Starting phenix.real_space_refine on Mon Sep 23 12:47:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xiu_38390/09_2024/8xiu_38390.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xiu_38390/09_2024/8xiu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xiu_38390/09_2024/8xiu_38390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xiu_38390/09_2024/8xiu_38390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xiu_38390/09_2024/8xiu_38390.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xiu_38390/09_2024/8xiu_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-5461/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: 2.36, per 1000 atoms: 0.90 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: 0.61 Conformation dependent library (CDL) restraints added in 354.4 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: 0.27 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: 0.71 Time building geometry restraints manager: 0.73 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.620 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.510 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 0.294 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: 0.1212 time to fit residues: 15.2727 Evaluate side-chains 90 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.313 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 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 fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.274 Fit side-chains REVERT: A 151 MET cc_start: 0.7795 (mmm) cc_final: 0.7578 (mmp) REVERT: A 157 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.6366 (m-80) REVERT: A 229 MET cc_start: 0.8990 (mtp) cc_final: 0.8596 (mmt) REVERT: A 341 LEU cc_start: 0.8750 (tp) cc_final: 0.8532 (tp) REVERT: A 364 MET cc_start: 0.7834 (mtp) cc_final: 0.7368 (mtm) REVERT: A 428 PHE cc_start: 0.8326 (t80) cc_final: 0.7778 (t80) outliers start: 12 outliers final: 8 residues processed: 95 average time/residue: 0.1026 time to fit residues: 12.2111 Evaluate side-chains 95 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 0.023 2673 Z= 0.182 Angle : 0.634 9.433 3627 Z= 0.301 Chirality : 0.041 0.118 437 Planarity : 0.006 0.055 441 Dihedral : 5.357 50.934 369 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.30 % Allowed : 21.86 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.48), residues: 336 helix: 1.81 (0.32), residues: 276 sheet: None (None), residues: 0 loop : -0.81 (0.81), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 357 HIS 0.005 0.002 HIS A 352 PHE 0.024 0.001 PHE A 237 TYR 0.009 0.001 TYR A 421 ARG 0.001 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 fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 0.283 Fit side-chains REVERT: A 151 MET cc_start: 0.7817 (mmm) cc_final: 0.7585 (mmp) REVERT: A 157 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.6428 (m-80) REVERT: A 229 MET cc_start: 0.9001 (mtp) cc_final: 0.8586 (mmt) REVERT: A 341 LEU cc_start: 0.8762 (tp) cc_final: 0.8557 (tp) REVERT: A 364 MET cc_start: 0.7870 (mtp) cc_final: 0.7343 (mtm) REVERT: A 396 MET cc_start: 0.7338 (tpt) cc_final: 0.6939 (tpp) REVERT: A 428 PHE cc_start: 0.8346 (t80) cc_final: 0.8110 (t80) outliers start: 12 outliers final: 10 residues processed: 96 average time/residue: 0.1191 time to fit residues: 14.0755 Evaluate side-chains 99 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 16 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 0.0030 chunk 32 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2201 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= 0.227 Angle : 0.656 8.809 3627 Z= 0.320 Chirality : 0.042 0.122 437 Planarity : 0.006 0.058 441 Dihedral : 5.601 50.543 369 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 5.38 % Allowed : 24.37 % Favored : 70.25 % 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: 1.95 (0.47), residues: 336 helix: 1.77 (0.32), residues: 270 sheet: None (None), residues: 0 loop : -0.63 (0.75), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 450 HIS 0.004 0.002 HIS A 352 PHE 0.019 0.001 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 fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 0.281 Fit side-chains REVERT: A 157 TYR cc_start: 0.6763 (OUTLIER) cc_final: 0.6440 (m-80) REVERT: A 229 MET cc_start: 0.9006 (mtp) cc_final: 0.8598 (mmt) REVERT: A 319 MET cc_start: 0.7683 (tpp) cc_final: 0.7204 (ttp) REVERT: A 396 MET cc_start: 0.7364 (tpt) cc_final: 0.7108 (tpt) REVERT: A 401 MET cc_start: 0.8248 (tpp) cc_final: 0.8007 (tpp) REVERT: A 428 PHE cc_start: 0.8487 (t80) cc_final: 0.8148 (t80) outliers start: 15 outliers final: 13 residues processed: 97 average time/residue: 0.1132 time to fit residues: 13.4965 Evaluate side-chains 102 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 