Starting phenix.real_space_refine on Wed Nov 13 23:46:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zrt_60404/11_2024/8zrt_60404.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zrt_60404/11_2024/8zrt_60404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zrt_60404/11_2024/8zrt_60404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zrt_60404/11_2024/8zrt_60404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zrt_60404/11_2024/8zrt_60404.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zrt_60404/11_2024/8zrt_60404.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 1545 2.51 5 N 363 2.21 5 O 393 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2322 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2158 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain breaks: 3 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "L" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 164 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.15, per 1000 atoms: 0.93 Number of scatterers: 2322 At special positions: 0 Unit cell: (60.69, 71.4, 79.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 393 8.00 N 363 7.00 C 1545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 300.5 milliseconds 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 586 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 2 sheets defined 80.9% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 97 through 128 removed outlier: 3.870A pdb=" N VAL R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 164 Proline residue: R 156 - end of helix removed outlier: 3.837A pdb=" N LEU R 162 " --> pdb=" O ASN R 158 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 205 Proline residue: R 178 - end of helix removed outlier: 3.796A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 238 removed outlier: 3.698A pdb=" N LEU R 224 " --> pdb=" O VAL R 220 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A) Proline residue: R 235 - end of helix removed outlier: 3.695A pdb=" N ILE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 272 removed outlier: 3.511A pdb=" N GLN R 267 " --> pdb=" O THR R 263 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA R 272 " --> pdb=" O PHE R 268 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 301 removed outlier: 4.471A pdb=" N LEU R 284 " --> pdb=" O PHE R 280 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 319 through 349 Proline residue: R 338 - end of helix Processing helix chain 'R' and resid 356 through 388 removed outlier: 3.884A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 399 removed outlier: 3.704A pdb=" N SER R 399 " --> pdb=" O ASN R 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 18 Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 243 Processing sheet with id=AA2, first strand: chain 'R' and resid 246 through 247 181 hydrogen bonds defined for protein. 537 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: 0.62 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 693 1.34 - 1.46: 576 1.46 - 1.58: 1080 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 2376 Sorted by residual: bond pdb=" CB ASP R 147 " pdb=" CG ASP R 147 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.82e+00 bond pdb=" C ILE R 222 " pdb=" O ILE R 222 " ideal model delta sigma weight residual 1.233 1.243 -0.010 1.22e-02 6.72e+03 6.90e-01 bond pdb=" CA ASN R 373 " pdb=" C ASN R 373 " ideal model delta sigma weight residual 1.524 1.514 0.010 1.28e-02 6.10e+03 6.36e-01 bond pdb=" CB PRO R 93 " pdb=" CG PRO R 93 " ideal model delta sigma weight residual 1.492 1.530 -0.038 5.00e-02 4.00e+02 5.91e-01 bond pdb=" C VAL R 234 " pdb=" N PRO R 235 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.28e-02 6.10e+03 5.23e-01 ... (remaining 2371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 3149 1.70 - 3.40: 74 3.40 - 5.10: 13 5.10 - 6.80: 6 6.80 - 8.50: 3 Bond angle restraints: 3245 Sorted by residual: angle pdb=" CA PRO R 93 " pdb=" N PRO R 93 " pdb=" CD PRO R 93 " ideal model delta sigma weight residual 112.00 106.33 5.67 1.40e+00 5.10e-01 1.64e+01 angle pdb=" C VAL R 234 " pdb=" CA VAL R 234 " pdb=" CB VAL R 234 " ideal model delta sigma weight residual 113.70 110.87 2.83 9.50e-01 1.11e+00 8.87e+00 angle pdb=" C ASN R 373 " pdb=" N MET R 374 " pdb=" CA MET R 374 " ideal model delta sigma weight residual 121.58 116.12 5.46 1.95e+00 2.63e-01 7.85e+00 angle pdb=" N GLY R 92 " pdb=" CA GLY R 92 " pdb=" C GLY R 92 " ideal model delta sigma weight residual 112.34 117.90 -5.56 2.04e+00 2.40e-01 7.42e+00 angle pdb=" CB MET R 374 " pdb=" CG MET R 374 " pdb=" SD MET R 374 " ideal model delta sigma weight residual 112.70 104.75 7.95 3.00e+00 1.11e-01 7.02e+00 ... (remaining 3240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1229 17.96 - 35.92: 127 35.92 - 53.88: 39 53.88 - 71.84: 4 71.84 - 89.80: 2 Dihedral angle restraints: 1401 sinusoidal: 506 harmonic: 895 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 15 " pdb=" CB