Starting phenix.real_space_refine on Mon Jan 13 14:37:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xiu_38390/01_2025/8xiu_38390.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xiu_38390/01_2025/8xiu_38390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xiu_38390/01_2025/8xiu_38390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xiu_38390/01_2025/8xiu_38390.map" model { file = "/net/cci-nas-00/data/ceres_data/8xiu_38390/01_2025/8xiu_38390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xiu_38390/01_2025/8xiu_38390.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 30 5.16 5 C 1745 2.51 5 N 401 2.21 5 O 439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 2615 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2615 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 18, 'TRANS': 329} Chain breaks: 5 Time building chain proxies: 2.52, per 1000 atoms: 0.96 Number of scatterers: 2615 At special positions: 0 Unit cell: (72.25, 57.8, 69.7, 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 30 16.00 O 439 8.00 N 401 7.00 C 1745 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.86 Conformation dependent library (CDL) restraints added in 433.6 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 628 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 89.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 39 removed outlier: 3.930A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 49 removed outlier: 3.689A pdb=" N TYR A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 155 removed outlier: 3.849A pdb=" N PHE A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Proline residue: A 146 - end of helix Proline residue: A 150 - end of helix removed outlier: 4.086A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 173 removed outlier: 4.099A pdb=" N ILE A 173 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 180 through 210 removed outlier: 3.541A pdb=" N TYR A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 244 Proline residue: A 235 - end of helix removed outlier: 4.126A pdb=" N GLU A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 244 " --> pdb=" O ILE A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 269 removed outlier: 4.111A pdb=" N LEU A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 322 removed outlier: 3.865A pdb=" N LEU A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Proline residue: A 312 - end of helix Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 333 through 348 removed outlier: 4.054A pdb=" N ASN A 345 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 355 through 374 removed outlier: 4.379A pdb=" N CYS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 412 removed outlier: 3.827A pdb=" N PHE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Proline residue: A 403 - end of helix removed outlier: 4.211A pdb=" N GLY A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 435 removed outlier: 4.357A pdb=" N GLY A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 432 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.503A pdb=" N VAL A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 removed outlier: 4.448A pdb=" N PHE A 468 " --> pdb=" O LEU A 465 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 573 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: 0.82 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 779 1.35 - 1.46: 616 1.46 - 1.58: 1225 1.58 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 2673 Sorted by residual: bond pdb=" C VAL A 374 " pdb=" N PRO A 375 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.30e-02 5.92e+03 5.73e-01 bond pdb=" C PRO A 235 " pdb=" N PRO A 236 " ideal model delta sigma weight residual 1.336 1.344 -0.008 1.20e-02 6.94e+03 4.26e-01 bond pdb=" CA ASN A 145 " pdb=" C ASN A 145 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 4.02e-01 bond pdb=" C LEU A 314 " pdb=" N PRO A 315 " ideal model delta sigma weight residual 1.335 1.343 -0.008 1.28e-02 6.10e+03 3.90e-01 bond pdb=" CA MET A 402 " pdb=" C MET A 402 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.72e-01 ... (remaining 2668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 3539 1.41 - 2.82: 66 2.82 - 4.23: 12 4.23 - 5.64: 7 5.64 - 7.05: 3 Bond angle restraints: 3627 Sorted by residual: angle pdb=" N PRO A 235 " pdb=" CA PRO A 235 " pdb=" C PRO A 235 " ideal model delta sigma weight residual 110.70 113.20 -2.50 1.22e+00 6.72e-01 4.19e+00 angle pdb=" CA PRO A 235 " pdb=" C PRO A 235 " pdb=" N PRO A 236 " ideal model delta sigma weight residual 117.93 120.28 -2.35 1.20e+00 6.94e-01 3.82e+00 angle pdb=" C PRO A 235 " pdb=" N PRO A 236 " pdb=" CD PRO A 236 " ideal model delta sigma weight residual 125.00 132.05 -7.05 4.10e+00 5.95e-02 2.96e+00 angle pdb=" CA LEU A 461 " pdb=" CB LEU A 461 " pdb=" CG LEU A 461 " ideal model delta sigma weight residual 116.30 122.02 -5.72 3.50e+00 8.16e-02 2.67e+00 angle pdb=" N PHE A 434 " pdb=" CA PHE A 434 " pdb=" C PHE A 434 " ideal model delta sigma weight residual 110.61 112.65 -2.04 1.25e+00 6.40e-01 2.66e+00 ... (remaining 3622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.17: 1417 11.17 - 22.35: 81 22.35 - 33.52: 34 33.52 - 44.69: 19 44.69 - 55.86: 6 Dihedral angle restraints: 1557 sinusoidal: 575 harmonic: 982 Sorted by residual: dihedral pdb=" CA VAL A 374 " pdb=" C VAL A 374 " pdb=" N PRO A 375 " pdb=" CA PRO A 375 " ideal model delta harmonic sigma weight residual 180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA GLN A 141 " pdb=" CB GLN A 141 " pdb=" CG GLN A 141 " pdb=" CD GLN A 141 " ideal model delta sinusoidal sigma weight residual -180.00 -124.14 -55.86 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" N TYR A 157 " pdb=" CA TYR A 157 " pdb=" CB TYR A 157 " pdb=" CG TYR A 157 " ideal model delta sinusoidal sigma weight residual -60.00 -6.46 -53.54 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 1554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 267 0.026 - 0.053: 96 0.053 - 0.079: 42 0.079 - 0.106: 24 0.106 - 0.132: 8 Chirality restraints: 437 Sorted by residual: chirality pdb=" CA VAL A 374 " pdb=" N VAL A 374 " pdb=" C VAL A 374 " pdb=" CB VAL A 374 " both_signs ideal model delta sigma weight residual False 2.44 2.31 0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA MET A 402 " pdb=" N MET A 402 " pdb=" C MET A 402 " pdb=" CB MET A 402 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 434 not shown) Planarity restraints: 441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 234 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 235 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 159 " 0.028 5.00e-02 4.00e+02 4.25e-02 2.89e+00 pdb=" N PRO A 160 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 160 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 160 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 44 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 45 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " -0.021 5.00e-02 4.00e+02 ... (remaining 438 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 898 2.87 - 3.37: 2904 3.37 - 3.88: 4170 3.88 - 4.39: 4163 4.39 - 4.90: 7407 Nonbonded interactions: 19542 Sorted by model distance: nonbonded pdb=" O TRP A 317 " pdb=" OG1 THR A 321 " model vdw 2.357 3.040 nonbonded pdb=" OG SER A 339 " pdb=" O PHE A 388 " model vdw 2.379 3.040 nonbonded pdb=" N ASP A 213 " pdb=" OD1 ASP A 213 " model vdw 2.411 3.120 nonbonded pdb=" O TYR A 210 " pdb=" NE ARG A 216 " model vdw 2.469 3.120 nonbonded pdb=" O VAL A 140 " pdb=" OG1 THR A 144 " model vdw 2.480 3.040 ... (remaining 19537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.120 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 12.880 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 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 : 0.002 0.022 2673 Z= 0.143 Angle : 0.554 7.054 3627 Z= 0.277 Chirality : 0.039 0.132 437 Planarity : 0.005 0.047 441 Dihedral : 10.636 55.863 929 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.08 % Allowed : 11.83 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.48), residues: 336 helix: 2.30 (0.33), residues: 274 sheet: None (None), residues: 0 loop : -0.79 (0.83), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 317 HIS 0.001 0.000 HIS A 413 PHE 0.010 0.001 PHE A 134 TYR 0.007 0.001 TYR A 340 ARG 0.001 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.283 Fit side-chains REVERT: A 20 LYS cc_start: 0.6381 (mtmt) cc_final: 0.6093 (mtmm) REVERT: A 157 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.6530 (m-80) REVERT: A 168 MET cc_start: 0.8309 (mmt) cc_final: 0.7958 (mmt) REVERT: A 229 MET cc_start: 0.8948 (mtp) cc_final: 0.8541 (mmt) REVERT: A 309 MET cc_start: 0.8693 (tpp) cc_final: 0.8482 (tpp) REVERT: A 341 LEU cc_start: 0.8797 (tp) cc_final: 0.8493 (tp) REVERT: A 364 MET cc_start: 0.7739 (mtp) cc_final: 0.7428 (mtm) REVERT: A 401 MET cc_start: 0.7252 (ttm) cc_final: 0.6760 (ttm) REVERT: A 428 PHE cc_start: 0.8264 (t80) cc_final: 0.7692 (t80) outliers start: 3 outliers final: 2 residues processed: 105 average time/residue: 0.1300 time to fit residues: 16.3984 Evaluate side-chains 90 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 165 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.165154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.151123 restraints weight = 6807.