Starting phenix.real_space_refine on Thu Sep 26 01:10:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/09_2024/7unl_26626.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/09_2024/7unl_26626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/09_2024/7unl_26626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/09_2024/7unl_26626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/09_2024/7unl_26626.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7unl_26626/09_2024/7unl_26626.cif" } resolution = 2.45 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= 0.035 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 8 8.98 5 S 38 5.16 5 C 3754 2.51 5 N 938 2.21 5 O 1086 1.98 5 H 5900 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11724 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Time building chain proxies: 6.85, per 1000 atoms: 0.58 Number of scatterers: 11724 At special positions: 0 Unit cell: (104.55, 70.55, 78.2, 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 8 19.00 S 38 16.00 O 1086 8.00 N 938 7.00 C 3754 6.00 H 5900 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 905.6 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 89.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 66 through 102 Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 257 through 284 removed outlier: 5.037A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 306 through 332 removed outlier: 3.565A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 368 through 399 removed outlier: 3.711A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (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: 4.932A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.522A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 461 removed outlier: 4.520A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'B' and resid 33 through 49 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 66 through 102 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 257 through 284 removed outlier: 5.036A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.566A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 368 through 399 removed outlier: 3.710A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (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: 4.932A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.523A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 461 removed outlier: 4.521A pdb=" N VAL B 445 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N GLY B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 466 hydrogen bonds defined for protein. 1368 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: 4.10 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5882 1.03 - 1.22: 18 1.22 - 1.42: 2382 1.42 - 1.61: 3390 1.61 - 1.81: 58 Bond restraints: 11730 Sorted by residual: bond pdb=" CD1 PHE B 314 " pdb=" HD1 PHE B 314 " ideal model delta sigma weight residual 0.930 0.965 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C THR B 306 " pdb=" N GLY B 307 " ideal model delta sigma weight residual 1.340 1.329 0.011 6.60e-03 2.30e+04 2.64e+00 bond pdb=" C THR A 306 " pdb=" N GLY A 307 " ideal model delta sigma weight residual 1.340 1.329 0.011 6.60e-03 2.30e+04 2.64e+00 bond pdb=" NE2 GLN A 34 " pdb="HE21 GLN A 34 " ideal model delta sigma weight residual 0.860 0.831 0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" CE1 PHE B 314 " pdb=" HE1 PHE B 314 " ideal model delta sigma weight residual 0.930 0.904 0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 11725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 19828 1.14 - 2.27: 1356 2.27 - 3.41: 47 3.41 - 4.54: 29 4.54 - 5.68: 4 Bond angle restraints: 21264 Sorted by residual: angle pdb=" CA GLN A 34 " pdb=" CB GLN A 34 " pdb=" CG GLN A 34 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.06e+00 angle pdb=" CA GLN B 34 " pdb=" CB GLN B 34 " pdb=" CG GLN B 34 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.02e+00 angle pdb=" N PHE A 314 " pdb=" CA PHE A 314 " pdb=" CB PHE A 314 " ideal model delta sigma weight residual 109.72 105.67 4.05 1.70e+00 3.46e-01 5.67e+00 angle pdb=" N PHE B 314 " pdb=" CA PHE B 314 " pdb=" CB PHE B 314 " ideal model delta sigma weight residual 109.72 105.76 3.96 1.70e+00 3.46e-01 5.44e+00 angle pdb=" C GLN B 34 " pdb=" CA GLN B 34 " pdb=" CB GLN B 34 " ideal model delta sigma weight residual 110.88 114.45 -3.57 1.57e+00 4.06e-01 5.17e+00 ... (remaining 21259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4995 17.53 - 35.05: 365 35.05 - 52.58: 128 52.58 - 70.11: 32 70.11 - 87.63: 4 Dihedral angle restraints: 5524 sinusoidal: 2932 harmonic: 2592 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 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+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 180.00 158.28 21.72 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ASP A 283 " pdb=" C ASP A 283 " pdb=" N ASN A 284 " pdb=" CA ASN A 284 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 5521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 581 0.026 - 0.051: 242 0.051 - 0.077: 94 0.077 - 0.103: 48 0.103 - 0.129: 13 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA VAL A 285 " pdb=" N VAL A 285 " pdb=" C VAL A 285 " pdb=" CB VAL A 285 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL B 285 " pdb=" N VAL B 285 " pdb=" C VAL B 285 " pdb=" CB VAL B 285 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 975 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 314 " 0.026 2.00e-02 2.50e+03 2.83e-02 2.41e+01 pdb=" CG PHE A 314 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 314 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 PHE A 314 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 314 