Starting phenix.real_space_refine on Sun Mar 10 23:58:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5c_13198/03_2024/7p5c_13198.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5c_13198/03_2024/7p5c_13198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5c_13198/03_2024/7p5c_13198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5c_13198/03_2024/7p5c_13198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5c_13198/03_2024/7p5c_13198.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p5c_13198/03_2024/7p5c_13198.pdb" } resolution = 3.2 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 4038 2.51 5 N 1012 2.21 5 O 1146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6222 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3055 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} Chain breaks: 1 Chain: "B" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3055 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 14, 'TRANS': 377} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.96, per 1000 atoms: 0.64 Number of scatterers: 6222 At special positions: 0 Unit cell: (79.422, 71.61, 127.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 1146 8.00 N 1012 7.00 C 4038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 366 " distance=2.04 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 366 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 601 " - " ASN A 144 " " NAG A 602 " - " ASN A 351 " " NAG B 601 " - " ASN B 144 " " NAG B 602 " - " ASN B 351 " " NAG C 1 " - " ASN A 126 " " NAG D 1 " - " ASN B 126 " Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.3 seconds 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1464 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 87.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 removed outlier: 3.579A pdb=" N ARG A 17 " --> pdb=" O SER A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 66 removed outlier: 3.608A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 158 removed outlier: 4.456A pdb=" N GLU A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 161 through 185 removed outlier: 3.595A pdb=" N ILE A 185 " --> pdb=" O TYR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 234 Processing helix chain 'A' and resid 235 through 273 removed outlier: 4.042A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.784A pdb=" N TYR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 307 through 336 removed outlier: 3.521A pdb=" N THR A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 339 through 364 removed outlier: 4.286A pdb=" N GLY A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 409 removed outlier: 4.283A pdb=" N LEU A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'B' and resid 9 through 17 removed outlier: 3.572A pdb=" N ARG B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 66 removed outlier: 3.583A pdb=" N ALA B 42 " --> pdb=" O ASP B 38 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 145 Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 161 through 184 Processing helix chain 'B' and resid 194 through 233 Processing helix chain 'B' and resid 235 through 273 removed outlier: 3.547A pdb=" N PHE B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ASP B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.879A pdb=" N TYR B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 307 through 330 Processing helix chain 'B' and resid 331 through 336 removed outlier: 4.284A pdb=" N GLU B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 364 Processing helix chain 'B' and resid 365 through 383 removed outlier: 4.179A pdb=" N LEU B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 407 removed outlier: 3.677A pdb=" N ALA B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 removed outlier: 3.684A pdb=" N TRP B 413 " --> pdb=" O PRO B 410 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1638 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: 2.00 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1950 1.34 - 1.46: 1139 1.46 - 1.58: 3249 1.58 - 1.70: 0 1.70 - 1.81: 32 Bond restraints: 6370 Sorted by residual: bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C1 NAG B 601 " pdb=" O5 NAG B 601 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 ... (remaining 6365 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.29: 207 107.29 - 113.96: 3736 113.96 - 120.64: 2811 120.64 - 127.31: 1869 127.31 - 133.99: 93 Bond angle restraints: 8716 Sorted by residual: angle pdb=" C PHE B 21 " pdb=" N ASP B 22 " pdb=" CA ASP B 22 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+01 angle pdb=" CA LEU A 250 " pdb=" CB LEU A 250 " pdb=" CG LEU A 250 " ideal model delta sigma weight residual 116.30 126.24 -9.94 3.50e+00 8.16e-02 8.06e+00 angle pdb=" N VAL A 332 " pdb=" CA VAL A 332 " pdb=" C VAL A 332 " ideal model delta sigma weight residual 108.88 114.50 -5.62 2.16e+00 2.14e-01 6.78e+00 angle pdb=" N ASP B 22 " pdb=" CA ASP B 22 " pdb=" CB ASP B 22 " ideal model delta sigma weight residual 110.49 114.74 -4.25 1.69e+00 3.50e-01 6.33e+00 angle pdb=" N VAL B 332 " pdb=" CA VAL B 332 " pdb=" C VAL B 332 " ideal model delta sigma