Starting phenix.real_space_refine on Sun Mar 10 15:51:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/03_2024/7tx6_26155_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/03_2024/7tx6_26155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/03_2024/7tx6_26155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/03_2024/7tx6_26155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/03_2024/7tx6_26155_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tx6_26155/03_2024/7tx6_26155_updated.pdb" } resolution = 3.3 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= 0.002 sd= 0.033 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 10 5.16 5 C 2122 2.51 5 N 503 2.21 5 O 534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 67": "OE1" <-> "OE2" 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: 3169 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3169 Unusual residues: {'AJP': 1, 'MTX': 1} Classifications: {'peptide': 398, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 13, 'TRANS': 384, None: 2} Not linked: pdbres="GLN A 459 " pdbres="MTX A2644 " Not linked: pdbres="MTX A2644 " pdbres="AJP A2501 " Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'MTX:plan-3': 1, 'ARG:plan': 10, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 65 Time building chain proxies: 2.73, per 1000 atoms: 0.86 Number of scatterers: 3169 At special positions: 0 Unit cell: (72.36, 61.56, 79.92, 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 10 16.00 O 534 8.00 N 503 7.00 C 2122 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.31 Conformation dependent library (CDL) restraints added in 676.0 milliseconds 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 24 through 39 removed outlier: 3.894A pdb=" N LEU A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 68 through 89 removed outlier: 3.835A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.986A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 Processing helix chain 'A' and resid 116 through 131 Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.580A pdb=" N TYR A 136 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 137 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 143 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 176 removed outlier: 5.402A pdb=" N GLN A 150 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER A 168 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A 174 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR A 176 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.616A pdb=" N PHE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.936A pdb=" N ARG A 263 " --> pdb=" O GLY A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 3.573A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 327 removed outlier: 4.015A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 333 removed outlier: 4.097A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 336 through 355 Processing helix chain 'A' and resid 359 through 390 removed outlier: 5.284A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 4.095A pdb=" N SER A 389 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 390 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 418 removed outlier: 3.726A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 458 224 hydrogen bonds defined for protein. 519 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: 0.80 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 446 1.31 - 1.43: 993 1.43 - 1.56: 1806 1.56 - 1.68: 5 1.68 - 1.81: 15 Bond restraints: 3265 Sorted by residual: bond pdb=" C VAL A 410 " pdb=" N LYS A 411 " ideal model delta sigma weight residual 1.335 1.449 -0.114 1.31e-02 5.83e+03 7.53e+01 bond pdb=" C4 MTX A2644 " pdb=" NA4 MTX A2644 " ideal model delta sigma weight residual 1.328 1.449 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N MTX A2644 " pdb=" C MTX A2644 " ideal model delta sigma weight residual 1.339 1.455 -0.116 2.00e-02 2.50e+03 3.36e+01 bond pdb=" C2 MTX A2644 " pdb=" NA2 MTX