Starting phenix.real_space_refine on Sun Mar 10 15:41:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugj_26489/03_2024/7ugj_26489_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugj_26489/03_2024/7ugj_26489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugj_26489/03_2024/7ugj_26489.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugj_26489/03_2024/7ugj_26489.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugj_26489/03_2024/7ugj_26489_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ugj_26489/03_2024/7ugj_26489_updated.pdb" } resolution = 2.81 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= 0.036 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: 6 Type Number sf(0) Gaussians S 16 5.16 5 Na 2 4.78 5 C 2035 2.51 5 N 504 2.21 5 O 537 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3095 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3095 Unusual residues: {' NA': 2, 'TB1': 1} Classifications: {'peptide': 416, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 397, None: 3} Not linked: pdbres="GLY A 417 " pdbres="TB1 A 501 " Not linked: pdbres="TB1 A 501 " pdbres=" NA A 502 " Not linked: pdbres=" NA A 502 " pdbres=" NA A 503 " Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.25, per 1000 atoms: 0.73 Number of scatterers: 3095 At special positions: 0 Unit cell: (63.9, 79.236, 83.496, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 16 16.00 Na 2 11.00 F 1 9.00 O 537 8.00 N 504 7.00 C 2035 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 618.0 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.737A pdb=" N ILE A 8 " --> pdb=" O TYR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 32 Processing helix chain 'A' and resid 36 through 72 removed outlier: 4.197A pdb=" N LYS A 44 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 3.663A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix Processing helix chain 'A' and resid 75 through 107 removed outlier: 3.552A pdb=" N ARG A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 137 removed outlier: 3.955A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 148 removed outlier: 3.591A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.506A pdb=" N THR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 224 removed outlier: 3.645A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 5.367A pdb=" N VAL A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N HIS A 223 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.719A pdb=" N VAL A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 254 Processing helix chain 'A' and resid 258 through 275 removed outlier: 3.614A pdb=" N HIS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 273 " --> pdb=" O MET A 269 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 292 Proline residue: A 283 - end of helix removed outlier: 3.538A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 309 removed outlier: 4.144A pdb=" N PHE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 3.712A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.759A pdb=" N PHE A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.550A pdb=" N VAL A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 369 Processing helix chain 'A' and resid 377 through 416 removed outlier: 3.779A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 663 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: 0.92 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.37: 983 1.37 - 1.55: 2141 1.55 - 1.73: 0 1.73 - 1.92: 30 1.92 - 2.10: 1 Bond restraints: 3155 Sorted by residual: bond pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 2.054 2.101 -0.047 2.00e-02 2.50e+03 5.52e+00 bond pdb=" C EFC A 385 " pdb=" O EFC A 385 " ideal model delta sigma weight residual 1.231 1.185 0.046 2.00e-02 2.50e+03 5.20e+00 bond pdb=" C1 TB1 A 501 " pdb=" C4 TB1 A 501 " ideal model delta sigma weight residual 1.503 1.528 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C2 EFC A 385 " pdb=" F2 EFC A 385 " ideal model delta sigma weight residual 1.388 1.364 0.024 2.00e-02 2.50e+03 1.40e+00 bond pdb=" C1 EFC A 385 " pdb=" C2 EFC A 385 " ideal model delta sigma weight residual 1.506 1.526 -0.020 2.00e-02 2.50e+03 1.05e+00 ... (remaining 3150 not shown) Histogram of bond angle deviations from ideal: 100.74 - 106.84: 97 106.84 - 112.94: 1769 112.94 - 119.04: 775 119.04 - 125.14: 1632 125.14 - 131.23: 30 Bond angle restraints: 4303 Sorted by residual: angle pdb=" CB EFC A 385 " pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " ideal model delta sigma weight residual 101.65 110.59 -8.94 3.00e+00 1.11e-01 8.88e+00 angle pdb=" C LEU A 245 " pdb=" N VAL A 246 " pdb=" CA VAL A 246 " ideal model delta sigma weight residual 122.97 120.65 2.32 9.80e-01 1.04e+00 5.63e+00 angle pdb=" O1 