Starting phenix.real_space_refine on Thu Feb 15 22:24:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9g_25757/02_2024/7t9g_25757.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9g_25757/02_2024/7t9g_25757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9g_25757/02_2024/7t9g_25757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9g_25757/02_2024/7t9g_25757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9g_25757/02_2024/7t9g_25757.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9g_25757/02_2024/7t9g_25757.pdb" } resolution = 2.83 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 52 5.16 5 Na 4 4.78 5 C 4456 2.51 5 N 1046 2.21 5 O 1133 1.98 5 H 6958 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 249": "OE1" <-> "OE2" Residue "Y PHE 273": "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-5238/modules/chem_data/mon_lib" Total number of atoms: 13649 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6820 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 6820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 6820 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 15, 'TRANS': 429} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 6.16, per 1000 atoms: 0.45 Number of scatterers: 13649 At special positions: 0 Unit cell: (88.81, 102.09, 76.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 52 16.00 Na 4 11.00 O 1133 8.00 N 1046 7.00 C 4456 6.00 H 6958 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: 10.81 Conformation dependent library (CDL) restraints added in 1.4 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1656 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 85.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 Processing helix chain 'A' and resid 42 through 62 Processing helix chain 'A' and resid 65 through 79 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 94 through 114 removed outlier: 3.601A pdb=" N PHE A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 130 through 149 removed outlier: 3.517A pdb=" N VAL A 135 " --> pdb=" O MET A 131 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TRP A 148 " --> pdb=" O LEU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.587A pdb=" N ALA A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 174 through 193 removed outlier: 3.618A pdb=" N TYR A 178 " --> pdb=" O GLN A 174 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.592A pdb=" N ALA A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 240 removed outlier: 3.634A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Proline residue: A 223 - end of helix Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 260 through 277 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 290 through 307 Processing helix chain 'A' and resid 310 through 318 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.771A pdb=" N LEU A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 4.696A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N MET A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 377 through 396 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.703A pdb=" N SER A 404 " --> pdb=" O PRO A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 420 Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 434 through 461 Processing helix chain 'Y' and resid 19 through 38 Processing helix chain 'Y' and resid 42 through 62 Processing helix chain 'Y' and resid 65 through 79 Proline residue: Y 74 - end of helix Processing helix chain 'Y' and resid 84 through 90 Processing helix chain 'Y' and resid 91 through 93 No H-bonds generated for 'chain 'Y' and resid 91 through 93' Processing helix chain 'Y' and resid 94 through 114 removed outlier: 3.602A pdb=" N PHE Y 98 " --> pdb=" O ASN Y 94 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 127 Processing helix chain 'Y' and resid 130 through 149 removed outlier: 3.517A pdb=" N VAL Y 135 " --> pdb=" O MET Y 131 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N PHE Y 136 " --> pdb=" O SER Y 132 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP Y 148 " --> pdb=" O LEU Y 144 " (cutoff:3.500A) Processing helix chain 'Y' and resid 151 through 166 removed outlier: 3.587A pdb=" N ALA Y 155 " --> pdb=" O ASN Y 151 " (cutoff:3.500A) Proline residue: Y 160 - end of helix Processing helix chain 'Y' and resid 174 through 193 removed outlier: 3.618A pdb=" N TYR Y 178 " --> pdb=" O GLN Y 174 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL Y 185 " --> pdb=" O VAL Y 181 " (cutoff:3.500A) Processing helix chain 'Y' and resid 200 through 211 removed outlier: 3.592A pdb=" N ALA Y 204 " --> pdb=" O SER Y 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 213 through 240 removed outlier: 3.633A pdb=" N