weight residual 108.88 114.25 -5.37 2.16e+00 2.14e-01 6.18e+00 ... (remaining 8711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3364 17.69 - 35.37: 358 35.37 - 53.06: 58 53.06 - 70.75: 19 70.75 - 88.44: 3 Dihedral angle restraints: 3802 sinusoidal: 1526 harmonic: 2276 Sorted by residual: dihedral pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" N THR A 353 " pdb=" CA THR A 353 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA HIS B 145 " pdb=" C HIS B 145 " pdb=" N THR B 146 " pdb=" CA THR B 146 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CB GLU A 335 " pdb=" CG GLU A 335 " pdb=" CD GLU A 335 " pdb=" OE1 GLU A 335 " ideal model delta sinusoidal sigma weight residual 0.00 88.44 -88.44 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 3799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 976 0.070 - 0.140: 76 0.140 - 0.209: 0 0.209 - 0.279: 1 0.279 - 0.349: 1 Chirality restraints: 1054 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 126 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 126 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CG LEU A 293 " pdb=" CB LEU A 293 " pdb=" CD1 LEU A 293 " pdb=" CD2 LEU A 293 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1051 not shown) Planarity restraints: 1078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 381 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C CYS A 381 " 0.028 2.00e-02 2.50e+03 pdb=" O CYS A 381 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR A 382 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 352 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C GLY A 352 " 0.028 2.00e-02 2.50e+03 pdb=" O GLY A 352 " -0.010 2.00e-02 2.50e+03 pdb=" N THR A 353 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 380 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.79e+00 pdb=" C PHE A 380 " 0.023 2.00e-02 2.50e+03 pdb=" O PHE A 380 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS A 381 " -0.008 2.00e-02 2.50e+03 ... (remaining 1075 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1033 2.76 - 3.29: 6302 3.29 - 3.83: 10690 3.83 - 4.36: 12122 4.36 - 4.90: 21329 Nonbonded interactions: 51476 Sorted by model distance: nonbonded pdb=" O VAL A 12 " pdb=" OG SER A 268 " model vdw 2.220 2.440 nonbonded pdb=" OD1 ASN A 126 " pdb=" N2 NAG C 1 " model vdw 2.228 2.520 nonbonded pdb=" OD1 ASP B 275 " pdb=" OH TYR B 373 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP A 275 " pdb=" OH TYR A 373 " model vdw 2.261 2.440 nonbonded pdb=" O VAL B 12 " pdb=" OG SER B 268 " model vdw 2.291 2.440 ... (remaining 51471 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 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 0.470 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: 0.010 Extract box with map and model: 2.750 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 21.640 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 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 : 0.004 0.038 6370 Z= 0.280 Angle : 0.604 9.939 8716 Z= 0.285 Chirality : 0.041 0.349 1054 Planarity : 0.003 0.026 1072 Dihedral : 14.521 88.436 2326 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 2.41 (0.29), residues: 776 helix: 1.91 (0.20), residues: 646 sheet: None (None), residues: 0 loop : 0.16 (0.56), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.003 0.001 HIS A 20 PHE 0.007 0.001 PHE A 394 TYR 0.010 0.001 TYR A 390 ARG 0.006 0.001 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 106 TYR cc_start: 0.8214 (t80) cc_final: 0.7807 (t80) REVERT: B 229 VAL cc_start: 0.8989 (t) cc_final: 0.8759 (t) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1966 time to fit residues: 26.6531 Evaluate side-chains 90 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6370 Z= 0.240 Angle : 0.584 8.891 8716 Z= 0.286 Chirality : 0.039 0.267 1054 Planarity : 0.004 0.035 1072 Dihedral : 5.389 48.980 1014 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.07 % Allowed : 6.40 % Favored : 92.53 % 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: 3.37 (0.29), residues: 776 helix: 2.64 (0.19), residues: 650 sheet: None (None), residues: 0 loop : -0.09 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.003 0.001 HIS A 20 PHE 0.008 0.001 PHE A 394 TYR 0.009 0.001 TYR A 373 ARG 0.006 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 0.887 Fit side-chains REVERT: A 35 GLU cc_start: 0.7346 (pm20) cc_final: 0.7146 (pm20) REVERT: A 106 TYR cc_start: 0.8059 (t80) cc_final: 0.7836 (t80) REVERT: B 120 TYR cc_start: 0.8741 (t80) cc_final: 0.8533 (t80) REVERT: B 320 GLU cc_start: 0.7785 (tp30) cc_final: 0.7561 (tp30) outliers start: 7 outliers final: 3 residues processed: 106 average time/residue: 0.1874 time to fit residues: 26.2840 Evaluate side-chains 99 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 53 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: A 375 GLN B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6370 Z= 0.217 Angle : 0.538 8.146 8716 Z= 0.263 Chirality : 0.037 0.158 1054 Planarity : 0.003 0.034 1072 Dihedral : 4.876 44.029 1014 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.52 % Allowed : 8.54 