TB1 A 501 " pdb=" C9 TB1 A 501 " pdb=" O5 TB1 A 501 " ideal model delta sigma weight residual 126.71 119.71 7.00 3.00e+00 1.11e-01 5.44e+00 angle pdb=" O3 TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" O4 TB1 A 501 " ideal model delta sigma weight residual 126.45 119.88 6.57 3.00e+00 1.11e-01 4.80e+00 angle pdb=" SG EFC A 385 " pdb=" SD EFC A 385 " pdb=" C1 EFC A 385 " ideal model delta sigma weight residual 103.98 110.34 -6.36 3.00e+00 1.11e-01 4.50e+00 ... (remaining 4298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 1749 17.49 - 34.98: 82 34.98 - 52.47: 14 52.47 - 69.96: 3 69.96 - 87.46: 2 Dihedral angle restraints: 1850 sinusoidal: 672 harmonic: 1178 Sorted by residual: dihedral pdb=" CB MET A 59 " pdb=" CG MET A 59 " pdb=" SD MET A 59 " pdb=" CE MET A 59 " ideal model delta sinusoidal sigma weight residual 180.00 122.19 57.81 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB MET A 194 " pdb=" CG MET A 194 " pdb=" SD MET A 194 " pdb=" CE MET A 194 " ideal model delta sinusoidal sigma weight residual 180.00 123.09 56.91 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ARG A 105 " pdb=" CB ARG A 105 " pdb=" CG ARG A 105 " pdb=" CD ARG A 105 " ideal model delta sinusoidal sigma weight residual -180.00 -135.03 -44.97 3 1.50e+01 4.44e-03 8.09e+00 ... (remaining 1847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 344 0.028 - 0.055: 127 0.055 - 0.083: 45 0.083 - 0.111: 19 0.111 - 0.138: 2 Chirality restraints: 537 Sorted by residual: chirality pdb=" C7 TB1 A 501 " pdb=" N TB1 A 501 " pdb=" C10 TB1 A 501 " pdb=" C11 TB1 A 501 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA PRO A 45 " pdb=" N PRO A 45 " pdb=" C PRO A 45 " pdb=" CB PRO A 45 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.13e-01 chirality pdb=" CA MET A 59 " pdb=" N MET A 59 " pdb=" C MET A 59 " pdb=" CB MET A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.66e-01 ... (remaining 534 not shown) Planarity restraints: 532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 44 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 45 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 355 " -0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO A 356 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 356 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 356 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 376 " 0.016 5.00e-02 4.00e+02 2.38e-02 9.04e-01 pdb=" N PRO A 377 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 377 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 377 " 0.013 5.00e-02 4.00e+02 ... (remaining 529 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 826 2.81 - 3.33: 3292 3.33 - 3.85: 4685 3.85 - 4.38: 5619 4.38 - 4.90: 9592 Nonbonded interactions: 24014 Sorted by model distance: nonbonded pdb=" N TB1 A 501 " pdb=" O1 TB1 A 501 " model vdw 2.285 2.520 nonbonded pdb=" OG1 THR A 92 " pdb="NA NA A 503 " model vdw 2.348 2.470 nonbonded pdb=" OD1 ASN A 378 " pdb=" N VAL A 379 " model vdw 2.414 2.520 nonbonded pdb=" O VAL A 346 " pdb=" OG SER A 349 " model vdw 2.444 2.440 nonbonded pdb=" O ASN A 401 " pdb="NA NA A 502 " model vdw 2.463 2.470 ... (remaining 24009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.290 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: 11.450 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 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 0.047 3155 Z= 0.162 Angle : 0.498 8.940 4303 Z= 0.234 Chirality : 0.035 0.138 537 Planarity : 0.003 0.030 532 Dihedral : 10.716 87.456 1104 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: 2.01 (0.39), residues: 411 helix: 1.51 (0.26), residues: 331 sheet: None (None), residues: 0 loop : 0.92 (0.75), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 219 PHE 0.005 0.001 PHE A 261 TYR 0.008 0.001 TYR A 7 ARG 0.002 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.340 Fit side-chains REVERT: A 108 ASN cc_start: 0.8987 (t0) cc_final: 0.8729 (t0) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 1.0819 time to fit residues: 59.0867 Evaluate side-chains 33 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.0670 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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: 0.8484 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3155 Z= 0.199 Angle : 0.557 4.868 4303 Z= 0.302 Chirality : 0.039 0.186 537 Planarity : 0.004 0.029 532 Dihedral : 7.816 76.757 459 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.27 % Allowed : 7.62 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.40), residues: 411 helix: 2.06 (0.26), residues: 348 sheet: None (None), residues: 0 loop : 0.69 (0.79), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 114 PHE 0.010 0.001 PHE A 323 TYR 0.014 0.001 TYR A 89 