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.154439 restraints weight = 4119.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.157005 restraints weight = 2788.809| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2673 Z= 0.192 Angle : 0.656 9.450 3627 Z= 0.309 Chirality : 0.042 0.139 437 Planarity : 0.006 0.055 441 Dihedral : 5.364 52.942 369 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 4.30 % Allowed : 20.79 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.48), residues: 336 helix: 2.04 (0.32), residues: 276 sheet: None (None), residues: 0 loop : -0.71 (0.82), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 450 HIS 0.007 0.002 HIS A 352 PHE 0.024 0.001 PHE A 237 TYR 0.012 0.001 TYR A 421 ARG 0.001 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.280 Fit side-chains REVERT: A 157 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: A 229 MET cc_start: 0.8968 (mtp) cc_final: 0.8612 (mmt) REVERT: A 341 LEU cc_start: 0.8817 (tp) cc_final: 0.8616 (tp) REVERT: A 364 MET cc_start: 0.7519 (mtp) cc_final: 0.7256 (mtm) REVERT: A 428 PHE cc_start: 0.8162 (t80) cc_final: 0.7638 (t80) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.1071 time to fit residues: 12.6845 Evaluate side-chains 95 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 465 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.162879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.148610 restraints weight = 6644.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152057 restraints weight = 4048.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.154439 restraints weight = 2675.578| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2673 Z= 0.189 Angle : 0.644 9.163 3627 Z= 0.306 Chirality : 0.041 0.117 437 Planarity : 0.006 0.055 441 Dihedral : 5.397 51.173 369 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.30 % Allowed : 22.22 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.48), residues: 336 helix: 1.79 (0.32), residues: 276 sheet: None (None), residues: 0 loop : -0.79 (0.81), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 357 HIS 0.006 0.002 HIS A 352 PHE 0.023 0.001 PHE A 237 TYR 0.009 0.001 TYR A 421 ARG 0.002 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.276 Fit side-chains REVERT: A 157 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: A 229 MET cc_start: 0.8991 (mtp) cc_final: 0.8619 (mmt) REVERT: A 364 MET cc_start: 0.7591 (mtp) cc_final: 0.7245 (mtm) REVERT: A 396 MET cc_start: 0.7392 (tpt) cc_final: 0.7155 (tpt) REVERT: A 428 PHE cc_start: 0.8182 (t80) cc_final: 0.7938 (t80) outliers start: 12 outliers final: 10 residues processed: 96 average time/residue: 0.1119 time to fit residues: 13.2671 Evaluate side-chains 99 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 465 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146373 restraints weight = 6624.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.149911 restraints weight = 3935.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.152263 restraints weight = 2562.620| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2673 Z= 0.237 Angle : 0.676 8.519 3627 Z= 0.329 Chirality : 0.043 0.124 437 Planarity : 0.006 0.058 441 Dihedral : 5.693 50.884 369 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.73 % Allowed : 23.66 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.47), residues: 336 helix: 1.68 (0.32), residues: 271 sheet: None (None), residues: 0 loop : -0.46 (0.75), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 450 HIS 0.004 0.002 HIS A 352 PHE 0.019 0.002 PHE A 237 TYR 0.011 0.001 TYR A 421 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.344 Fit side-chains REVERT: A 157 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6617 (m-80) REVERT: A 229 MET cc_start: 0.8985 (mtp) cc_final: 0.8759 (mmt) REVERT: A 319 MET cc_start: 0.7594 (tpp) cc_final: 0.7170 (ttp) REVERT: A 396 MET cc_start: 0.7427 (tpt) cc_final: 0.7165 (tpt) REVERT: A 401 MET cc_start: 0.8229 (tpp) cc_final: 0.8006 (tpp) REVERT: A 428 PHE cc_start: 0.8316 (t80) cc_final: 0.8071 (t80) outliers start: 16 outliers final: 14 residues processed: 97 average time/residue: 0.1169 time to fit residues: 13.9413 Evaluate side-chains 102 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 465 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 0.0010 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.163152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148886 restraints weight = 6232.