Starting phenix.real_space_refine on Thu Sep 26 01:08:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/09_2024/6wc9_21603.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/09_2024/6wc9_21603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/09_2024/6wc9_21603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/09_2024/6wc9_21603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/09_2024/6wc9_21603.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wc9_21603/09_2024/6wc9_21603.cif" } resolution = 2.64 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= 0.725 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 7 8.98 5 S 38 5.16 5 C 3754 2.51 5 N 938 2.21 5 O 1072 1.98 5 H 5904 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11713 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5800 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 5800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5800 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Time building chain proxies: 8.85, per 1000 atoms: 0.76 Number of scatterers: 11713 At special positions: 0 Unit cell: (104.992, 71.264, 76.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 7 19.00 S 38 16.00 O 1072 8.00 N 938 7.00 C 3754 6.00 H 5904 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 33 through 49 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 66 through 102 removed outlier: 3.632A pdb=" N VAL A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 257 through 284 removed outlier: 5.202A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.690A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 332 removed outlier: 3.555A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 399 removed outlier: 3.673A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 439 removed outlier: 5.116A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 508 Processing helix chain 'B' and resid 33 through 49 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 66 through 102 removed outlier: 3.632A pdb=" N VAL B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 257 through 284 removed outlier: 5.202A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.690A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.555A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 399 removed outlier: 3.672A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 439 removed outlier: 5.116A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 466 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 3.62 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: 5886 1.03 - 1.22: 18 1.22 - 1.42: 2380 1.42 - 1.61: 3392 1.61 - 1.81: 58 Bond restraints: 11734 Sorted by residual: bond pdb=" C THR B 472 " pdb=" N LEU B 473 " ideal model delta sigma weight residual 1.335 1.544 -0.209 1.32e-02 5.74e+03 2.51e+02 bond pdb=" C THR A 472 " pdb=" N LEU A 505 " ideal model delta sigma weight residual 1.335 1.544 -0.209 1.32e-02 5.74e+03 2.51e+02 bond pdb=" CB GLN B 65 " pdb=" CG GLN B 65 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" CB GLN A 65 " pdb=" CG GLN A 65 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" C VAL B 409 " pdb=" O VAL B 409 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.19e-02 7.06e+03 6.92e-01 ... (remaining 11729 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 19807 1.10 - 2.21: 1381 2.21 - 3.31: 54 3.31 - 4.41: 23 4.41 - 5.51: 3 Bond angle restraints: 21268 Sorted by residual: angle pdb=" N PHE A 66 " pdb=" CA PHE A 66 " pdb=" C PHE A 66 " ideal model delta sigma weight residual 112.72 109.17 3.55 1.36e+00 5.41e-01 6.80e+00 angle pdb=" N PHE B 66 " pdb=" CA PHE B 66 " pdb=" C PHE B 66 " ideal model delta sigma weight residual 112.72 109.17 3.55 1.36e+00 5.41e-01 6.80e+00 angle pdb=" CA TRP A 394 " pdb=" CB TRP A 394 " pdb=" CG TRP A 394 " ideal model delta sigma weight residual 113.60 117.90 -4.30 1.90e+00 2.77e-01 5.13e+00 angle pdb=" CA TRP B 394 " pdb=" CB TRP B 394 " pdb=" CG TRP B 394 " ideal model delta sigma weight residual 113.60 117.87 -4.27 1.90e+00 2.77e-01 5.06e+00 angle pdb=" CD GLN A 65 " pdb=" CG GLN A 65 " pdb=" HG3 GLN A 65 " ideal model delta sigma weight residual 108.00 102.49 5.51 3.00e+00 1.11e-01 3.38e+00 ... (remaining 