88 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2412 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= 0.188 Angle : 0.646 9.566 3627 Z= 0.311 Chirality : 0.042 0.119 437 Planarity : 0.006 0.056 441 Dihedral : 5.546 49.343 369 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 6.09 % Allowed : 24.01 % Favored : 69.89 % 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: 1.93 (0.47), residues: 336 helix: 1.78 (0.32), residues: 270 sheet: None (None), residues: 0 loop : -0.75 (0.73), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 450 HIS 0.004 0.001 HIS A 352 PHE 0.020 0.001 PHE A 237 TYR 0.009 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 108 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.439 Fit side-chains REVERT: A 157 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6461 (m-80) REVERT: A 229 MET cc_start: 0.9023 (mtp) cc_final: 0.8534 (mmt) REVERT: A 319 MET cc_start: 0.7691 (tpp) cc_final: 0.7210 (ttm) REVERT: A 396 MET cc_start: 0.7357 (tpt) cc_final: 0.7027 (tpt) REVERT: A 428 PHE cc_start: 0.8516 (t80) cc_final: 0.8290 (t80) outliers start: 17 outliers final: 15 residues processed: 99 average time/residue: 0.1083 time to fit residues: 13.5380 Evaluate side-chains 103 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 299 SER Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 333 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 2 optimal weight: 0.1980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 18 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2509 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= 0.176 Angle : 0.656 9.625 3627 Z= 0.315 Chirality : 0.041 0.123 437 Planarity : 0.006 0.056 441 Dihedral : 5.428 47.546 369 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 6.09 % Allowed : 25.09 % 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: 1.82 (0.47), residues: 336 helix: 1.75 (0.33), residues: 269 sheet: None (None), residues: 0 loop : -0.99 (0.70), residues: 67 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 0.018 0.001 PHE A 237 TYR 0.007 0.001 TYR A 421 ARG 0.003 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 111 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.286 Fit side-chains REVERT: A 157 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6553 (m-80) REVERT: A 191 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 229 MET cc_start: 0.8969 (mtp) cc_final: 0.8504 (mmt) REVERT: A 318 MET cc_start: 0.6941 (ttp) cc_final: 0.6472 (ptm) REVERT: A 396 MET cc_start: 0.7279 (tpt) cc_final: 0.7004 (tpt) outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 0.1092 time to fit residues: 13.8770 Evaluate side-chains 105 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 333 PHE Chi-restraints excluded: chain A residue 357 TRP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 0.0470 chunk 20 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2673 Z= 0.179 Angle : 0.697 10.416 3627 Z= 0.331 Chirality : 0.042 0.133 437 Planarity : 0.006 0.056 441 Dihedral : 5.385 46.558 369 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 6.81 % Allowed : 24.37 % 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: 1.82 (0.47), residues: 336 helix: 1.74 (0.33), residues: 267 sheet: None (None), residues: 0 loop : -0.87 (0.70), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 317 HIS 0.002 0.001 HIS A 352 PHE 0.017 0.001 PHE A 237 TYR 0.010 0.001 TYR A 340 ARG 0.004 0.000 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 109 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.6588 (m-80) REVERT: A 191 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8736 (tm-30) REVERT: A 229 MET cc_start: 0.8972 (mtp) cc_final: 0.8622 (mmm) REVERT: A 318 MET cc_start: 0.6951 (ttp) cc_final: 0.6491 (ptm) REVERT: A 357 TRP cc_start: 0.7147 (OUTLIER) cc_final: 0.6540 (m-10) outliers start: 19 outliers final: 17 residues processed: 100 average time/residue: 0.1032 time to fit residues: 12.9224 Evaluate side-chains 107 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 162 PHE 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 333 PHE Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 358 LEU 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 3 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.0670 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2673 Z= 0.178 Angle : 0.679 10.638 3627 Z= 0.323 Chirality : 0.041 0.119 437 Planarity : 0.006 0.057 441 Dihedral : 5.365 45.912 369 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % 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: 1.73 (0.47), residues: 336 helix: 1.68 (0.32), residues: 267 sheet: None (None), residues: 0 loop : -0.90 (0.71), 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 0.012 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 