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 314 " -0.036 2.00e-02 2.50e+03 pdb=" CZ PHE A 314 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 314 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 314 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 314 " -0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 314 " 0.027 2.00e-02 2.50e+03 pdb=" HZ PHE A 314 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 314 " 0.000 2.00e-02 2.50e+03 2.20e-02 1.45e+01 pdb=" CG PHE B 314 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE B 314 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 314 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 314 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 314 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 314 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE B 314 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE B 314 " 0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE B 314 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE B 314 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 314 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 133 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 134 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 134 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 134 " -0.022 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.19: 570 2.19 - 2.92: 30654 2.92 - 3.66: 44464 3.66 - 4.40: 68468 4.40 - 5.14: 107342 Nonbonded interactions: 251498 Sorted by model distance: nonbonded pdb=" OE1 GLU A 259 " pdb=" H GLU A 259 " model vdw 1.448 2.450 nonbonded pdb=" OE1 GLU B 259 " pdb=" H GLU B 259 " model vdw 1.449 2.450 nonbonded pdb=" HG SER A 45 " pdb=" O HOH A 802 " model vdw 1.657 2.450 nonbonded pdb=" HG SER B 45 " pdb=" O HOH B 802 " model vdw 1.659 2.450 nonbonded pdb=" O PHE A 434 " pdb=" HG1 THR A 437 " model vdw 1.660 2.450 ... (remaining 251493 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 476 or resid 701 through 703)) 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: 9.390 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: 0.230 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.690 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.003 0.036 5830 Z= 0.226 Angle : 0.559 5.676 7946 Z= 0.319 Chirality : 0.037 0.129 978 Planarity : 0.004 0.039 974 Dihedral : 14.663 87.635 2034 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.94 % Allowed : 8.74 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.34), residues: 726 helix: 1.58 (0.22), residues: 608 sheet: None (None), residues: 0 loop : 1.68 (0.72), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 394 HIS 0.005 0.001 HIS B 328 PHE 0.054 0.002 PHE A 314 TYR 0.011 0.002 TYR A 81 ARG 0.002 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 99 average time/residue: 2.3027 time to fit residues: 240.6667 Evaluate side-chains 68 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain B residue 145 VAL 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: 0.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5830 Z= 0.281 Angle : 0.547 4.837 7946 Z= 0.292 Chirality : 0.037 0.129 978 Planarity : 0.004 0.032 974 Dihedral : 4.601 33.881 782 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.46 % Allowed : 12.94 % Favored : 85.60 % 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: 3.48 (0.33), residues: 726 helix: 2.42 (0.21), residues: 606 sheet: None (None), residues: 0 loop : 1.88 (0.71), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.003 0.001 HIS A 328 PHE 0.012 0.001 PHE A 99 TYR 0.009 0.002 TYR A 313 ARG 0.001 0.000 ARG A 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 2.8055 time to fit residues: 187.1794 Evaluate side-chains 59 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 373 LEU 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: 0.9990 chunk 54 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 chunk 64 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5830 Z= 0.215 Angle : 0.491 4.409 7946 Z= 0.257 Chirality : 0.036 0.125 978 Planarity : 0.004 0.032 974 Dihedral : 4.364 30.812 782 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.13 % Allowed : 13.11 % Favored : 85.76 % 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: 3.72 (0.33), residues: 726 helix: 2.65 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.51 (0.70), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.012 0.001 PHE B 99 TYR 0.010 0.001 TYR B 359 ARG 0.001 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.968 Fit side-chains REVERT: A 289 LYS cc_start: 0.8106 (mppt) cc_final: 0.7819 (mtmm) REVERT: B 289 LYS cc_start: 0.8103 (mppt) cc_final: 0.7805 (mtmm) outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 2.9963 time to fit residues: 200.1666 Evaluate side-chains 55 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5830 Z= 0.261 Angle : 0.503 4.341 7946 Z= 0.265 Chirality : 0.036 0.129 978 Planarity : 0.004 0.031 974 Dihedral : 4.248 27.598 782 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 0.97 % Allowed : 13.27 % Favored : 85.76 % 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: 3.84 (0.32), residues: 726 helix: 2.79 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.24 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.002 TYR B 359 ARG 0.001 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.880 Fit side-chains REVERT: A 289 LYS cc_start: 0.8097 (mppt) cc_final: 0.7763 (mtmm) REVERT: B 289 LYS cc_start: 0.8110 (mppt) cc_final: 0.7774 (mtmm) outliers start: 6 outliers final: 2 residues processed: 56 average time/residue: 2.8398 time to fit residues: 166.5817 Evaluate side-chains 54 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 373 LEU 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: 