21263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4861 16.03 - 32.06: 453 32.06 - 48.10: 128 48.10 - 64.13: 76 64.13 - 80.16: 10 Dihedral angle restraints: 5528 sinusoidal: 2936 harmonic: 2592 Sorted by residual: dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 159.17 20.83 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE A 99 " pdb=" C PHE A 99 " pdb=" N GLN A 100 " pdb=" CA GLN A 100 " ideal model delta harmonic sigma weight residual 180.00 159.23 20.77 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA GLN A 65 " pdb=" C GLN A 65 " pdb=" N PHE A 66 " pdb=" CA PHE A 66 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 552 0.024 - 0.047: 237 0.047 - 0.071: 127 0.071 - 0.094: 30 0.094 - 0.118: 32 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA VAL B 285 " pdb=" N VAL B 285 " pdb=" C VAL B 285 " pdb=" CB VAL B 285 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA VAL A 285 " pdb=" N VAL A 285 " pdb=" C VAL A 285 " pdb=" CB VAL A 285 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA PHE A 99 " pdb=" N PHE A 99 " pdb=" C PHE A 99 " pdb=" CB PHE A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 975 not shown) Planarity restraints: 1672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 472 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.02e+00 pdb=" N LEU A 505 " -0.024 2.00e-02 2.50e+03 pdb=" CA LEU A 505 " 0.006 2.00e-02 2.50e+03 pdb=" H LEU A 505 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 307 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 308 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 308 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 308 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 307 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO B 308 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.017 5.00e-02 4.00e+02 ... (remaining 1669 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.31: 2625 2.31 - 3.02: 32108 3.02 - 3.72: 44488 3.72 - 4.43: 66574 4.43 - 5.14: 103031 Nonbonded interactions: 248826 Sorted by model distance: nonbonded pdb=" HE2 HIS A 95 " pdb=" OD1 ASN A 113 " model vdw 1.601 2.450 nonbonded pdb=" HE2 HIS B 95 " pdb=" OD1 ASN B 113 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP A 266 " pdb=" HE1 TRP A 324 " model vdw 1.614 2.450 nonbonded pdb=" OD1 ASP B 266 " pdb=" HE1 TRP B 324 " model vdw 1.614 2.450 nonbonded pdb=" OE2 GLU A 282 " pdb=" HD1 HIS B 57 " model vdw 1.664 2.450 ... (remaining 248821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 508 or resid 701 through 703)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 43.710 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.000 Set scattering table: 0.090 Process input model: 31.350 Find NCS groups from input model: 0.390 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.006 0.209 5830 Z= 0.425 Angle : 0.537 4.603 7946 Z= 0.304 Chirality : 0.037 0.118 978 Planarity : 0.003 0.030 974 Dihedral : 15.749 80.161 2034 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.10 % Allowed : 15.37 % Favored : 82.52 % 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: -0.42 (0.30), residues: 726 helix: 0.31 (0.20), residues: 595 sheet: None (None), residues: 0 loop : -2.68 (0.52), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 394 HIS 0.008 0.001 HIS B 328 PHE 0.013 0.001 PHE A 99 TYR 0.006 0.001 TYR B 359 ARG 0.004 0.000 ARG B 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.794 Fit side-chains REVERT: A 34 GLN cc_start: 0.7379 (tt0) cc_final: 0.6849 (tm-30) REVERT: A 106 ASP cc_start: 0.8089 (p0) cc_final: 0.7549 (p0) REVERT: A 415 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7060 (mm-30) REVERT: A 444 SER cc_start: 0.6049 (OUTLIER) cc_final: 0.5758 (p) REVERT: B 34 GLN cc_start: 0.7379 (tt0) cc_final: 0.6851 (tm-30) REVERT: B 106 ASP cc_start: 0.8093 (p0) cc_final: 0.7539 (p0) REVERT: B 415 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7061 (mm-30) REVERT: B 434 PHE cc_start: 0.7190 (t80) cc_final: 0.6963 (t80) REVERT: B 444 SER cc_start: 0.6032 (OUTLIER) cc_final: 0.5755 (p) outliers start: 13 outliers final: 4 residues processed: 106 average time/residue: 2.1498 time to fit residues: 240.9766 Evaluate side-chains 