A2644 " ideal model delta sigma weight residual 1.341 1.451 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C14 MTX A2644 " pdb=" N10 MTX A2644 " ideal model delta sigma weight residual 1.368 1.453 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 3260 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.41: 78 106.41 - 113.31: 1823 113.31 - 120.21: 1248 120.21 - 127.12: 1294 127.12 - 134.02: 37 Bond angle restraints: 4480 Sorted by residual: angle pdb=" C VAL A 410 " pdb=" N LYS A 411 " pdb=" CA LYS A 411 " ideal model delta sigma weight residual 120.28 114.07 6.21 1.34e+00 5.57e-01 2.15e+01 angle pdb=" CA ILE A 48 " pdb=" C ILE A 48 " pdb=" O ILE A 48 " ideal model delta sigma weight residual 121.17 116.45 4.72 1.06e+00 8.90e-01 1.98e+01 angle pdb=" CA ILE A 417 " pdb=" C ILE A 417 " pdb=" O ILE A 417 " ideal model delta sigma weight residual 120.85 116.34 4.51 1.06e+00 8.90e-01 1.81e+01 angle pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 120.57 116.30 4.27 1.07e+00 8.73e-01 1.59e+01 angle pdb=" N PHE A 416 " pdb=" CA PHE A 416 " pdb=" C PHE A 416 " ideal model delta sigma weight residual 111.28 106.94 4.34 1.09e+00 8.42e-01 1.58e+01 ... (remaining 4475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 1837 24.23 - 48.46: 81 48.46 - 72.69: 8 72.69 - 96.92: 8 96.92 - 121.14: 8 Dihedral angle restraints: 1942 sinusoidal: 769 harmonic: 1173 Sorted by residual: dihedral pdb=" N MTX A2644 " pdb=" C MTX A2644 " pdb=" CA MTX A2644 " pdb=" CB MTX A2644 " ideal model delta harmonic sigma weight residual 122.80 10.81 111.99 0 2.50e+00 1.60e-01 2.01e+03 dihedral pdb=" C MTX A2644 " pdb=" N MTX A2644 " pdb=" CA MTX A2644 " pdb=" CB MTX A2644 " ideal model delta harmonic sigma weight residual -122.60 -172.60 50.00 0 2.50e+00 1.60e-01 4.00e+02 dihedral pdb=" C02 AJP A2501 " pdb=" C85 AJP A2501 " pdb=" O84 AJP A2501 " pdb=" C05 AJP A2501 " ideal model delta sinusoidal sigma weight residual -57.60 63.54 -121.14 1 3.00e+01 1.11e-03 1.62e+01 ... (remaining 1939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 469 0.070 - 0.141: 50 0.141 - 0.211: 12 0.211 - 0.281: 6 0.281 - 0.352: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" C11 AJP A2501 " pdb=" C10 AJP A2501 " pdb=" C12 AJP A2501 " pdb=" C16 AJP A2501 " both_signs ideal model delta sigma weight residual False 2.20 2.56 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C15 AJP A2501 " pdb=" C14 AJP A2501 " pdb=" C16 AJP A2501 " pdb=" C20 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.42 -2.70 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C23 AJP A2501 " pdb=" C22 AJP A2501 " pdb=" C24 AJP A2501 " pdb=" O25 AJP A2501 " both_signs ideal model delta sigma weight residual False -2.50 -2.78 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 535 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 62 " -0.016 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C GLU A 62 " 0.053 2.00e-02 2.50e+03 pdb=" O GLU A 62 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN A 63 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 93 " -0.047 5.00e-02 4.00e+02 7.08e-02 8.03e+00 pdb=" N PRO A 94 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 68 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.50e+00 pdb=" C ILE A 68 " -0.032 2.00e-02 2.50e+03 pdb=" O ILE A 68 " 0.012 2.00e-02 2.50e+03 pdb=" N THR A 69 " 0.011 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1094 2.84 - 3.36: 3440 3.36 - 3.87: 5073 3.87 - 4.39: 5561 4.39 - 4.90: 9416 Nonbonded interactions: 24584 Sorted by model distance: nonbonded pdb=" OD1 ASN A 300 " pdb=" N SER A 301 " model vdw 2.327 2.520 nonbonded pdb=" OD1 ASP A 56 " pdb=" N LYS A 57 " model vdw 2.386 2.520 nonbonded pdb=" O SER A 102 " pdb=" OG SER A 105 " model vdw 2.421 2.440 nonbonded pdb=" O LEU A 440 " pdb=" OG SER A 443 " model vdw 2.482 2.440 nonbonded pdb=" O THR A 87 " pdb=" O LEU A 90 " model vdw 2.484 3.040 ... (remaining 24579 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.770 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.960 