2.9990 chunk 1 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5830 Z= 0.260 Angle : 0.498 4.290 7946 Z= 0.263 Chirality : 0.036 0.126 978 Planarity : 0.004 0.031 974 Dihedral : 3.978 23.820 780 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.81 % Allowed : 12.94 % Favored : 86.25 % 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: 3.88 (0.32), residues: 726 helix: 2.83 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.14 (0.67), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.012 0.001 PHE B 99 TYR 0.010 0.002 TYR A 313 ARG 0.001 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.866 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 2.7719 time to fit residues: 162.7976 Evaluate side-chains 53 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 373 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5830 Z= 0.263 Angle : 0.513 6.227 7946 Z= 0.273 Chirality : 0.037 0.130 978 Planarity : 0.004 0.028 974 Dihedral : 3.967 23.838 780 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.81 % Allowed : 12.94 % Favored : 86.25 % 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: 3.95 (0.32), residues: 726 helix: 2.89 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.11 (0.65), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.009 0.002 TYR A 313 ARG 0.002 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.806 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 56 average time/residue: 3.0897 time to fit residues: 180.3318 Evaluate side-chains 53 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.0870 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5830 Z= 0.225 Angle : 0.495 6.471 7946 Z= 0.262 Chirality : 0.036 0.126 978 Planarity : 0.004 0.029 974 Dihedral : 3.927 23.532 780 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 12.94 % Favored : 86.25 % 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: 4.07 (0.31), residues: 726 helix: 2.97 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.15 (0.64), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.001 TYR A 313 ARG 0.003 0.000 ARG B 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.942 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 2.8686 time to fit residues: 165.4839 Evaluate side-chains 54 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5830 Z= 0.202 Angle : 0.505 7.029 7946 Z= 0.266 Chirality : 0.036 0.128 978 Planarity : 0.004 0.029 974 Dihedral : 3.891 23.264 780 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.81 % Allowed : 12.62 % Favored : 86.57 % 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: 4.18 (0.31), residues: 726 helix: 3.03 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.24 (0.64), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.009 0.001 TYR A 313 ARG 0.003 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 52 time to evaluate : 0.778 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 54 average time/residue: 2.9620 time to fit residues: 167.4093 Evaluate side-chains 54 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 426 TYR 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: 0.9980 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 61 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5830 Z= 0.233 Angle : 0.505 6.848 7946 Z= 0.266 Chirality : 0.036 0.127 978 Planarity : 0.004 0.029 974 Dihedral : 3.865 23.137 780 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.49 % Allowed : 12.94 % Favored : 86.57 % 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: 4.20 (0.31), residues: 726 helix: 3.04 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.28 (0.64), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.009 0.001 TYR A 313 ARG 0.004 0.000 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.901 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 2.8921 time to fit residues: 160.4188 Evaluate side-chains 51 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 TYR 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: 0.5980 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5830 Z= 0.236 Angle : 0.511 7.418 7946 Z= 0.269 Chirality : 0.036 0.126 978 Planarity : 0.004 0.029 974 Dihedral : 3.851 23.255 780 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.49 % Allowed : 13.11 % Favored : 86.41 % 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: 4.24 (0.31), residues: 726 helix: 3.07 (0.21), residues: 608 sheet: None (None), residues: 0 loop : 1.30 (0.64), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 394 HIS 0.004 0.001 HIS A 328 PHE 0.013 0.001 PHE B 99 TYR 0.010 0.002 TYR A 313 ARG 0.003 0.000 ARG A 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.939 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 53 average time/residue: 2.4491 time to fit residues: 135.9273 Evaluate side-chains 51 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.100998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.069615 restraints weight = 22534.843| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.30 r_work: 0.2716 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5830 Z= 0.182 Angle : 0.496 7.431 7946 Z= 0.259 Chirality : 0.035 0.127 978 Planarity : 0.004 0.029 974 Dihedral : 3.812 23.028 780 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.49 % Allowed : 13.11 % Favored : 86.41 % 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: 4.31 (0.32), residues: 726 helix: 3.13 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 1.21 (0.65), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 394 HIS 0.004 0.001 HIS A 328 PHE 0.012 0.001 PHE A 99 TYR 0.010 0.001 TYR A 313 ARG 0.003 0.000 ARG A 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4593.71 seconds wall clock time: 88 minutes 40.55 seconds (5320.55 seconds total)