Starting phenix.real_space_refine on Fri Mar 15 12:38:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unm_26627/03_2024/7unm_26627.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unm_26627/03_2024/7unm_26627.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unm_26627/03_2024/7unm_26627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unm_26627/03_2024/7unm_26627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unm_26627/03_2024/7unm_26627.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unm_26627/03_2024/7unm_26627.pdb" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.034 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 K 5 8.98 5 S 38 5.16 5 C 3764 2.51 5 N 942 2.21 5 O 1025 1.98 5 H 5920 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11694 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 5817 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 16, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 5817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 5817 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 16, 'TRANS': 351} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Time building chain proxies: 5.54, per 1000 atoms: 0.47 Number of scatterers: 11694 At special positions: 0 Unit cell: (106.25, 67.15, 80.75, 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) K 5 19.00 S 38 16.00 O 1025 8.00 N 942 7.00 C 3764 6.00 H 5920 1.00 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: 9.93 Conformation dependent library (CDL) restraints added in 1.2 seconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'B' and resid 33 through 51 removed outlier: 4.383A pdb=" N MET B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.350A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 67 through 103 removed outlier: 3.593A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.556A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 257 through 284 removed outlier: 3.523A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 4.029A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 302 through 333 Proline residue: B 308 - end of helix removed outlier: 3.739A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.548A pdb=" N ALA B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 400 removed outlier: 3.738A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.975A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.631A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 removed outlier: 3.644A pdb=" N GLY B 467 " --> pdb=" O ARG B 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 51 removed outlier: 4.379A pdb=" N MET A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.363A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 67 through 103 removed outlier: 3.596A pdb=" N GLN A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.557A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 257 through 284 removed outlier: 3.522A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 4.029A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 302 through 333 Proline residue: A 308 - end of helix removed outlier: 3.742A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.555A pdb=" N ALA A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 400 removed outlier: 3.736A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.978A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.647A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 removed outlier: 3.647A pdb=" N GLY A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1350 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: 4.26 Time building geometry restraints manager: 10.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5902 1.03 - 1.23: 18 1.23 - 1.42: 2390 1.42 - 1.61: 3400 1.61 - 1.81: 58 Bond restraints: 11768 Sorted by residual: bond pdb=" C VAL A 272 " pdb=" O VAL A 272 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.13e-02 7.83e+03 4.88e-01 bond pdb=" C VAL B 272 " pdb=" O VAL B 272 " ideal model delta sigma weight residual 1.237 1.244 -0.007 1.13e-02 7.83e+03 4.28e-01 bond pdb=" CB THR A 362 " pdb=" CG2 THR A 362 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.20e-01 bond pdb=" CG LEU A 278 " pdb=" CD1 LEU A 278 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.08e-01 bond pdb=" CG LEU B 278 " pdb=" CD1 LEU B 278 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.07e-01 ... (remaining 11763 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.17: 268 107.17 - 113.87: 14077 113.87 - 120.57: 4147 120.57 - 127.27: 2772 127.27 - 133.96: 66 Bond angle restraints: 21330 Sorted by residual: angle pdb=" C HIS B 400 " pdb=" N GLN B 401 " pdb=" CA GLN B 401 " ideal model delta sigma weight residual 120.38 122.72 -2.34 1.37e+00 5.33e-01 2.92e+00 angle pdb=" C HIS A 400 " pdb=" N GLN A 401 " pdb=" CA GLN A 401 " ideal model delta sigma weight residual 120.38 122.71 -2.33 1.46e+00 4.69e-01 2.54e+00 angle pdb=" C LEU A 123 " pdb=" CA LEU A 123 " pdb=" CB LEU A 123 " ideal model delta sigma weight residual 112.76 109.85 2.91 1.86e+00 2.89e-01 2.45e+00 angle pdb=" C LEU B 123 " pdb=" CA LEU B 123 " pdb=" CB LEU B 123 " ideal model delta sigma weight residual 112.76 109.91 2.85 1.86e+00 2.89e-01 2.34e+00 angle pdb=" CA ARG A 97 " pdb=" CB ARG A 97 " pdb=" CG ARG A 97 " ideal model delta sigma weight residual 114.10 117.07 -2.97 2.00e+00 2.50e-01 2.21e+00 ... (remaining 21325 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 5061 16.12 - 32.25: 356 32.25 - 48.37: 77 48.37 - 64.50: 42 64.50 - 80.62: 2 Dihedral angle restraints: 5538 sinusoidal: 2940 harmonic: 2598 Sorted by residual: dihedral pdb=" CA PHE A 99 " pdb=" C PHE A 99 " pdb=" N GLN A 100 " pdb=" CA GLN A 100 " ideal model delta harmonic sigma weight residual 180.00 155.85 24.15 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 156.17 23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA ASP B 283 " pdb=" C