 Dihedral : 8.995 72.200 298 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.45 % Allowed : 24.49 % Favored : 73.06 % 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: 2.92 (0.51), residues: 258 helix: 2.77 (0.33), residues: 215 sheet: None (None), residues: 0 loop : -2.87 (0.75), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 301 HIS 0.002 0.001 HIS C 114 PHE 0.009 0.001 PHE C 231 TYR 0.011 0.001 TYR C 238 ARG 0.001 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 59 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: C 170 GLN cc_start: 0.7380 (mm-40) cc_final: 0.7116 (mt0) REVERT: C 195 LYS cc_start: 0.4145 (mptt) cc_final: 0.3279 (tppt) outliers start: 6 outliers final: 4 residues processed: 57 average time/residue: 0.1556 time to fit residues: 10.3505 Evaluate side-chains 55 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 18 optimal weight: 0.0050 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4657 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= 0.185 Angle : 1.045 24.331 3058 Z= 0.410 Chirality : 0.119 2.146 363 Planarity : 0.003 0.036 353 Dihedral : 8.887 72.618 298 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.63 % Allowed : 24.90 % 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: 2.91 (0.52), residues: 258 helix: 2.74 (0.33), residues: 218 sheet: None (None), residues: 0 loop : -3.17 (0.79), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 301 HIS 0.001 0.000 HIS C 83 PHE 0.006 0.001 PHE C 134 TYR 0.010 0.001 TYR C 238 ARG 0.002 0.000 ARG C 286 ********************** 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 57 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 170 GLN cc_start: 0.7276 (mm-40) cc_final: 0.7031 (mt0) REVERT: C 195 LYS cc_start: 0.4161 (mptt) cc_final: 0.3306 (tppt) outliers start: 4 outliers final: 4 residues processed: 56 average time/residue: 0.1690 time to fit residues: 11.0390 Evaluate side-chains 57 residues out of total 245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 17 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4028 r_free = 0.4028 target = 0.156820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123016 restraints weight = 3602.735| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.77 r_work: 0.3374 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4761 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= 0.201 Angle : 1.069 24.282 3058 Z= 0.417 Chirality : 0.119 2.144 363 Planarity : 0.003 0.036 353 Dihedral : 8.832 71.414 298 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.63 % Allowed : 25.31 % Favored : 73.06 % 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 (0.52), residues: 258 helix: 2.74 (0.33), residues: 219 sheet: None (None), residues: 0 loop : -3.02 (0.80), residues: 39 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 301 HIS 0.001 0.000 HIS C 114 PHE 0.007 0.001 PHE C 134 TYR 0.010 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: 999.72 seconds wall clock time: 18 minutes 37.29 seconds (1117.29 seconds total)