Starting phenix.real_space_refine on Mon Jan 13 13:52:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrt_60404/01_2025/8zrt_60404.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrt_60404/01_2025/8zrt_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/cci-nas-00/data/ceres_data/8zrt_60404/01_2025/8zrt_60404.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrt_60404/01_2025/8zrt_60404.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrt_60404/01_2025/8zrt_60404.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrt_60404/01_2025/8zrt_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-5571/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: 2.07, per 1000 atoms: 0.89 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: 0.63 Conformation dependent library (CDL) restraints added in 295.5 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: 0.18 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: 0.61 Time building geometry restraints manager: 0.72 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.880 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.050 ------------------------------------------------------------------------------- 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 : 0.254 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: 0.1010 time to fit residues: 7.1255 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 : 0.271 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.200946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.188845 restraints weight = 3087.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.192562 restraints weight = 1576.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.195045 restraints weight = 929.214| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- 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 : 0.277 Fit side-chains REVERT: R 236 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7097 (tp30) REVERT: R 266 MET cc_start: 0.7339 (tpp) cc_final: 0.7014 (mmm) outliers start: 13 outliers final: 9 residues processed: 66 average time/residue: 0.1088 time to fit residues: 8.9834 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 : 0.252 ------------------------------------------------------------------------------- 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 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.200537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.188172 restraints weight = 3068.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.191898 restraints weight = 1624.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.194418 restraints weight = 973.568| |-----------------------------------------------------------------------------| r_work (final): 0.4264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1196 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= 0.232 Angle : 0.639 10.724 3245 Z= 0.324 Chirality : 0.042 0.206 402 Planarity : 0.007 0.108 388 Dihedral : 5.050 49.472 319 Min Nonbonded Distance : 2.584 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: 0.68 (0.48), residues: 293 helix: 1.46 (0.33), residues: 229 sheet: None (None), residues: 0 loop : -3.43 (0.61), 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 0.011 0.001 TYR R 387 ARG 0.000 0.000 ARG R 343 *********************** 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 : 0.366 Fit side-chains REVERT: R 236 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7141 (tp30) REVERT: R 266 MET cc_start: 0.7327 (tpp) cc_final: 0.7017 (mmm) outliers start: 24 outliers final: 16 residues processed: 75 average time/residue: 0.0984 time to fit residues: 9.2709 Evaluate side-chains 68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 256 LEU 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 28 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 373 ASN R 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.202305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.190131 restraints weight = 3072.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.193709 restraints weight = 1596.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.196242 restraints weight = 960.238| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1368 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= 0.212 Angle : 0.632 10.307 3245 Z= 0.318 Chirality : 0.041 0.206 402 Planarity : 0.007 0.103 388 Dihedral : 5.045 50.152 319 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.41 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: 1.57 (0.33), residues: 230 sheet: None (None), residues: 0 loop : -3.37 (0.63), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 276 HIS 0.002 0.001 HIS R 258 PHE 0.010 0.001 PHE R 100 TYR 0.009 0.001 TYR R 387 ARG 0.000 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 79 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.272 Fit side-chains REVERT: R 225 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7780 (mp) REVERT: R 266 MET cc_start: 0.7299 (tpp) cc_final: 0.6998 (mmm) outliers start: 22 outliers final: 16 residues processed: 76 average time/residue: 0.1122 time to fit residues: 10.6016 Evaluate side-chains 67 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 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 379 SER Chi-restraints excluded: chain R residue 386 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.0670 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.203882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.191556 restraints weight = 3089.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.195442 restraints weight = 1569.