ASP B 283 " pdb=" N ASN B 284 " pdb=" CA ASN B 284 " ideal model delta harmonic sigma weight residual -180.00 -162.96 -17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 629 0.024 - 0.048: 180 0.048 - 0.072: 105 0.072 - 0.096: 47 0.096 - 0.120: 19 Chirality restraints: 980 Sorted by residual: chirality pdb=" CA ILE B 60 " pdb=" N ILE B 60 " pdb=" C ILE B 60 " pdb=" CB ILE B 60 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA ILE A 60 " pdb=" N ILE A 60 " pdb=" C ILE A 60 " pdb=" CB ILE A 60 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA PHE B 99 " pdb=" N PHE B 99 " pdb=" C PHE B 99 " pdb=" CB PHE B 99 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 977 not shown) Planarity restraints: 1678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 123 " 0.025 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 124 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 123 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO B 124 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 124 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 124 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 136 " -0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO A 137 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " -0.015 5.00e-02 4.00e+02 ... (remaining 1675 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 1548 2.27 - 2.99: 32756 2.99 - 3.71: 44560 3.71 - 4.42: 66753 4.42 - 5.14: 104491 Nonbonded interactions: 250108 Sorted by model distance: nonbonded pdb=" HE2 HIS A 95 " pdb=" OD1 ASN A 113 " model vdw 1.553 1.850 nonbonded pdb=" HE2 HIS B 95 " pdb=" OD1 ASN B 113 " model vdw 1.571 1.850 nonbonded pdb=" O PHE A 434 " pdb=" HG1 THR A 437 " model vdw 1.601 1.850 nonbonded pdb=" O PHE B 434 " pdb=" HG1 THR B 437 " model vdw 1.620 1.850 nonbonded pdb=" OD1 ASP A 266 " pdb=" HE1 TRP A 324 " model vdw 1.669 1.850 ... (remaining 250103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 476 or resid 601)) selection = chain 'B' } 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: 3.220 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: 0.190 Extract box with map and model: 12.160 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 42.430 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 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 0.021 5848 Z= 0.143 Angle : 0.433 3.970 7970 Z= 0.237 Chirality : 0.035 0.120 980 Planarity : 0.004 0.039 978 Dihedral : 11.230 80.620 2042 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 3.34 (0.33), residues: 728 helix: 2.50 (0.22), residues: 580 sheet: None (None), residues: 0 loop : 1.14 (0.58), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 394 HIS 0.002 0.000 HIS A 95 PHE 0.012 0.001 PHE A 310 TYR 0.006 0.001 TYR A 81 ARG 0.002 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 2.6176 time to fit residues: 314.7444 Evaluate side-chains 65 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 GLN A 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5848 Z= 0.238 Angle : 0.532 4.076 7970 Z= 0.289 Chirality : 0.037 0.129 980 Planarity : 0.004 0.042 978 Dihedral : 3.683 19.558 782 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.32 % Allowed : 11.45 % Favored : 88.23 % 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: 3.70 (0.32), residues: 728 helix: 2.82 (0.22), residues: 584 sheet: None (None), residues: 0 loop : 0.89 (0.59), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.002 PHE A 310 TYR 0.019 0.002 TYR B 313 ARG 0.010 0.000 ARG B 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 71 average time/residue: 1.8181 time to fit residues: 138.0788 Evaluate side-chains 63 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain A residue 131 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.8275 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5848 Z= 0.241 Angle : 0.506 3.954 7970 Z= 0.272 Chirality : 0.037 0.132 980 Planarity : 0.004 0.042 978 Dihedral : 3.712 19.445 782 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.29 % Allowed : 11.13 % Favored : 87.58 % 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: 3.77 (0.32), residues: 728 helix: 2.93 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.61 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 324 HIS 0.004 0.001 HIS A 328 PHE 0.025 0.001 PHE B 310 TYR 0.013 0.002 TYR A 125 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 70 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 2.1130 time to fit residues: 159.2562 Evaluate side-chains 67 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5848 Z= 0.237 Angle : 0.499 3.956 7970 Z= 0.268 Chirality : 0.037 0.144 980 Planarity : 0.004 0.043 978 Dihedral : 3.742 19.074 782 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.61 % Allowed : 11.94 % Favored : 86.45 % 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: 3.80 (0.32), residues: 728 helix: 2.96 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.61 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.022 0.001 PHE A 310 TYR 0.010 0.002 TYR B 125 ARG 0.001 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7243 (m-80) outliers start: 10 outliers final: 4 residues processed: 71 average time/residue: 2.0608 time to fit residues: 155.5087 Evaluate side-chains 61 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.0040 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5848 Z= 0.187 Angle : 0.481 3.955 7970 Z= 0.259 Chirality : 0.036 0.128 980 Planarity : 0.004 0.043 978 Dihedral : 3.689 18.832 782 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.77 % Allowed : 13.23 % Favored : 85.00 % 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: 3.93 (0.32), residues: 728 helix: 3.05 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.66 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.021 0.001 PHE B 310 TYR 0.009 0.002 TYR A 313 ARG 0.001 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.6913 (tp30) cc_final: 0.6677 (tp30) REVERT: B 127 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: A 127 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7255 (m-80) outliers start: 11 outliers final: 5 residues processed: 67 average time/residue: 1.9110 time to fit residues: 135.9072 Evaluate side-chains 68 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 292 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5848 Z= 0.248 Angle : 0.501 3.898 7970 Z= 0.270 Chirality : 0.037 0.137 980 Planarity : 0.004 0.042 978 Dihedral : 3.711 18.958 782 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.61 % Allowed : 13.39 % Favored : 85.00 % 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: 3.89 (0.32), residues: 728 helix: 3.03 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.63 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 324 HIS 0.005 0.001 HIS B 328 PHE 0.022 0.002 PHE B 310 TYR 0.012 0.002 TYR B 125 ARG 0.002 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: A 127 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7268 (m-80) outliers start: 10 outliers final: 6 residues processed: 63 average time/residue: 2.1633 time to fit residues: 144.3476 Evaluate side-chains 64 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 293 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.0870 chunk 69 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.0980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5848 Z= 0.152 Angle : 0.474 5.696 7970 Z= 0.253 Chirality : 0.035 0.121 980 Planarity : 0.004 0.045 978 Dihedral : 3.636 19.003 782 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.13 % Allowed : 14.03 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.14 (0.32), residues: 728 helix: 3.20 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.71 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 324 HIS 0.003 0.001 HIS A 328 PHE 0.021 0.001 PHE B 310 TYR 0.013 0.002 TYR B 125 ARG 0.001 0.000 ARG B 414 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.6944 (tp30) cc_final: 0.6668 (tp30) REVERT: B 127 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: A 127 PHE cc_start: 0.7607 (OUTLIER) cc_final: 0.7270 (m-80) outliers start: 7 outliers final: 4 residues processed: 70 average time/residue: 2.1531 time to fit residues: 159.5440 Evaluate side-chains 69 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5848 Z= 0.232 Angle : 0.503 5.891 7970 Z= 0.269 Chirality : 0.036 0.134 980 Planarity : 0.004 0.043 978 Dihedral : 3.659 19.003 782 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.97 % Allowed : 14.68 % Favored : 84.35 % 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: 4.08 (0.32), residues: 728 helix: 3.17 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.64 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 324 HIS 0.004 0.001 HIS A 328 PHE 0.021 0.001 PHE B 310 TYR 0.013 0.002 TYR A 125 ARG 0.001 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.6967 (tp30) cc_final: 0.6709 (tp30) REVERT: B 127 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7357 (m-80) REVERT: A 127 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7281 (m-80) outliers start: 6 outliers final: 3 residues processed: 60 average time/residue: 2.4266 time to fit residues: 153.4646 Evaluate side-chains 63 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5848 Z= 0.230 Angle : 0.506 6.588 7970 Z= 0.272 Chirality : 0.036 0.151 980 Planarity : 0.004 0.043 978 Dihedral : 3.700 19.387 782 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.97 % Allowed : 14.52 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.05 (0.32), residues: 728 helix: 3.16 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.60 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.005 0.001 HIS A 328 PHE 0.021 0.001 PHE B 310 TYR 0.010 0.002 TYR A 125 ARG 0.001 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7640 (OUTLIER) cc_final: 0.7336 (m-80) outliers start: 6 outliers final: 3 residues processed: 63 average time/residue: 2.3140 time to fit residues: 153.8688 Evaluate side-chains 64 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.0870 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 HIS ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5848 Z= 0.209 Angle : 0.499 6.737 7970 Z= 0.268 Chirality : 0.036 0.132 980 Planarity : 0.004 0.043 978 Dihedral : 3.690 19.381 782 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.48 % Allowed : 15.00 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.32), residues: 728 helix: 3.21 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.63 (0.57), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.021 0.001 PHE B 310 TYR 0.009 0.001 TYR A 125 ARG 0.001 0.000 ARG A 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 2.3793 time to fit residues: 151.1753 Evaluate side-chains 62 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 131 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.0370 chunk 50 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.119339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.080247 restraints weight = 26479.478| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.66 r_work: 0.3026 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5848 Z= 0.225 Angle : 0.505 6.420 7970 Z= 0.271 Chirality : 0.036 0.133 980 Planarity : 0.004 0.043 978 Dihedral : 3.690 19.517 782 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.65 % Allowed : 15.00 % Favored : 84.35 % 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: 4.14 (0.32), residues: 728 helix: 3.22 (0.22), residues: 582 sheet: None (None), residues: 0 loop : 0.61 (0.56), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.021 0.001 PHE B 310 TYR 0.009 0.001 TYR A 125 ARG 0.001 0.000 ARG A 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4443.26 seconds wall clock time: 78 minutes 9.71 seconds (4689.71 seconds total)