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.28), residues: 776 helix: 2.89 (0.18), residues: 648 sheet: None (None), residues: 0 loop : -0.03 (0.55), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 10 HIS 0.003 0.001 HIS B 20 PHE 0.008 0.001 PHE A 394 TYR 0.013 0.001 TYR A 373 ARG 0.003 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.682 Fit side-chains REVERT: A 56 LEU cc_start: 0.8047 (tt) cc_final: 0.7736 (tp) REVERT: B 344 LEU cc_start: 0.8996 (mm) cc_final: 0.8789 (mm) outliers start: 10 outliers final: 8 residues processed: 108 average time/residue: 0.1812 time to fit residues: 25.8726 Evaluate side-chains 102 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 20 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6370 Z= 0.178 Angle : 0.517 7.778 8716 Z= 0.254 Chirality : 0.036 0.229 1054 Planarity : 0.003 0.035 1072 Dihedral : 4.451 35.221 1014 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.68 % Allowed : 11.13 % Favored : 87.20 % 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: 3.99 (0.28), residues: 776 helix: 3.03 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.12 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 11 HIS 0.003 0.001 HIS A 370 PHE 0.005 0.001 PHE B 394 TYR 0.021 0.001 TYR B 120 ARG 0.003 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.707 Fit side-chains REVERT: A 56 LEU cc_start: 0.8265 (tt) cc_final: 0.8011 (tp) REVERT: B 22 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7717 (p0) REVERT: B 35 GLU cc_start: 0.6840 (tt0) cc_final: 0.6516 (tt0) REVERT: B 344 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8697 (mm) outliers start: 11 outliers final: 7 residues processed: 100 average time/residue: 0.1979 time to fit residues: 25.9580 Evaluate side-chains 103 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 0.0050 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6370 Z= 0.184 Angle : 0.505 7.475 8716 Z= 0.248 Chirality : 0.036 0.212 1054 Planarity : 0.003 0.035 1072 Dihedral : 4.099 23.652 1014 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.29 % Allowed : 12.20 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.12 (0.28), residues: 776 helix: 3.12 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.15 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 67 HIS 0.002 0.001 HIS B 20 PHE 0.006 0.001 PHE B 394 TYR 0.019 0.001 TYR B 120 ARG 0.003 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 0.733 Fit side-chains REVERT: A 35 GLU cc_start: 0.7608 (pm20) cc_final: 0.7281 (pm20) REVERT: A 56 LEU cc_start: 0.8275 (tt) cc_final: 0.8027 (tp) REVERT: A 95 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6310 (mp) REVERT: B 22 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7763 (p0) REVERT: B 35 GLU cc_start: 0.7163 (tt0) cc_final: 0.6848 (tt0) REVERT: B 344 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8670 (mm) outliers start: 15 outliers final: 10 residues processed: 104 average time/residue: 0.2101 time to fit residues: 28.4852 Evaluate side-chains 107 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 375 GLN Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6370 Z= 0.265 Angle : 0.537 7.171 8716 Z= 0.262 Chirality : 0.037 0.193 1054 Planarity : 0.003 0.036 1072 Dihedral : 4.125 24.294 1014 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.44 % Allowed : 13.87 % Favored : 83.69 % 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: 3.98 (0.28), residues: 776 helix: 3.01 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.17 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.003 0.001 HIS A 20 PHE 0.009 0.001 PHE B 394 TYR 0.017 0.001 TYR B 120 ARG 0.002 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.699 Fit side-chains REVERT: A 35 GLU cc_start: 0.7634 (pm20) cc_final: 0.7367 (pm20) REVERT: A 56 LEU cc_start: 0.8327 (tt) cc_final: 0.8047 (tp) REVERT: A 95 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6316 (mp) REVERT: B 22 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7864 (p0) REVERT: B 339 THR cc_start: 0.8860 (p) cc_final: 0.8605 (p) REVERT: B 344 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8758 (mm) outliers start: 16 outliers final: 11 residues processed: 100 average time/residue: 0.1988 time to fit residues: 25.7602 Evaluate side-chains 104 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6370 Z= 0.199 Angle : 0.519 9.663 8716 Z= 0.251 Chirality : 0.036 0.186 1054 Planarity : 0.003 0.037 1072 Dihedral : 3.993 23.966 1014 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.44 % Allowed : 14.33 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.11 (0.28), residues: 776 helix: 3.11 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.18 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.002 0.001 HIS B 20 PHE 0.006 0.001 PHE B 394 TYR 0.017 0.001 TYR B 120 ARG 0.002 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.673 Fit side-chains REVERT: A 35 GLU cc_start: 0.7678 (pm20) cc_final: 0.7400 (pm20) REVERT: A 56 LEU cc_start: 0.8321 (tt) cc_final: 0.8042 (tp) REVERT: A 95 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6495 (mp) REVERT: B 22 