87 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 64 GLN A 360 GLN B 34 GLN B 64 GLN B 360 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5830 Z= 0.249 Angle : 0.547 4.969 7946 Z= 0.297 Chirality : 0.038 0.150 978 Planarity : 0.004 0.039 974 Dihedral : 5.073 30.306 786 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.43 % Allowed : 17.31 % Favored : 80.26 % 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: 1.29 (0.31), residues: 726 helix: 1.46 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.98 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.002 PHE A 389 TYR 0.013 0.003 TYR A 359 ARG 0.001 0.000 ARG A 442 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.963 Fit side-chains REVERT: A 34 GLN cc_start: 0.7454 (tt0) cc_final: 0.6820 (tm-30) REVERT: A 408 SER cc_start: 0.7954 (OUTLIER) cc_final: 0.7491 (p) REVERT: A 415 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6934 (mm-30) REVERT: B 34 GLN cc_start: 0.7452 (tt0) cc_final: 0.6818 (tm-30) REVERT: B 306 THR cc_start: 0.7314 (p) cc_final: 0.7015 (m) REVERT: B 408 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7500 (p) REVERT: B 415 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6932 (mm-30) outliers start: 15 outliers final: 4 residues processed: 99 average time/residue: 1.9190 time to fit residues: 201.0945 Evaluate side-chains 82 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 408 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5830 Z= 0.261 Angle : 0.535 4.778 7946 Z= 0.288 Chirality : 0.039 0.151 978 Planarity : 0.004 0.040 974 Dihedral : 4.929 33.566 784 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.53 % Allowed : 15.21 % Favored : 80.26 % 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 (0.31), residues: 726 helix: 1.72 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.87 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP A 324 HIS 0.006 0.002 HIS A 328 PHE 0.021 0.002 PHE B 99 TYR 0.014 0.003 TYR A 359 ARG 0.001 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 75 time to evaluate : 0.905 Fit side-chains REVERT: A 34 GLN cc_start: 0.7525 (tt0) cc_final: 0.6822 (tm-30) REVERT: A 152 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7776 (t) REVERT: A 408 SER cc_start: 0.7969 (OUTLIER) cc_final: 0.7523 (p) REVERT: A 415 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6942 (mm-30) REVERT: A 444 SER cc_start: 0.6136 (OUTLIER) cc_final: 0.5887 (p) REVERT: A 460 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7799 (tt) REVERT: B 34 GLN cc_start: 0.7531 (tt0) cc_final: 0.6827 (tm-30) REVERT: B 152 VAL cc_start: 0.8076 (OUTLIER) cc_final: 0.7766 (t) REVERT: B 306 THR cc_start: 0.7393 (p) cc_final: 0.7066 (m) REVERT: B 408 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7528 (p) REVERT: B 415 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6953 (mm-30) REVERT: B 444 SER cc_start: 0.6122 (OUTLIER) cc_final: 0.5886 (p) REVERT: B 460 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7816 (tt) outliers start: 28 outliers final: 10 residues processed: 95 average time/residue: 2.2573 time to fit residues: 227.0671 Evaluate side-chains 90 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 65 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5830 Z= 0.182 Angle : 0.485 4.415 7946 Z= 0.258 Chirality : 0.036 0.133 978 Planarity : 0.004 0.040 974 Dihedral : 4.696 34.756 784 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.24 % Allowed : 16.34 % Favored : 80.42 % 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: 2.27 (0.32), residues: 726 helix: 2.15 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.71 (0.56), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.018 0.001 PHE B 99 TYR 0.013 0.002 TYR A 359 ARG 0.002 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7465 (tt0) cc_final: 0.6799 (tm-30) REVERT: A 152 VAL cc_start: 0.8109 (OUTLIER) cc_final: 0.7782 (t) REVERT: A 306 THR cc_start: 0.7411 (p) cc_final: 0.7066 (m) REVERT: A 444 SER cc_start: 0.6098 (OUTLIER) cc_final: 0.5867 (p) REVERT: A 460 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7748 (tt) REVERT: B 34 GLN cc_start: 0.7468 (tt0) cc_final: 0.6803 (tm-30) REVERT: B 152 