CYS L 15 " ideal model delta sinusoidal sigma weight residual -86.00 -136.24 50.24 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CA MET R 374 " pdb=" C MET R 374 " pdb=" N ALA R 375 " pdb=" CA ALA R 375 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CB GLU R 299 " pdb=" CG GLU R 299 " pdb=" CD GLU R 299 " pdb=" OE1 GLU R 299 " ideal model delta sinusoidal sigma weight residual 0.00 89.80 -89.80 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 1398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 301 0.043 - 0.086: 83 0.086 - 0.129: 14 0.129 - 0.172: 3 0.172 - 0.215: 1 Chirality restraints: 402 Sorted by residual: chirality pdb=" CB ILE R 187 " pdb=" CA ILE R 187 " pdb=" CG1 ILE R 187 " pdb=" CG2 ILE R 187 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA MET R 374 " pdb=" N MET R 374 " pdb=" C MET R 374 " pdb=" CB MET R 374 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA PRO R 338 " pdb=" N PRO R 338 " pdb=" C PRO R 338 " pdb=" CB PRO R 338 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 399 not shown) Planarity restraints: 388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 92 " 0.102 5.00e-02 4.00e+02 1.52e-01 3.71e+01 pdb=" N PRO R 93 " -0.263 5.00e-02 4.00e+02 pdb=" CA PRO R 93 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO R 93 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 372 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C ILE R 372 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 372 " -0.014 2.00e-02 2.50e+03 pdb=" N ASN R 373 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 366 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C VAL R 366 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL R 366 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU R 367 " -0.011 2.00e-02 2.50e+03 ... (remaining 385 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 421 2.76 - 3.30: 2406 3.30 - 3.83: 3994 3.83 - 4.37: 4137 4.37 - 4.90: 7507 Nonbonded interactions: 18465 Sorted by model distance: nonbonded pdb=" O PRO R 285 " pdb=" OG1 THR R 289 " model vdw 2.227 3.040 nonbonded pdb=" OD1 ASN R 134 " pdb=" ND2 ASN R 137 " model vdw 2.230 3.120 nonbonded pdb=" O SER R 376 " pdb=" OG SER R 379 " model vdw 2.236 3.040 nonbonded pdb=" O ASP R 154 " pdb=" ND2 ASN R 158 " model vdw 2.312 3.120 nonbonded pdb=" O GLU R 165 " pdb=" NE2 HIS L 16 " model vdw 2.315 3.120 ... (remaining 18460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.100 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 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 : 0.003 0.038 2376 Z= 0.221 Angle : 0.693 8.503 3245 Z= 0.363 Chirality : 0.041 0.215 402 Planarity : 0.009 0.152 388 Dihedral : 16.251 89.801 803 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.81 % Allowed : 33.06 % Favored : 66.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.48), residues: 293 helix: 0.89 (0.34), residues: 228 sheet: None (None), residues: 0 loop : -3.20 (0.64), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 276 HIS 0.002 0.001 HIS R 258 PHE 0.013 0.001 PHE R 100 TYR 0.008 0.001 TYR R 269 ARG 0.004 0.001 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.303 Fit side-chains REVERT: R 236 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7026 (tp30) REVERT: R 266 MET cc_start: 0.7246 (tpp) cc_final: 0.6853 (mmm) outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 0.0973 time to fit residues: 6.8892 Evaluate side-chains 53 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN R 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2376 Z= 0.215 Angle : 0.645 11.242 3245 Z= 0.324 Chirality : 0.041 0.208 402 Planarity : 0.007 0.121 388 Dihedral : 4.950 48.014 319 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 5.24 % Allowed : 27.02 % Favored : 67.74 % 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: 0.60 (0.48), residues: 293 helix: 1.36 (0.33), residues: 229 sheet: None (None), residues: 0 loop : -3.29 (0.63), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 21 HIS 0.003 0.001 HIS L 16 PHE 0.011 0.001 PHE R 397 TYR 0.007 0.001 TYR R 269 ARG 0.003 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.272 Fit side-chains REVERT: R 236 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7104 (tp30) REVERT: R 266 MET cc_start: 0.7330 (tpp) cc_final: 0.7005 (mmm) outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.1026 time to fit residues: 8.4906 Evaluate side-chains 61 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 181 GLN ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2376 Z= 0.226 Angle : 0.632 10.570 3245 Z= 0.319 Chirality : 0.041 0.210 402 Planarity : 0.007 0.107 388 Dihedral : 5.002 48.997 319 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 9.68 % Allowed : 25.00 % Favored : 65.32 % 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: 0.73 (0.48), residues: 293 helix: 1.50 (0.33), residues: 229 sheet: None (None), residues: 0 loop : -3.41 (0.62), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 