PHE Y 220 " --> pdb=" O ASP Y 216 " (cutoff:3.500A) Proline residue: Y 223 - end of helix Proline residue: Y 230 - end of helix Processing helix chain 'Y' and resid 260 through 277 Processing helix chain 'Y' and resid 277 through 284 Processing helix chain 'Y' and resid 290 through 307 Processing helix chain 'Y' and resid 310 through 318 Processing helix chain 'Y' and resid 319 through 339 removed outlier: 3.770A pdb=" N LEU Y 323 " --> pdb=" O ASP Y 319 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 356 removed outlier: 4.695A pdb=" N ASP Y 351 " --> pdb=" O ASN Y 347 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N MET Y 352 " --> pdb=" O ALA Y 348 " (cutoff:3.500A) Processing helix chain 'Y' and resid 357 through 373 Processing helix chain 'Y' and resid 377 through 396 Proline residue: Y 387 - end of helix Processing helix chain 'Y' and resid 400 through 413 removed outlier: 3.703A pdb=" N SER Y 404 " --> pdb=" O PRO Y 400 " (cutoff:3.500A) Processing helix chain 'Y' and resid 417 through 420 Processing helix chain 'Y' and resid 421 through 429 Processing helix chain 'Y' and resid 434 through 461 516 hydrogen bonds defined for protein. 1542 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: 4.90 Time building geometry restraints manager: 11.19 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: 6952 1.03 - 1.23: 6 1.23 - 1.42: 2758 1.42 - 1.61: 3984 1.61 - 1.81: 98 Bond restraints: 13798 Sorted by residual: bond pdb=" CG LEU Y 250 " pdb=" CD2 LEU Y 250 " ideal model delta sigma weight residual 1.521 1.548 -0.027 3.30e-02 9.18e+02 6.55e-01 bond pdb=" CB VAL A 427 " pdb=" CG2 VAL A 427 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.17e-01 bond pdb=" CB VAL Y 427 " pdb=" CG2 VAL Y 427 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.12e-01 bond pdb=" CG LEU A 250 " pdb=" CD2 LEU A 250 " ideal model delta sigma weight residual 1.521 1.547 -0.026 3.30e-02 9.18e+02 6.10e-01 bond pdb=" CG PRO A 423 " pdb=" CD PRO A 423 " ideal model delta sigma weight residual 1.503 1.478 0.025 3.40e-02 8.65e+02 5.20e-01 ... (remaining 13793 not shown) Histogram of bond angle deviations from ideal: 79.48 - 90.38: 14 90.38 - 101.29: 36 101.29 - 112.19: 16532 112.19 - 123.09: 7310 123.09 - 134.00: 1192 Bond angle restraints: 25084 Sorted by residual: angle pdb=" CG LEU Y 445 " pdb=" CD2 LEU Y 445 " pdb="HD23 LEU Y 445 " ideal model delta sigma weight residual 109.00 79.48 29.52 3.00e+00 1.11e-01 9.68e+01 angle pdb=" CG LEU A 445 " pdb=" CD2 LEU A 445 " pdb="HD23 LEU A 445 " ideal model delta sigma weight residual 109.00 79.48 29.52 3.00e+00 1.11e-01 9.68e+01 angle pdb=" CG LEU A 445 " pdb=" CD2 LEU A 445 " pdb="HD22 LEU A 445 " ideal model delta sigma weight residual 109.00 79.65 29.35 3.00e+00 1.11e-01 9.57e+01 angle pdb=" CG LEU Y 445 " pdb=" CD2 LEU Y 445 " pdb="HD22 LEU Y 445 " ideal model delta sigma weight residual 109.00 79.70 29.30 3.00e+00 1.11e-01 9.54e+01 angle pdb="HD21 LEU A 445 " pdb=" CD2 LEU A 445 " pdb="HD23 LEU A 445 " ideal model delta sigma weight residual 110.00 81.03 28.97 3.00e+00 1.11e-01 9.33e+01 ... (remaining 25079 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.34: 5834 16.34 - 32.68: 447 32.68 - 49.02: 107 49.02 - 65.37: 74 65.37 - 81.71: 8 Dihedral angle restraints: 6470 sinusoidal: 3394 harmonic: 3076 Sorted by residual: dihedral pdb=" CA PHE A 396 " pdb=" C PHE A 396 " pdb=" N GLY A 397 " pdb=" CA GLY A 397 " ideal model delta harmonic sigma weight residual -180.00 -159.32 -20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE Y 396 " pdb=" C PHE Y 396 " pdb=" N GLY Y 397 " pdb=" CA GLY Y 397 " ideal model delta harmonic sigma weight residual -180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLY Y 397 " pdb=" C GLY Y 397 " pdb=" N MET Y 398 " pdb=" CA MET Y 398 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 6467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.338: 1156 0.338 - 0.677: 0 0.677 - 1.015: 0 1.015 - 1.353: 0 1.353 - 1.691: 2 Chirality restraints: 1158 Sorted by residual: chirality pdb=" CG LEU Y 250 " pdb=" CB LEU Y 250 " pdb=" CD1 LEU Y 250 " pdb=" CD2 LEU Y 250 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.15e+01 chirality pdb=" CG LEU A 250 " pdb=" CB LEU A 250 " pdb=" CD1 LEU A 250 " pdb=" CD2 LEU A 250 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 chirality pdb=" CA VAL A 309 " pdb=" N VAL A 309 " pdb=" C VAL A 309 " pdb=" CB VAL A 309 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1155 not shown) Planarity restraints: 1986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Y 421 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO Y 422 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO Y 422 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO Y 422 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 421 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO A 422 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 201 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 202 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 202 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 202 " 0.018 5.00e-02 4.00e+02 ... (remaining 1983 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 672 2.19 - 2.79: 28214 2.79 - 3.40: 40397 3.40 - 4.00: 52000 4.00 - 4.60: 81891 Nonbonded interactions: 203174 Sorted by model distance: nonbonded pdb=" O MET Y 147 " pdb=" HG1 THR Y 196 " model vdw 1.590 1.850 nonbonded pdb=" O MET A 147 " pdb=" HG1 THR A 196 " model vdw 1.591 1.850 nonbonded pdb="HD22 ASN A 282 " pdb=" O PHE A 288 " model vdw 1.624 1.850 nonbonded pdb="HD22 ASN Y 282 " pdb=" O PHE Y 288 " model vdw 1.624 1.850 nonbonded pdb=" HG SER Y 146 " pdb=" O ALA Y 189 " model vdw 1.667 1.850 ... (remaining 203169 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' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.210 Extract box with map and model: 4.170 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 46.390 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 0.033 6840 Z= 0.174 Angle : 0.550 10.025 9326 Z= 0.282 Chirality : 0.078 1.691 1158 Planarity : 0.004 0.052 1128 Dihedral : 12.680 81.706 2300 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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: 1.69 (0.30), residues: 886 helix: 2.01 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.95 (0.40), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 461 HIS 0.007 0.001 HIS A 355 PHE 0.018 0.001 PHE A 100 TYR 0.005 0.001 TYR A 36 ARG 0.001 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 101 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 101 average time/residue: 2.4222 time to fit residues: 258.9135 Evaluate side-chains 85 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 MET Chi-restraints excluded: chain Y residue 157 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8641 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6840 Z= 0.204 Angle : 0.550 10.761 9326 Z= 0.280 Chirality : 0.077 1.671 1158 Planarity : 0.005 0.057 1128 Dihedral : 4.845 44.012 914 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.85 % Allowed : 5.97 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.30), residues: 886 helix: 1.93 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -2.84 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 311 HIS 0.003 0.001 HIS Y 310 PHE 0.014 0.001 PHE A 277 TYR 0.005 0.001 TYR A 36 ARG 0.005 0.001 ARG Y 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 97 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 84 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7851 (pp) REVERT: Y 240 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7378 (pp) outliers start: 13 outliers final: 3 residues processed: 92 average time/residue: 2.3866 time to fit residues: 233.4807 Evaluate side-chains 83 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 355 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 0.0030 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.0270 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.0054 ------------------------------------------------------------------------------- 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: 0.8663 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6840 Z= 0.173 Angle : 0.524 10.518 9326 Z= 0.263 Chirality : 0.077 1.684 1158 Planarity : 0.004 0.056 1128 Dihedral : 4.298 21.773 908 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.56 % Allowed : 7.67 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.30), residues: 886 helix: 1.96 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -3.01 (0.41), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Y 311 HIS 0.002 0.001 HIS Y 65 PHE 0.009 0.001 PHE Y 277 TYR 0.004 0.001 TYR Y 36 ARG 0.004 0.001 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 91 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 240 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7315 (pp) REVERT: Y 240 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7335 (pp) outliers start: 11 outliers final: 3 residues processed: 87 average time/residue: 2.4190 time to fit residues: 223.0318 Evaluate side-chains 81 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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: 0.8726 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6840 Z= 0.241 Angle : 0.546 10.462 9326 Z= 0.282 Chirality : 0.078 1.667 1158 Planarity : 0.005 0.058 1128 Dihedral : 