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.198026 restraints weight = 913.608| |-----------------------------------------------------------------------------| r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1500 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 : 0.651 10.607 3245 Z= 0.328 Chirality : 0.042 0.206 402 Planarity : 0.006 0.099 388 Dihedral : 5.028 50.305 319 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 8.87 % Allowed : 26.21 % 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: 0.91 (0.48), residues: 293 helix: 1.59 (0.33), residues: 230 sheet: None (None), residues: 0 loop : -3.29 (0.64), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 206 HIS 0.002 0.001 HIS R 258 PHE 0.010 0.001 PHE R 100 TYR 0.017 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 79 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.281 Fit side-chains REVERT: R 225 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7709 (mp) REVERT: R 266 MET cc_start: 0.7266 (tpp) cc_final: 0.6984 (mmm) outliers start: 22 outliers final: 19 residues processed: 73 average time/residue: 0.0882 time to fit residues: 8.2532 Evaluate side-chains 71 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 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 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 330 LEU 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 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 8 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 ** 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 = 0.4353 r_free = 0.4353 target = 0.204388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.192385 restraints weight = 3040.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.196432 restraints weight = 1558.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.198877 restraints weight = 902.818| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1711 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= 0.213 Angle : 0.697 10.102 3245 Z= 0.352 Chirality : 0.042 0.201 402 Planarity : 0.006 0.098 388 Dihedral : 5.250 51.475 319 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 10.48 % Allowed : 25.40 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.48), residues: 293 helix: 1.51 (0.33), residues: 230 sheet: None (None), residues: 0 loop : -3.30 (0.64), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 167 HIS 0.001 0.001 HIS R 258 PHE 0.015 0.001 PHE R 100 TYR 0.016 0.001 TYR R 387 ARG 0.001 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 79 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.283 Fit side-chains REVERT: R 101 LYS cc_start: 0.6001 (mmtp) cc_final: 0.5575 (mttm) REVERT: R 225 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7682 (mp) REVERT: R 266 MET cc_start: 0.7258 (tpp) cc_final: 0.6963 (mmm) outliers start: 26 outliers final: 21 residues processed: 73 average time/residue: 0.0927 time to fit residues: 8.5630 Evaluate side-chains 73 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.272 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.3980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 378 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 = 0.4343 r_free = 0.4343 target = 0.201715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.189949 restraints weight = 3085.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.193731 restraints weight = 1577.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.196158 restraints weight = 918.076| |-----------------------------------------------------------------------------| r_work (final): 0.4295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1780 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= 0.207 Angle : 0.677 9.880 3245 Z= 0.341 Chirality : 0.042 0.201 402 Planarity : 0.006 0.097 388 Dihedral : 5.295 52.214 319 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 9.27 % Allowed : 26.21 % 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: 0.77 (0.49), residues: 293 helix: 1.53 (0.33), residues: 230 sheet: -3.72 (1.06), residues: 14 loop : -3.10 (0.78), 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 0.016 0.001 PHE R 100 TYR 0.018 0.001 TYR R 387 ARG 0.001 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 74 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.281 Fit side-chains REVERT: R 101 LYS cc_start: 0.5672 (mmtp) cc_final: 0.5315 (mttm) REVERT: R 225 ILE cc_start: 0.7964 (OUTLIER) cc_final: 0.7676 (mp) REVERT: R 266 MET cc_start: 0.7279 (tpp) cc_final: 0.6975 (mmm) outliers start: 23 outliers final: 20 residues processed: 69 average time/residue: 0.0990 time to fit residues: 8.7414 Evaluate side-chains 71 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 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 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 29 optimal weight: 0.0370 chunk 26 optimal weight: 0.0020 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 overall best weight: 0.4066 ------------------------------------------------------------------------------- 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 373 ASN ** R 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.204952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.193174 restraints weight = 3105.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.196929 restraints weight = 1568.