276 HIS 0.002 0.001 HIS R 258 PHE 0.013 0.001 PHE R 100 TYR 0.010 0.001 TYR R 387 ARG 0.001 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.285 Fit side-chains REVERT: R 236 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7148 (tp30) REVERT: R 266 MET cc_start: 0.7357 (tpp) cc_final: 0.7039 (mmm) outliers start: 24 outliers final: 15 residues processed: 76 average time/residue: 0.0944 time to fit residues: 9.0736 Evaluate side-chains 68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 362 SER Chi-restraints excluded: chain R residue 379 SER Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain L residue 15 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2376 Z= 0.205 Angle : 0.629 10.173 3245 Z= 0.316 Chirality : 0.041 0.201 402 Planarity : 0.006 0.102 388 Dihedral : 4.961 49.258 319 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 8.87 % Allowed : 25.40 % Favored : 65.73 % 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: 0.85 (0.48), residues: 293 helix: 1.59 (0.33), residues: 229 sheet: None (None), residues: 0 loop : -3.40 (0.63), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 21 HIS 0.002 0.001 HIS L 16 PHE 0.011 0.001 PHE R 100 TYR 0.009 0.001 TYR R 387 ARG 0.001 0.000 ARG R 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.254 Fit side-chains REVERT: R 225 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7731 (mp) REVERT: R 266 MET cc_start: 0.7251 (tpp) cc_final: 0.6948 (mmm) outliers start: 22 outliers final: 17 residues processed: 76 average time/residue: 0.0945 time to fit residues: 8.9091 Evaluate side-chains 67 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 379 SER Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain L residue 19 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 26 optimal weight: 0.0040 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2376 Z= 0.208 Angle : 0.647 10.408 3245 Z= 0.326 Chirality : 0.041 0.202 402 Planarity : 0.006 0.099 388 Dihedral : 4.975 49.749 319 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 7.66 % Allowed : 26.61 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.49), residues: 293 helix: 1.61 (0.33), residues: 229 sheet: None (None), residues: 0 loop : -3.33 (0.64), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 206 HIS 0.002 0.001 HIS L 16 PHE 0.010 0.001 PHE R 397 TYR 0.016 0.001 TYR R 387 ARG 0.001 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.258 Fit side-chains REVERT: R 225 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7703 (mp) REVERT: R 266 MET cc_start: 0.7238 (tpp) cc_final: 0.6950 (mmm) outliers start: 19 outliers final: 17 residues processed: 69 average time/residue: 0.0892 time to fit residues: 7.9494 Evaluate side-chains 68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain L residue 19 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN R 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2376 Z= 0.215 Angle : 0.687 9.807 3245 Z= 0.349 Chirality : 0.042 0.202 402 Planarity : 0.006 0.097 388 Dihedral : 5.219 51.033 319 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 10.08 % Allowed : 24.19 % Favored : 65.73 % 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: 0.82 (0.48), residues: 293 helix: 1.53 (0.33), residues: 230 sheet: None (None), residues: 0 loop : -3.32 (0.64), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 167 HIS 0.001 0.001 HIS L 16 PHE 0.015 0.001 PHE R 100 TYR 0.016 0.001 TYR R 387 ARG 0.000 0.000 ARG R 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.279 Fit side-chains REVERT: R 225 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7688 (mp) REVERT: R 266 MET cc_start: 0.7251 (tpp) cc_final: 0.6956 (mmm) outliers start: 25 outliers final: 21 residues processed: 73 average time/residue: 0.0955 time to fit residues: 8.8259 Evaluate side-chains 71 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain R residue 362 SER Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain L residue 19 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.0570 chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2376 Z= 0.203 Angle : 0.697 10.087 3245 Z= 0.348 Chirality : 0.042 0.203 402 Planarity : 0.006 0.096 388 Dihedral : 5.242 51.458 319 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 9.68 % Allowed : 24.60 % Favored : 65.73 % 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: 0.94 (0.49), residues: 293 helix: 1.58 (0.33), residues: 230 sheet: None (None), residues: 0 loop : -3.13 (0.67), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 167 HIS 0.002 0.001 HIS R 258 PHE 0.012 0.001 PHE R 100 TYR 0.015 0.001 TYR R 387 ARG 0.000 0.000 ARG R 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.290 Fit side-chains REVERT: R 225 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7655 (mp) REVERT: R 266 MET cc_start: 0.7250 (tpp) cc_final: 0.6953 (mmm) outliers start: 24 outliers final: 20 residues processed: 73 average time/residue: 0.0998 