4.371 22.005 908 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.13 % Allowed : 8.10 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.29), residues: 886 helix: 1.91 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -2.98 (0.41), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Y 311 HIS 0.003 0.001 HIS Y 65 PHE 0.014 0.001 PHE Y 277 TYR 0.004 0.001 TYR Y 237 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 1.031 Fit side-chains REVERT: A 240 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7322 (pp) REVERT: A 313 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: Y 42 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: Y 240 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7303 (pp) REVERT: Y 313 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7927 (mt-10) outliers start: 15 outliers final: 6 residues processed: 83 average time/residue: 2.6118 time to fit residues: 228.7290 Evaluate side-chains 83 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8734 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6840 Z= 0.230 Angle : 0.540 10.325 9326 Z= 0.276 Chirality : 0.077 1.661 1158 Planarity : 0.004 0.060 1128 Dihedral : 4.378 21.759 908 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.56 % Allowed : 9.23 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.29), residues: 886 helix: 1.92 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.06 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Y 311 HIS 0.004 0.001 HIS Y 65 PHE 0.010 0.001 PHE Y 277 TYR 0.003 0.001 TYR A 36 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.030 Fit side-chains REVERT: A 240 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7293 (pp) REVERT: A 313 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: Y 240 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7296 (pp) REVERT: Y 313 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7912 (mt-10) outliers start: 11 outliers final: 5 residues processed: 83 average time/residue: 2.6990 time to fit residues: 236.0103 Evaluate side-chains 82 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8729 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6840 Z= 0.200 Angle : 0.529 10.343 9326 Z= 0.269 Chirality : 0.077 1.662 1158 Planarity : 0.004 0.059 1128 Dihedral : 4.349 21.814 908 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.85 % Allowed : 10.51 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.29), residues: 886 helix: 1.98 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.07 (0.40), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 311 HIS 0.003 0.001 HIS Y 65 PHE 0.010 0.001 PHE Y 277 TYR 0.004 0.001 TYR A 36 ARG 0.002 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 1.040 Fit side-chains REVERT: A 240 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7285 (pp) REVERT: A 313 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: Y 42 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: Y 240 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7280 (pp) REVERT: Y 313 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7883 (mt-10) outliers start: 13 outliers final: 6 residues processed: 82 average time/residue: 2.7721 time to fit residues: 239.2362 Evaluate side-chains 84 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 ASN Y 446 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6840 Z= 0.284 Angle : 0.556 10.261 9326 Z= 0.288 Chirality : 0.077 1.659 1158 Planarity : 0.005 0.059 1128 Dihedral : 4.412 21.343 908 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.42 % Allowed : 10.94 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.29), residues: 886 helix: 1.91 (0.20), residues: 718 sheet: None (None), residues: 0 loop : -2.79 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 311 HIS 0.003 0.001 HIS Y 65 PHE 0.013 0.001 PHE Y 277 TYR 0.003 0.001 TYR A 237 ARG 0.004 0.001 ARG Y 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.043 Fit side-chains REVERT: A 240 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7197 (pp) REVERT: A 313 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: Y 42 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: Y 240 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7210 (pp) REVERT: Y 313 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7957 (mt-10) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 2.8609 time to fit residues: 255.5675 Evaluate side-chains 85 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 0.0770 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- 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: 0.8748 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6840 Z= 0.219 Angle : 0.541 10.300 9326 Z= 0.277 Chirality : 