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7775 (t) REVERT: B 306 THR cc_start: 0.7417 (p) cc_final: 0.7078 (m) REVERT: B 460 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7772 (tt) outliers start: 20 outliers final: 8 residues processed: 92 average time/residue: 2.1435 time to fit residues: 208.8019 Evaluate side-chains 91 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5830 Z= 0.238 Angle : 0.517 4.664 7946 Z= 0.278 Chirality : 0.038 0.147 978 Planarity : 0.004 0.039 974 Dihedral : 4.687 36.396 782 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.56 % Allowed : 17.48 % Favored : 78.96 % 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: 2.21 (0.31), residues: 726 helix: 2.09 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.64 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 324 HIS 0.006 0.001 HIS A 328 PHE 0.022 0.002 PHE A 99 TYR 0.014 0.002 TYR B 359 ARG 0.001 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 79 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7514 (tt0) cc_final: 0.6851 (tm-30) REVERT: A 152 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7793 (t) REVERT: A 306 THR cc_start: 0.7440 (p) cc_final: 0.7077 (m) REVERT: A 444 SER cc_start: 0.6124 (OUTLIER) cc_final: 0.5884 (p) REVERT: B 34 GLN cc_start: 0.7507 (tt0) cc_final: 0.6804 (tm-30) REVERT: B 152 VAL cc_start: 0.8107 (OUTLIER) cc_final: 0.7786 (t) REVERT: B 306 THR cc_start: 0.7439 (p) cc_final: 0.7075 (m) REVERT: B 444 SER cc_start: 0.6108 (OUTLIER) cc_final: 0.5880 (p) REVERT: B 460 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7850 (tt) outliers start: 22 outliers final: 10 residues processed: 95 average time/residue: 2.0804 time to fit residues: 209.4413 Evaluate side-chains 94 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 460 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5830 Z= 0.215 Angle : 0.502 4.446 7946 Z= 0.268 Chirality : 0.037 0.143 978 Planarity : 0.004 0.039 974 Dihedral : 4.654 38.318 782 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.88 % Allowed : 16.67 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.31), residues: 726 helix: 2.25 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.61 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.002 PHE B 99 TYR 0.014 0.002 TYR A 359 ARG 0.002 0.000 ARG B 474 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7514 (tt0) cc_final: 0.6847 (tm-30) REVERT: A 152 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7794 (t) REVERT: A 306 THR cc_start: 0.7462 (p) cc_final: 0.7091 (m) REVERT: A 444 SER cc_start: 0.6151 (OUTLIER) cc_final: 0.5892 (p) REVERT: B 34 GLN cc_start: 0.7520 (tt0) cc_final: 0.6855 (tm-30) REVERT: B 152 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7786 (t) REVERT: B 306 THR cc_start: 0.7462 (p) cc_final: 0.7093 (m) REVERT: B 444 SER cc_start: 0.6141 (OUTLIER) cc_final: 0.5899 (p) outliers start: 24 outliers final: 11 residues processed: 97 average time/residue: 2.0974 time to fit residues: 215.4599 Evaluate side-chains 93 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5830 Z= 0.196 Angle : 0.491 4.445 7946 Z= 0.262 Chirality : 0.037 0.138 978 Planarity : 0.004 0.039 974 Dihedral : 4.612 38.877 782 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.40 % Allowed : 17.48 % Favored : 79.13 % 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: 2.60 (0.31), residues: 726 helix: 2.34 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.44 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.002 PHE A 99 TYR 0.013 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7506 (tt0) cc_final: 0.6850 (tm-30) REVERT: A 129 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7900 (mt) REVERT: A 152 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7791 (t) REVERT: A 306 THR cc_start: 0.7462 (p) cc_final: 0.7096 (m) REVERT: A 363 SER cc_start: 0.7401 (OUTLIER) cc_final: 0.7146 (m) REVERT: A 408 SER cc_start: 0.7980 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 444 SER cc_start: 0.6147 (OUTLIER) cc_final: 0.5882 (p) REVERT: B 34 GLN cc_start: 0.7512 (tt0) cc_final: 0.6847 (tm-30) REVERT: B 152 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7785 (t) REVERT: B 306 THR cc_start: 0.7461 (p) cc_final: 