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.199431 restraints weight = 913.754| |-----------------------------------------------------------------------------| r_work (final): 0.4322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1946 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= 0.194 Angle : 0.676 9.614 3245 Z= 0.339 Chirality : 0.042 0.208 402 Planarity : 0.006 0.097 388 Dihedral : 5.267 52.196 319 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 9.27 % Allowed : 25.40 % 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: 0.93 (0.49), residues: 293 helix: 1.61 (0.33), residues: 230 sheet: -4.13 (0.94), residues: 12 loop : -2.83 (0.79), 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 0.019 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 72 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.272 Fit side-chains REVERT: R 225 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7635 (mp) outliers start: 23 outliers final: 19 residues processed: 66 average time/residue: 0.1000 time to fit residues: 8.3341 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 : 0.272 ------------------------------------------------------------------------------- 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 330 LEU Chi-restraints excluded: chain R residue 378 ASN Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain R residue 388 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 27 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.0570 chunk 18 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.203493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.191880 restraints weight = 2975.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.195485 restraints weight = 1515.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.198033 restraints weight = 893.363| |-----------------------------------------------------------------------------| r_work (final): 0.4308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.1943 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= 0.214 Angle : 0.690 9.744 3245 Z= 0.347 Chirality : 0.043 0.201 402 Planarity : 0.006 0.095 388 Dihedral : 5.321 53.444 319 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 8.47 % Allowed : 26.61 % 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: 0.92 (0.49), residues: 293 helix: 1.59 (0.33), residues: 230 sheet: -4.13 (0.94), residues: 12 loop : -2.74 (0.81), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 167 HIS 0.001 0.001 HIS R 258 PHE 0.010 0.001 PHE R 100 TYR 0.019 0.001 TYR R 387 ARG 0.001 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 72 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.279 Fit side-chains REVERT: R 225 ILE cc_start: 0.7958 (OUTLIER) cc_final: 0.7655 (mp) REVERT: R 266 MET cc_start: 0.7283 (tpp) cc_final: 0.6970 (mmm) REVERT: R 268 PHE cc_start: 0.8288 (t80) cc_final: 0.7161 (t80) outliers start: 21 outliers final: 19 residues processed: 66 average time/residue: 0.0882 time to fit residues: 7.5394 Evaluate side-chains 68 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 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 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 378 ASN Chi-restraints excluded: chain R residue 386 LEU Chi-restraints excluded: chain R residue 388 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.0010 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.206905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.195386 restraints weight = 2986.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.199118 restraints weight = 1505.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.201557 restraints weight = 867.180| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2145 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= 0.191 Angle : 0.667 9.386 3245 Z= 0.334 Chirality : 0.042 0.201 402 Planarity : 0.006 0.095 388 Dihedral : 5.227 53.119 319 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 8.06 % Allowed : 27.02 % 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: 1.13 (0.49), residues: 293 helix: 1.66 (0.33), residues: 232 sheet: -3.91 (1.06), residues: 12 loop : -2.41 (0.85), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 167 HIS 0.002 0.001 HIS L 16 PHE 0.010 0.001 PHE R 100 TYR 0.019 0.001 TYR R 387 ARG 0.001 0.000 ARG R 343 ********************** 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 70 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.259 Fit side-chains REVERT: R 225 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7511 (mp) outliers start: 20 outliers final: 17 residues processed: 66 average time/residue: 0.0899 time to fit residues: 7.7080 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 : 0.225 ------------------------------------------------------------------------------- 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 220 VAL 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 R residue 388 LEU Chi-restraints excluded: chain L residue 19 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 11 optimal weight: 0.0070 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 overall best weight: 0.3536 ------------------------------------------------------------------------------- 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 = 0.4395 r_free = 0.4395 target = 0.208049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.196399 restraints weight = 2936.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.200147 restraints weight = 1491.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.202634 restraints weight = 861.453| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.2269 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= 0.187 Angle : 0.662 9.270 3245 Z= 0.331 Chirality : 0.041 0.202 402 Planarity : 0.006 0.094 388 Dihedral : 5.190 53.541 319 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: 1.18 (0.49), residues: 293 helix: 1.68 (0.33), residues: 232 sheet: -3.73 (1.15), residues: 12 loop : -2.38 (0.85), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 167 HIS 0.002 0.001 HIS L 16 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: 1065.16 seconds wall clock time: 20 minutes 28.88 seconds (1228.88 seconds total)