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152419 restraints weight = 3670.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.154755 restraints weight = 2362.097| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2673 Z= 0.182 Angle : 0.647 9.786 3627 Z= 0.309 Chirality : 0.041 0.116 437 Planarity : 0.006 0.057 441 Dihedral : 5.542 49.093 369 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 5.73 % Allowed : 25.09 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.47), residues: 336 helix: 1.76 (0.32), residues: 270 sheet: None (None), residues: 0 loop : -0.78 (0.72), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 450 HIS 0.003 0.001 HIS A 352 PHE 0.019 0.001 PHE A 237 TYR 0.008 0.001 TYR A 421 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.304 Fit side-chains REVERT: A 157 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: A 229 MET cc_start: 0.8950 (mtp) cc_final: 0.8746 (mmt) REVERT: A 396 MET cc_start: 0.7411 (tpt) cc_final: 0.7111 (tpt) REVERT: A 428 PHE cc_start: 0.8315 (t80) cc_final: 0.8071 (t80) outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 0.1058 time to fit residues: 12.9515 Evaluate side-chains 101 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 465 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.163012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.148361 restraints weight = 6536.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151852 restraints weight = 3907.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154289 restraints weight = 2559.137| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2673 Z= 0.191 Angle : 0.655 9.706 3627 Z= 0.318 Chirality : 0.042 0.130 437 Planarity : 0.006 0.058 441 Dihedral : 5.549 48.578 369 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.73 % Allowed : 25.45 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.46), residues: 336 helix: 1.66 (0.32), residues: 269 sheet: None (None), residues: 0 loop : -0.97 (0.71), residues: 67 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 450 HIS 0.003 0.001 HIS A 352 PHE 0.022 0.001 PHE A 392 TYR 0.012 0.001 TYR A 340 ARG 0.004 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.275 Fit side-chains REVERT: A 157 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: A 229 MET cc_start: 0.8999 (mtp) cc_final: 0.8688 (mmm) REVERT: A 243 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7463 (tm-30) REVERT: A 396 MET cc_start: 0.7354 (tpt) cc_final: 0.6895 (tpp) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.1128 time to fit residues: 14.0098 Evaluate side-chains 106 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 465 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.163037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.148535 restraints weight = 7078.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152170 restraints weight = 4133.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.154585 restraints weight = 2627.289| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2673 Z= 0.194 Angle : 0.698 9.791 3627 Z= 0.334 Chirality : 0.042 0.121 437 Planarity : 0.006 0.057 441 Dihedral : 5.562 47.942 369 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 6.45 % Allowed : 26.16 % Favored : 67.38 % 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: 1.63 (0.46), residues: 336 helix: 1.61 (0.32), residues: 267 sheet: None (None), residues: 0 loop : -0.93 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 450 HIS 0.003 0.001 HIS A 352 PHE 0.017 0.001 PHE A 392 TYR 0.013 0.001 TYR A 340 ARG 0.004 0.001 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: A 229 MET cc_start: 0.8969 (mtp) cc_final: 0.8733 (mmp) REVERT: A 243 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 318 MET cc_start: 0.7132 (ttp) cc_final: 0.6930 (ptm) REVERT: A 319 MET cc_start: 0.7650 (tpp) cc_final: 0.7433 (tpp) outliers start: 18 outliers final: 16 residues processed: 102 average time/residue: 0.1154 time to fit residues: 14.5129 Evaluate side-chains 108 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 465 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 27 optimal weight: 0.0670 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.149517 restraints weight = 6817.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153093 restraints weight = 4041.