ARG 0.004 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.340 Fit side-chains REVERT: A 48 ASP cc_start: 0.8211 (m-30) cc_final: 0.7944 (m-30) REVERT: A 311 MET cc_start: 0.7934 (mmt) cc_final: 0.7705 (mmm) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 1.1869 time to fit residues: 57.4742 Evaluate side-chains 38 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.8499 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3155 Z= 0.210 Angle : 0.519 5.883 4303 Z= 0.273 Chirality : 0.038 0.128 537 Planarity : 0.004 0.028 532 Dihedral : 7.060 66.161 459 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 2.54 % Allowed : 12.06 % Favored : 85.40 % 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: 2.79 (0.41), residues: 411 helix: 2.03 (0.27), residues: 356 sheet: None (None), residues: 0 loop : 0.87 (0.86), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.006 0.001 PHE A 156 TYR 0.010 0.001 TYR A 236 ARG 0.004 0.001 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.334 Fit side-chains REVERT: A 311 MET cc_start: 0.7980 (mmt) cc_final: 0.7660 (mmm) REVERT: A 401 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6418 (m-40) outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 1.1800 time to fit residues: 56.1858 Evaluate side-chains 40 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 401 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.0170 chunk 39 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- 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: 0.8502 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3155 Z= 0.217 Angle : 0.524 5.157 4303 Z= 0.270 Chirality : 0.038 0.154 537 Planarity : 0.004 0.027 532 Dihedral : 6.850 61.867 459 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.22 % Allowed : 14.29 % Favored : 83.49 % 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: 2.87 (0.41), residues: 411 helix: 2.13 (0.27), residues: 353 sheet: None (None), residues: 0 loop : 0.63 (0.82), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 114 PHE 0.007 0.001 PHE A 156 TYR 0.009 0.001 TYR A 236 ARG 0.002 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.344 Fit side-chains REVERT: A 311 MET cc_start: 0.7992 (mmt) cc_final: 0.7700 (mmm) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 1.1830 time to fit residues: 54.9015 Evaluate side-chains 41 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 10 optimal weight: 0.0060 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 338 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3155 Z= 0.161 Angle : 0.490 4.925 4303 Z= 0.249 Chirality : 0.036 0.146 537 Planarity : 0.003 0.028 532 Dihedral : 6.808 62.103 459 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.49 % Allowed : 13.97 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.41), residues: 411 helix: 2.24 (0.28), residues: 351 sheet: None (None), residues: 0 loop : 0.58 (0.81), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.007 0.001 PHE A 156 TYR 0.007 0.001 TYR A 236 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.283 Fit side-chains REVERT: A 311 MET cc_start: 0.7965 (mmt) cc_final: 0.7655 (mmt) REVERT: A 334 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8525 (p) outliers start: 11 outliers final: 3 residues processed: 43 average time/residue: 1.2390 time to fit residues: 54.8230 Evaluate side-chains 39 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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: 0.8453 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3155 Z= 0.177 Angle : 0.509 7.600 4303 Z= 0.253 Chirality : 0.037 0.139 537 Planarity : 0.003 0.027 532 Dihedral : 6.786 63.355 459 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.17 % Allowed : 15.24 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.41), residues: 411 helix: 2.23 (0.28), residues: 351 sheet: None (None), residues: 0 loop : 0.64 (0.80), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 219 PHE 0.006 0.001 PHE A 156 TYR 0.008 0.001 TYR A 236 ARG 0.001 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.586 Fit side-chains REVERT: A 48 ASP cc_start: 0.8015 (m-30) cc_final: 0.7776 (m-30) REVERT: A 311 MET cc_start: 0.7924 (mmt) cc_final: 0.7588 (mmt) REVERT: A 334 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8528 (p) REVERT: A 411 ILE cc_start: 0.8536 (mm) cc_final: 0.8335 (mt) outliers start: 10 outliers final: 7 residues processed: 47 average time/residue: 1.1733 time to fit residues: 56.9624 Evaluate side-chains 46 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 0.0070 chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3155 Z= 0.178 Angle : 0.523 7.050 4303 Z= 0.259 Chirality : 0.037 0.141 537 Planarity : 0.003 0.027 532 Dihedral : 6.702 63.209 459 