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7805 (p0) REVERT: B 339 THR cc_start: 0.8851 (p) cc_final: 0.8578 (p) REVERT: B 344 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8718 (mm) outliers start: 16 outliers final: 11 residues processed: 103 average time/residue: 0.2030 time to fit residues: 27.3733 Evaluate side-chains 107 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6370 Z= 0.221 Angle : 0.529 9.219 8716 Z= 0.257 Chirality : 0.037 0.181 1054 Planarity : 0.003 0.037 1072 Dihedral : 3.992 24.089 1014 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.74 % Allowed : 15.09 % Favored : 82.16 % 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: 4.06 (0.28), residues: 776 helix: 3.07 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.17 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.003 0.001 HIS B 20 PHE 0.007 0.001 PHE B 394 TYR 0.016 0.001 TYR B 120 ARG 0.002 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.631 Fit side-chains REVERT: A 35 GLU cc_start: 0.7655 (pm20) cc_final: 0.7383 (pm20) REVERT: A 56 LEU cc_start: 0.8329 (tt) cc_final: 0.8050 (tp) REVERT: A 95 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6476 (mp) REVERT: B 22 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7814 (p0) REVERT: B 339 THR cc_start: 0.8682 (p) cc_final: 0.8443 (p) REVERT: B 344 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8738 (mm) outliers start: 18 outliers final: 13 residues processed: 104 average time/residue: 0.2118 time to fit residues: 28.3989 Evaluate side-chains 108 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6370 Z= 0.185 Angle : 0.513 9.099 8716 Z= 0.250 Chirality : 0.036 0.185 1054 Planarity : 0.003 0.036 1072 Dihedral : 3.916 23.779 1014 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.59 % Allowed : 15.24 % Favored : 82.16 % 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: 4.15 (0.28), residues: 776 helix: 3.14 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.18 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 10 HIS 0.002 0.001 HIS B 20 PHE 0.006 0.001 PHE B 394 TYR 0.016 0.001 TYR B 120 ARG 0.002 0.000 ARG B 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 91 time to evaluate : 0.731 Fit side-chains REVERT: A 35 GLU cc_start: 0.7611 (pm20) cc_final: 0.7354 (pm20) REVERT: A 56 LEU cc_start: 0.8328 (tt) cc_final: 0.8048 (tp) REVERT: A 95 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6456 (mp) REVERT: B 22 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7773 (p0) REVERT: B 344 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8683 (mm) outliers start: 17 outliers final: 12 residues processed: 102 average time/residue: 0.1992 time to fit residues: 26.4971 Evaluate side-chains 108 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 375 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6370 Z= 0.182 Angle : 0.515 9.014 8716 Z= 0.251 Chirality : 0.036 0.185 1054 Planarity : 0.003 0.036 1072 Dihedral : 3.870 23.575 1014 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.44 % Allowed : 15.85 % Favored : 81.71 % 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: 4.17 (0.28), residues: 776 helix: 3.15 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.17 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 67 HIS 0.002 0.001 HIS B 370 PHE 0.005 0.001 PHE B 394 TYR 0.016 0.001 TYR B 120 ARG 0.002 0.000 ARG B 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1552 Ramachandran restraints generated. 776 Oldfield, 0 Emsley, 776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.700 Fit side-chains REVERT: A 35 GLU cc_start: 0.7608 (pm20) cc_final: 0.7349 (pm20) REVERT: A 56 LEU cc_start: 0.8330 (tt) cc_final: 0.8051 (tp) REVERT: A 95 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6461 (mp) REVERT: B 22 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7746 (p0) REVERT: B 344 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8679 (mm) outliers start: 16 outliers final: 11 residues processed: 101 average time/residue: 0.2027 time to fit residues: 26.5394 Evaluate side-chains 107 residues out of total 656 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 22 ASP Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 344 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.130186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.107768 restraints weight = 6826.304| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.53 r_work: 0.2985 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6370 Z= 0.190 Angle : 0.515 8.869 8716 Z= 0.250 Chirality : 0.036 0.183 1054 Planarity : 0.003 0.035 1072 Dihedral : 3.831 23.562 1014 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.29 % Allowed : 15.85 % Favored : 81.86 % 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: 4.16 (0.28), residues: 776 helix: 3.15 (0.18), residues: 660 sheet: None (None), residues: 0 loop : 0.16 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 67 HIS 0.002 0.001 HIS B 20 PHE 0.006 0.001 PHE B 394 TYR 0.016 0.001 TYR B 120 ARG 0.002 0.000 ARG B 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1493.67 seconds wall clock time: 27 minutes 40.20 seconds (1660.20 seconds total)