107 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.6582 (m-80) REVERT: A 191 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 229 MET cc_start: 0.8978 (mtp) cc_final: 0.8542 (mmt) REVERT: A 243 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 318 MET cc_start: 0.6906 (ttp) cc_final: 0.6457 (ptm) REVERT: A 357 TRP cc_start: 0.7183 (OUTLIER) cc_final: 0.6553 (m-10) outliers start: 18 outliers final: 16 residues processed: 97 average time/residue: 0.1034 time to fit residues: 12.5665 Evaluate side-chains 105 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 87 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 162 PHE 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 333 PHE Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 384 ILE 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 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 0.0030 chunk 31 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2673 Z= 0.179 Angle : 0.695 10.733 3627 Z= 0.330 Chirality : 0.042 0.118 437 Planarity : 0.006 0.056 441 Dihedral : 5.359 45.175 369 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: 1.71 (0.47), residues: 336 helix: 1.63 (0.32), residues: 267 sheet: None (None), residues: 0 loop : -0.74 (0.75), 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 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 106 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 88 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6618 (m-80) REVERT: A 191 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8703 (tm-30) REVERT: A 229 MET cc_start: 0.8981 (mtp) cc_final: 0.8540 (mmt) REVERT: A 318 MET cc_start: 0.6855 (ttp) cc_final: 0.6404 (ptm) REVERT: A 357 TRP cc_start: 0.7108 (OUTLIER) cc_final: 0.6514 (m-10) outliers start: 18 outliers final: 16 residues processed: 98 average time/residue: 0.1002 time to fit residues: 12.3672 Evaluate side-chains 104 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 162 PHE 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 333 PHE Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 380 ILE 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 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 0.0010 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2840 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= 0.192 Angle : 0.769 13.836 3627 Z= 0.355 Chirality : 0.042 0.118 437 Planarity : 0.006 0.056 441 Dihedral : 5.408 44.923 369 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 6.81 % Allowed : 26.16 % Favored : 67.03 % 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: 1.62 (0.47), residues: 336 helix: 1.59 (0.32), residues: 267 sheet: None (None), residues: 0 loop : -0.90 (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 0.015 0.001 PHE A 237 TYR 0.011 0.001 TYR A 340 ARG 0.006 0.001 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 106 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 157 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6657 (m-80) REVERT: A 229 MET cc_start: 0.8970 (mtp) cc_final: 0.8516 (mmt) REVERT: A 318 MET cc_start: 0.6842 (ttp) cc_final: 0.6389 (ptm) REVERT: A 357 TRP cc_start: 0.7099 (OUTLIER) cc_final: 0.6529 (m-10) outliers start: 19 outliers final: 17 residues processed: 96 average time/residue: 0.0995 time to fit residues: 11.9570 Evaluate side-chains 104 residues out of total 279 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 85 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 162 PHE 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 333 PHE Chi-restraints excluded: chain A residue 357 TRP Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 380 ILE 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 23 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4055 r_free = 0.4055 target = 0.164965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.150472 restraints weight = 6776.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154028 restraints weight = 4012.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.156348 restraints weight = 2634.767| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2881 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= 0.193 Angle : 0.756 13.610 3627 Z= 0.351 Chirality : 0.043 0.116 437 Planarity : 0.006 0.056 441 Dihedral : 5.447 45.036 369 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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 (0.47), residues: 336 helix: 1.57 (0.32), residues: 267 sheet: None (None), residues: 0 loop : -0.75 (0.75), 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 0.015 0.001 PHE A 237 TYR 0.012 0.001 TYR A 340 ARG 0.003 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1007.11 seconds wall clock time: 18 minutes 34.13 seconds (1114.13 seconds total)