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.155549 restraints weight = 2618.055| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2673 Z= 0.184 Angle : 0.672 10.392 3627 Z= 0.322 Chirality : 0.041 0.116 437 Planarity : 0.006 0.058 441 Dihedral : 5.503 46.973 369 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.45 % Allowed : 25.45 % Favored : 68.10 % 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: 1.63 (0.47), residues: 336 helix: 1.59 (0.32), residues: 267 sheet: None (None), residues: 0 loop : -0.84 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 450 HIS 0.003 0.001 HIS A 352 PHE 0.017 0.001 PHE A 237 TYR 0.012 0.001 TYR A 340 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6709 (m-80) REVERT: A 229 MET cc_start: 0.8980 (mtp) cc_final: 0.8775 (mmt) REVERT: A 318 MET cc_start: 0.7086 (ttp) cc_final: 0.6548 (ptm) REVERT: A 357 TRP cc_start: 0.7144 (OUTLIER) cc_final: 0.6940 (m-10) outliers start: 18 outliers final: 16 residues processed: 99 average time/residue: 0.1135 time to fit residues: 13.8445 Evaluate side-chains 107 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.149282 restraints weight = 6757.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152906 restraints weight = 4016.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155322 restraints weight = 2612.956| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2673 Z= 0.195 Angle : 0.707 10.423 3627 Z= 0.335 Chirality : 0.042 0.116 437 Planarity : 0.006 0.057 441 Dihedral : 5.521 46.478 369 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 7.17 % Allowed : 24.73 % Favored : 68.10 % 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: 1.55 (0.46), residues: 336 helix: 1.56 (0.32), residues: 267 sheet: None (None), residues: 0 loop : -0.95 (0.72), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 450 HIS 0.002 0.001 HIS A 352 PHE 0.016 0.001 PHE A 237 TYR 0.012 0.001 TYR A 340 ARG 0.003 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6746 (m-80) REVERT: A 229 MET cc_start: 0.8993 (mtp) cc_final: 0.8768 (mmt) REVERT: A 318 MET cc_start: 0.7229 (ttp) cc_final: 0.6628 (ptm) REVERT: A 357 TRP cc_start: 0.7134 (OUTLIER) cc_final: 0.6928 (m-10) outliers start: 20 outliers final: 16 residues processed: 100 average time/residue: 0.1192 time to fit residues: 14.5611 Evaluate side-chains 106 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 388 PHE Chi-restraints excluded: chain A residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.164021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.149346 restraints weight = 6699.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.152972 restraints weight = 3962.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.155404 restraints weight = 2593.224| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2673 Z= 0.188 Angle : 0.727 10.794 3627 Z= 0.343 Chirality : 0.042 0.117 437 Planarity : 0.006 0.057 441 Dihedral : 5.464 45.433 369 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 6.09 % Allowed : 26.52 % Favored : 67.38 % 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: 1.51 (0.47), residues: 336 helix: 1.51 (0.32), residues: 267 sheet: None (None), residues: 0 loop : -0.91 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 450 HIS 0.002 0.001 HIS A 352 PHE 0.017 0.001 PHE A 237 TYR 0.011 0.001 TYR A 340 ARG 0.003 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 229 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8775 (mmm) REVERT: A 357 TRP cc_start: 0.7087 (OUTLIER) cc_final: 0.6606 (m-10) REVERT: A 452 MET cc_start: 0.7965 (pmm) cc_final: 0.7463 (ptp) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.1049 time to fit residues: 12.9212 Evaluate side-chains 106 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 33 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.165366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.150765 restraints weight = 6880.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154166 restraints weight = 4107.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.156603 restraints weight = 2758.663| |-----------------------------------------------------------------------------| r_work (final): 0.3943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2673 Z= 0.190 Angle : 0.749 10.750 3627 Z= 0.348 Chirality : 0.042 0.135 437 Planarity : 0.006 0.055 441 Dihedral : 4.903 43.921 367 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 5.38 % Allowed : 28.32 % Favored : 66.31 % 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: 1.50 (0.46), residues: 336 helix: 1.50 (0.32), residues: 267 sheet: None (None), residues: 0 loop : -0.91 (0.73), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 450 HIS 0.002 0.001 HIS A 352 PHE 0.016 0.001 PHE A 237 TYR 0.011 0.001 TYR A 340 ARG 0.003 0.000 ARG A 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1193.70 seconds wall clock time: 22 minutes 12.64 seconds (1332.64 seconds total)