time to fit residues: 9.2517 Evaluate side-chains 72 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain R residue 362 SER Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain L residue 19 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 137 ASN ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2376 Z= 0.209 Angle : 0.696 10.008 3245 Z= 0.348 Chirality : 0.042 0.203 402 Planarity : 0.006 0.097 388 Dihedral : 5.265 52.034 319 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 8.47 % Allowed : 26.21 % Favored : 65.32 % 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: 0.91 (0.49), residues: 293 helix: 1.60 (0.33), residues: 230 sheet: -3.68 (1.09), residues: 14 loop : -2.89 (0.82), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 167 HIS 0.002 0.001 HIS R 258 PHE 0.011 0.001 PHE R 240 TYR 0.018 0.001 TYR R 387 ARG 0.001 0.000 ARG R 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.255 Fit side-chains REVERT: R 225 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7652 (mp) REVERT: R 266 MET cc_start: 0.7253 (tpp) cc_final: 0.6958 (mmm) outliers start: 21 outliers final: 18 residues processed: 69 average time/residue: 0.0927 time to fit residues: 8.2733 Evaluate side-chains 67 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain L residue 19 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN R 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2376 Z= 0.212 Angle : 0.696 9.770 3245 Z= 0.348 Chirality : 0.043 0.201 402 Planarity : 0.006 0.095 388 Dihedral : 5.307 52.771 319 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 8.06 % Allowed : 27.42 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.50), residues: 293 helix: 1.67 (0.33), residues: 230 sheet: -4.26 (0.89), residues: 12 loop : -2.74 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 167 HIS 0.002 0.001 HIS R 340 PHE 0.012 0.001 PHE R 100 TYR 0.020 0.001 TYR R 387 ARG 0.002 0.000 ARG R 199 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.298 Fit side-chains REVERT: R 225 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7662 (mp) REVERT: R 266 MET cc_start: 0.7262 (tpp) cc_final: 0.6989 (mmm) outliers start: 20 outliers final: 19 residues processed: 63 average time/residue: 0.0918 time to fit residues: 7.4448 Evaluate side-chains 66 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 330 LEU Chi-restraints excluded: chain R residue 362 SER Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.0270 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2376 Z= 0.209 Angle : 0.698 10.000 3245 Z= 0.347 Chirality : 0.042 0.201 402 Planarity : 0.006 0.094 388 Dihedral : 5.283 53.023 319 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 7.66 % Allowed : 27.82 % Favored : 64.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.50), residues: 293 helix: 1.68 (0.33), residues: 230 sheet: -4.13 (0.96), residues: 12 loop : -2.66 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 167 HIS 0.002 0.001 HIS R 258 PHE 0.012 0.001 PHE R 100 TYR 0.020 0.001 TYR R 387 ARG 0.001 0.000 ARG R 199 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.280 Fit side-chains REVERT: R 225 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7642 (mp) REVERT: R 266 MET cc_start: 0.7259 (tpp) cc_final: 0.6990 (mmm) outliers start: 19 outliers final: 18 residues processed: 63 average time/residue: 0.0864 time to fit residues: 7.0926 Evaluate side-chains 68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ILE Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 225 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 256 LEU Chi-restraints excluded: chain R residue 258 HIS Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 362 SER Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN ** R 378 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 = 0.4376 r_free = 0.4376 target = 0.205443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.193647 restraints weight = 2962.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.197500 restraints weight = 1523.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.199989 restraints weight = 878.712| |-----------------------------------------------------------------------------| r_work (final): 0.4331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2376 Z= 0.198 Angle : 0.681 9.624 3245 Z= 0.338 Chirality : 0.042 0.198 402 Planarity : 0.006 0.093 388 Dihedral : 5.253 53.563 319 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 7.66 % Allowed : 27.42 % Favored : 64.92 % 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: 1.11 (0.50), residues: 293 helix: 1.70 (0.33), residues: 230 sheet: -4.02 (1.01), residues: 12 loop : -2.56 (0.86), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 167 HIS 0.002 0.001 HIS R 258 PHE 0.011 0.001 PHE R 100 TYR 0.019 0.001 TYR R 387 ARG 0.001 0.000 ARG R 199 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 916.25 seconds wall clock time: 17 minutes 14.74 seconds (1034.74 seconds total)