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.81 % Allowed : 16.19 % Favored : 80.00 % 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: 2.95 (0.42), residues: 411 helix: 2.15 (0.28), residues: 356 sheet: None (None), residues: 0 loop : 0.74 (0.87), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.007 0.001 PHE A 156 TYR 0.008 0.001 TYR A 236 ARG 0.001 0.000 ARG A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.326 Fit side-chains REVERT: A 48 ASP cc_start: 0.8028 (m-30) cc_final: 0.7776 (m-30) REVERT: A 311 MET cc_start: 0.7908 (mmt) cc_final: 0.7578 (mmt) REVERT: A 334 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8546 (p) outliers start: 12 outliers final: 6 residues processed: 47 average time/residue: 1.1931 time to fit residues: 57.7753 Evaluate side-chains 42 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 394 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3155 Z= 0.193 Angle : 0.547 6.867 4303 Z= 0.274 Chirality : 0.037 0.141 537 Planarity : 0.003 0.027 532 Dihedral : 6.670 63.159 459 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.81 % Allowed : 15.56 % Favored : 80.63 % 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: 2.97 (0.42), residues: 411 helix: 2.17 (0.28), residues: 356 sheet: None (None), residues: 0 loop : 0.75 (0.87), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 32 PHE 0.006 0.001 PHE A 156 TYR 0.008 0.001 TYR A 299 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.343 Fit side-chains REVERT: A 48 ASP cc_start: 0.8029 (m-30) cc_final: 0.7777 (m-30) REVERT: A 311 MET cc_start: 0.7906 (mmt) cc_final: 0.7572 (mmt) REVERT: A 334 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8548 (p) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 1.1717 time to fit residues: 55.5921 Evaluate side-chains 44 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.8463 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3155 Z= 0.200 Angle : 0.556 7.084 4303 Z= 0.279 Chirality : 0.037 0.142 537 Planarity : 0.004 0.037 532 Dihedral : 6.615 62.963 459 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.17 % Allowed : 16.51 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.42), residues: 411 helix: 2.12 (0.28), residues: 356 sheet: None (None), residues: 0 loop : 0.72 (0.86), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 156 TYR 0.008 0.001 TYR A 299 ARG 0.005 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 35 time to evaluate : 0.337 Fit side-chains REVERT: A 48 ASP cc_start: 0.8050 (m-30) cc_final: 0.7799 (m-30) REVERT: A 311 MET cc_start: 0.7897 (mmt) cc_final: 0.7592 (mmm) REVERT: A 334 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8588 (p) outliers start: 10 outliers final: 8 residues processed: 39 average time/residue: 1.2409 time to fit residues: 49.9264 Evaluate side-chains 44 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8470 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3155 Z= 0.203 Angle : 0.554 7.474 4303 Z= 0.278 Chirality : 0.037 0.144 537 Planarity : 0.004 0.030 532 Dihedral : 6.573 62.871 459 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.54 % Allowed : 17.14 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.42), residues: 411 helix: 2.08 (0.28), residues: 356 sheet: None (None), residues: 0 loop : 0.70 (0.86), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.007 0.001 PHE A 156 TYR 0.008 0.001 TYR A 236 ARG 0.007 0.001 ARG A 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.370 Fit side-chains REVERT: A 48 ASP cc_start: 0.8052 (m-30) cc_final: 0.7795 (m-30) REVERT: A 334 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8592 (p) outliers start: 8 outliers final: 7 residues processed: 40 average time/residue: 1.1676 time to fit residues: 48.2722 Evaluate side-chains 43 residues out of total 322 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 416 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.111341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.074875 restraints weight = 5743.273| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.48 r_work: 0.2945 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3155 Z= 0.208 Angle : 0.552 6.215 4303 Z= 0.282 Chirality : 0.037 0.145 537 Planarity : 0.004 0.028 532 Dihedral : 6.551 62.840 459 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.86 % Allowed : 18.10 % Favored : 79.05 % 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: 2.78 (0.42), residues: 411 helix: 2.05 (0.28), residues: 354 sheet: None (None), residues: 0 loop : 0.65 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 40 PHE 0.006 0.001 PHE A 156 TYR 0.009 0.001 TYR A 236 ARG 0.007 0.001 ARG A 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1651.16 seconds wall clock time: 29 minutes 58.39 seconds (1798.39 seconds total)