0.077 1.655 1158 Planarity : 0.005 0.059 1128 Dihedral : 4.425 21.758 908 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.42 % Allowed : 11.51 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.29), residues: 886 helix: 1.96 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.79 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Y 311 HIS 0.003 0.001 HIS A 65 PHE 0.010 0.001 PHE Y 277 TYR 0.003 0.001 TYR A 36 ARG 0.005 0.001 ARG Y 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.020 Fit side-chains REVERT: A 240 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7197 (pp) REVERT: A 313 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7864 (mt-10) REVERT: Y 42 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: Y 240 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7192 (pp) REVERT: Y 313 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.7900 (mt-10) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 2.8900 time to fit residues: 245.9969 Evaluate side-chains 83 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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: 0.8720 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6840 Z= 0.158 Angle : 0.521 10.393 9326 Z= 0.263 Chirality : 0.077 1.661 1158 Planarity : 0.004 0.058 1128 Dihedral : 4.349 21.663 908 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.56 % Allowed : 11.65 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.30), residues: 886 helix: 2.14 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -3.00 (0.41), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 311 HIS 0.004 0.001 HIS Y 355 PHE 0.007 0.001 PHE A 54 TYR 0.004 0.001 TYR A 36 ARG 0.006 0.001 ARG Y 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.970 Fit side-chains REVERT: A 240 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7709 (pp) REVERT: Y 42 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: Y 240 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7224 (pp) REVERT: Y 313 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7839 (mt-10) outliers start: 11 outliers final: 5 residues processed: 80 average time/residue: 2.8317 time to fit residues: 238.2480 Evaluate side-chains 79 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 250 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN Y 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6840 Z= 0.373 Angle : 0.592 10.162 9326 Z= 0.311 Chirality : 0.078 1.658 1158 Planarity : 0.005 0.058 1128 Dihedral : 4.470 20.202 908 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.28 % Allowed : 12.07 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.29), residues: 886 helix: 1.86 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.74 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 311 HIS 0.004 0.001 HIS Y 65 PHE 0.016 0.002 PHE Y 277 TYR 0.005 0.001 TYR Y 237 ARG 0.003 0.001 ARG A 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 181 is missing expected H atoms. Skipping. Residue VAL 181 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.064 Fit side-chains REVERT: A 240 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7144 (pp) REVERT: Y 42 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: Y 240 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7155 (pp) REVERT: Y 313 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8038 (mt-10) outliers start: 9 outliers final: 5 residues processed: 80 average time/residue: 2.9171 time to fit residues: 244.9519 Evaluate side-chains 81 residues out of total 706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 355 HIS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 240 LEU Chi-restraints excluded: chain Y residue 313 GLU Chi-restraints excluded: chain Y residue 355 HIS Chi-restraints excluded: chain Y residue 421 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.095782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.084206 restraints weight = 33351.263| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.47 r_work: 0.2925 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6840 Z= 0.232 Angle : 0.550 10.374 9326 Z= 0.283 Chirality : 0.077 1.656 1158 Planarity : 0.005 0.059 1128 Dihedral : 4.471 21.314 908 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.99 % Allowed : 12.36 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.29), residues: 886 helix: 1.94 (0.20), residues: 720 sheet: None (None), residues: 0 loop : -2.79 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP Y 311 HIS 0.003 0.001 HIS A 65 PHE 0.011 0.001 PHE Y 277 TYR 0.003 0.001 TYR A 36 ARG 0.002 0.000 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5074.50 seconds wall clock time: 89 minutes 38.45 seconds (5378.45 seconds total)