Find NCS groups from input model: 0.080 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 : 0.008 0.121 3265 Z= 0.500 Angle : 0.902 7.786 4480 Z= 0.564 Chirality : 0.055 0.352 538 Planarity : 0.005 0.071 529 Dihedral : 17.014 121.145 1188 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.62 % Allowed : 6.88 % Favored : 92.50 % Cbeta Deviations : 0.27 % 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: 2.51 (0.42), residues: 394 helix: 2.27 (0.28), residues: 313 sheet: None (None), residues: 0 loop : -0.83 (0.73), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 355 PHE 0.010 0.001 PHE A 405 TYR 0.013 0.001 TYR A 438 ARG 0.002 0.000 ARG A 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 282 TYR cc_start: 0.8319 (m-80) cc_final: 0.8030 (m-10) REVERT: A 287 TYR cc_start: 0.8372 (m-80) cc_final: 0.7722 (m-80) REVERT: A 363 TRP cc_start: 0.2795 (m100) cc_final: 0.2102 (m100) REVERT: A 395 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7789 (tt) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.1533 time to fit residues: 19.2046 Evaluate side-chains 94 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3265 Z= 0.198 Angle : 0.723 17.822 4480 Z= 0.339 Chirality : 0.049 0.709 538 Planarity : 0.006 0.064 529 Dihedral : 10.668 87.847 571 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.88 % Allowed : 15.62 % Favored : 82.50 % Cbeta Deviations : 0.27 % 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: 2.09 (0.42), residues: 394 helix: 2.00 (0.28), residues: 311 sheet: None (None), residues: 0 loop : -0.99 (0.71), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 355 PHE 0.011 0.001 PHE A 432 TYR 0.015 0.001 TYR A 305 ARG 0.001 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 TRP cc_start: 0.2837 (m100) cc_final: 0.2044 (m100) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 0.1463 time to fit residues: 16.6284 Evaluate side-chains 88 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 375 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3265 Z= 0.202 Angle : 0.646 15.961 4480 Z= 0.310 Chirality : 0.047 0.706 538 Planarity : 0.006 0.060 529 Dihedral : 7.286 59.212 569 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 18.75 % Favored : 79.38 % Cbeta Deviations : 0.27 % 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 (0.42), residues: 394 helix: 1.63 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -0.85 (0.71), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 PHE 0.010 0.001 PHE A 34 TYR 0.017 0.001 TYR A 305 ARG 0.003 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8212 (tt0) REVERT: A 115 SER cc_start: 0.5975 (OUTLIER) cc_final: 0.5122 (p) REVERT: A 119 MET cc_start: 0.8215 (mmm) cc_final: 0.7968 (mmm) REVERT: A 133 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7372 (ptt180) REVERT: A 363 TRP cc_start: 0.2989 (m100) cc_final: 0.2411 (m100) REVERT: A 395 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7762 (tt) outliers start: 6 outliers final: 3 residues processed: 86 average time/residue: 0.1400 time to fit residues: 14.9128 Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3265 Z= 0.211 Angle : 0.630 16.354 4480 Z= 0.304 Chirality : 0.048 0.734 538 Planarity : 0.005 0.057 529 Dihedral : 6.804 56.820 569 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 20.94 % Favored : 76.88 % Cbeta Deviations : 0.27 % 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: 1.54 (0.42), residues: 394 helix: 1.53 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.01 (0.70), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 PHE 0.007 0.001 PHE A 432 TYR 0.012 0.001 TYR A 438 ARG 0.003 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8244 (tt0) REVERT: A 115 SER cc_start: 0.6122 (OUTLIER) cc_final: 0.5416 (p) REVERT: A 133 ARG cc_start: 0.8091 (ttp-170) cc_final: 0.7401 (ptt180) REVERT: A 363 TRP cc_start: 0.3219 (m100) cc_final: 0.2533 (m100) REVERT: A 395 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7817 (tt) outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 0.1420 time to fit residues: 14.5638 Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3265 Z= 0.174 Angle : 0.633 15.770 4480 Z= 0.295 Chirality : 0.047 0.729 538 Planarity : 0.005 0.056 529 Dihedral : 6.779 59.582 569 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 21.88 % Favored : 76.25 % 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: 1.64 (0.43), residues: 394 helix: 1.61 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -1.04 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.026 0.001 PHE A 322 TYR 0.010 0.001 TYR A 438 ARG 0.003 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8622 (tm-30) cc_final: 0.7907 (tt0) REVERT: A 102 SER cc_start: 0.8991 (m) cc_final: 0.8479 (p) REVERT: A 115 SER cc_start: 0.5899 (OUTLIER) cc_final: 0.4983 (p) REVERT: A 119 MET cc_start: 0.8169 (mmm) cc_final: 0.7873 (mmm) REVERT: A 133 ARG cc_start: 0.8110 (ttp-170) cc_final: 0.7469 (ptt180) REVERT: A 363 TRP cc_start: 0.3349 (m100) cc_final: 0.2615 (m100) REVERT: A 395 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7825 (tt) outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 0.1411 time to fit residues: 14.8311 Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3265 Z= 0.184 Angle : 0.631 15.880 4480 Z= 0.296 Chirality : 0.047 0.737 538 Planarity : 0.005 0.055 529 Dihedral : 6.571 58.960 569 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.19 % Allowed : 21.88 % Favored : 75.94 % 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: 1.65 (0.43), residues: 394 helix: 1.61 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.98 (0.71), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.017 0.001 PHE A 322 TYR 0.011 0.001 TYR A 438 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8622 (tm-30) cc_final: 0.7890 (tt0) REVERT: A 102 SER cc_start: 0.8955 (m) cc_final: 0.8461 (p) REVERT: A 115 SER cc_start: 0.5942 (OUTLIER) cc_final: 0.5054 (p) REVERT: A 119 MET cc_start: 0.8161 (mmm) cc_final: 0.7907 (mmm) REVERT: A 133 ARG cc_start: 0.8036 (ttp-170) cc_final: 0.7282 (ptt180) REVERT: A 363 TRP cc_start: 0.3297 (m100) cc_final: 0.3021 (m100) REVERT: A 395 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7783 (tt) outliers start: 7 outliers final: 4 residues processed: 82 average time/residue: 0.1392 time to fit residues: 14.1684 Evaluate side-chains 85 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.0060 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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: 0.7462 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3265 Z= 0.149 Angle : 0.629 16.158 4480 Z= 0.284 Chirality : 0.046 0.713 538 Planarity : 0.005 0.054 529 Dihedral : 6.501 60.970 569 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.56 % Allowed : 22.19 % Favored : 76.25 % Cbeta Deviations : 0.27 % 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: 1.72 (0.43), residues: 394 helix: 1.70 (0.29), residues: 319 sheet: None (None), residues: 0 loop : -1.24 (0.72), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 363 HIS 0.001 0.000 HIS A 358 PHE 0.014 0.001 PHE A 322 TYR 0.008 0.001 TYR A 438 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8596 (tm-30) cc_final: 0.7835 (tt0) REVERT: A 102 SER cc_start: 0.8917 (m) cc_final: 0.8506 (p) REVERT: A 363 TRP cc_start: 0.3262 (m100) cc_final: 0.2964 (m100) REVERT: A 395 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7778 (tt) outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 0.1275 time to fit residues: 13.5467 Evaluate side-chains 87 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 395 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3265 Z= 0.190 Angle : 0.656 16.015 4480 Z= 0.303 Chirality : 0.048 0.769 538 Planarity : 0.005 0.053 529 Dihedral : 6.432 55.879 569 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 21.88 % Favored : 75.94 % 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: 1.77 (0.43), residues: 394 helix: 1.71 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.96 (0.72), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.027 0.001 PHE A 141 TYR 0.011 0.001 TYR A 282 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8623 (tm-30) cc_final: 0.8070 (tt0) REVERT: A 102 SER cc_start: 0.8914 (m) cc_final: 0.8659 (p) REVERT: A 119 MET cc_start: 0.8117 (mmm) cc_final: 0.7834 (mmm) REVERT: A 133 ARG cc_start: 0.8057 (ttp-170) cc_final: 0.7444 (ptt180) REVERT: A 363 TRP cc_start: 0.3289 (m100) cc_final: 0.2954 (m100) outliers start: 7 outliers final: 4 residues processed: 83 average time/residue: 0.1412 time to fit residues: 14.4972 Evaluate side-chains 86 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 82 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7530 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3265 Z= 0.215 Angle : 0.697 16.329 4480 Z= 0.319 Chirality : 0.048 0.744 538 Planarity : 0.005 0.053 529 Dihedral : 6.351 56.761 569 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 22.19 % Favored : 75.94 % Cbeta Deviations : 0.27 % 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: 1.70 (0.43), residues: 394 helix: 1.63 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.91 (0.75), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 334 HIS 0.003 0.001 HIS A 358 PHE 0.010 0.001 PHE A 322 TYR 0.011 0.001 TYR A 438 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8638 (tm-30) cc_final: 0.7923 (tt0) REVERT: A 102 SER cc_start: 0.8919 (m) cc_final: 0.8528 (p) REVERT: A 119 MET cc_start: 0.8154 (mmm) cc_final: 0.7889 (mmm) REVERT: A 133 ARG cc_start: 0.7951 (ttp-170) cc_final: 0.7269 (ptt180) REVERT: A 363 TRP cc_start: 0.3345 (m100) cc_final: 0.2989 (m100) outliers start: 6 outliers final: 6 residues processed: 86 average time/residue: 0.1376 time to fit residues: 14.6655 Evaluate side-chains 90 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 1 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3265 Z= 0.203 Angle : 0.702 15.743 4480 Z= 0.319 Chirality : 0.047 0.722 538 Planarity : 0.005 0.052 529 Dihedral : 6.395 57.575 569 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.88 % Allowed : 22.50 % Favored : 75.62 % 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: 1.74 (0.43), residues: 394 helix: 1.66 (0.29), residues: 317 sheet: None (None), residues: 0 loop : -0.88 (0.75), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 334 HIS 0.002 0.001 HIS A 358 PHE 0.029 0.001 PHE A 141 TYR 0.011 0.001 TYR A 438 ARG 0.005 0.000 ARG A 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 788 Ramachandran restraints generated. 394 Oldfield, 0 Emsley, 394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.8625 (tm-30) cc_final: 0.7918 (tt0) REVERT: A 102 SER cc_start: 0.8911 (m) cc_final: 0.8519 (p) REVERT: A 119 MET cc_start: 0.8163 (mmm) cc_final: 0.7881 (mmm) REVERT: A 363 TRP cc_start: 0.3328 (m100) cc_final: 0.2968 (m100) outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.1345 time to fit residues: 14.5469 Evaluate side-chains 89 residues out of total 342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3737 r_free = 0.3737 target = 0.140686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.129762 restraints weight = 5264.493| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.44 r_work: 0.3503 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3265 Z= 0.195 Angle : 0.704 15.699 4480 Z= 0.319 Chirality : 0.047 0.725 538 Planarity : 0.005 0.052 529 Dihedral : 6.406 57.635 569 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.19 % Allowed : 22.19 % Favored : 75.62 % 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: 1.74 (0.43), residues: 394 helix: 1.67 (0.29), residues: 316 sheet: None (None), residues: 0 loop : -0.88 (0.74), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 363 HIS 0.002 0.001 HIS A 358 PHE 0.010 0.001 PHE A 322 TYR 0.010 0.001 TYR A 438 ARG 0.004 0.000 ARG A 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1089.92 seconds wall clock time: 20 minutes 7.68 seconds (1207.68 seconds total)