0.7090 (m) REVERT: B 363 SER cc_start: 0.7395 (OUTLIER) cc_final: 0.7153 (m) REVERT: B 408 SER cc_start: 0.7988 (OUTLIER) cc_final: 0.7572 (p) REVERT: B 444 SER cc_start: 0.6141 (OUTLIER) cc_final: 0.5889 (p) outliers start: 21 outliers final: 11 residues processed: 95 average time/residue: 2.1325 time to fit residues: 216.1418 Evaluate side-chains 99 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 79 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5830 Z= 0.195 Angle : 0.490 4.447 7946 Z= 0.261 Chirality : 0.037 0.138 978 Planarity : 0.004 0.039 974 Dihedral : 4.586 39.573 782 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.05 % Allowed : 16.83 % Favored : 79.13 % 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: 2.66 (0.31), residues: 726 helix: 2.38 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.41 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.002 PHE A 99 TYR 0.013 0.002 TYR B 359 ARG 0.001 0.000 ARG B 474 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7512 (tt0) cc_final: 0.6843 (tm-30) REVERT: A 152 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7789 (t) REVERT: A 306 THR cc_start: 0.7461 (p) cc_final: 0.7091 (m) REVERT: A 363 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.7172 (m) REVERT: A 408 SER cc_start: 0.7989 (OUTLIER) cc_final: 0.7577 (p) REVERT: A 444 SER cc_start: 0.6144 (OUTLIER) cc_final: 0.5882 (p) REVERT: B 34 GLN cc_start: 0.7515 (tt0) cc_final: 0.6848 (tm-30) REVERT: B 106 ASP cc_start: 0.8525 (p0) cc_final: 0.7999 (p0) REVERT: B 152 VAL cc_start: 0.8114 (OUTLIER) cc_final: 0.7780 (t) REVERT: B 306 THR cc_start: 0.7462 (p) cc_final: 0.7088 (m) REVERT: B 363 SER cc_start: 0.7382 (OUTLIER) cc_final: 0.7149 (m) REVERT: B 408 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7585 (p) REVERT: B 444 SER cc_start: 0.6134 (OUTLIER) cc_final: 0.5877 (p) outliers start: 25 outliers final: 10 residues processed: 99 average time/residue: 1.9881 time to fit residues: 208.8355 Evaluate side-chains 98 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 58 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5830 Z= 0.195 Angle : 0.490 4.501 7946 Z= 0.262 Chirality : 0.037 0.139 978 Planarity : 0.004 0.039 974 Dihedral : 4.587 39.995 782 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.40 % Allowed : 17.31 % Favored : 79.29 % 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: 2.69 (0.31), residues: 726 helix: 2.40 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.38 (0.56), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.002 PHE B 99 TYR 0.013 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7515 (tt0) cc_final: 0.6848 (tm-30) REVERT: A 152 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7784 (t) REVERT: A 306 THR cc_start: 0.7459 (p) cc_final: 0.7086 (m) REVERT: A 363 SER cc_start: 0.7418 (OUTLIER) cc_final: 0.7180 (m) REVERT: A 408 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7586 (p) REVERT: A 444 SER cc_start: 0.6155 (OUTLIER) cc_final: 0.5880 (p) REVERT: B 34 GLN cc_start: 0.7516 (tt0) cc_final: 0.6849 (tm-30) REVERT: B 152 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7779 (t) REVERT: B 306 THR cc_start: 0.7460 (p) cc_final: 0.7085 (m) REVERT: B 363 SER cc_start: 0.7376 (OUTLIER) cc_final: 0.7147 (m) REVERT: B 408 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7580 (p) REVERT: B 444 SER cc_start: 0.6137 (OUTLIER) cc_final: 0.5875 (p) outliers start: 21 outliers final: 9 residues processed: 96 average time/residue: 1.7409 time to fit residues: 177.2178 Evaluate side-chains 96 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5830 Z= 0.226 Angle : 0.512 4.580 7946 Z= 0.274 Chirality : 0.038 0.146 978 Planarity : 0.004 0.038 974 Dihedral : 4.669 40.767 782 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.72 % Allowed : 17.15 % Favored : 79.13 % 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: 2.52 (0.31), residues: 726 helix: 2.25 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -1.32 (0.56), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 324 HIS 0.006 0.001 HIS B 328 PHE 0.022 0.002 PHE B 99 TYR 0.014 0.002 TYR B 359 ARG 0.001 0.000 ARG A 463 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7533 (tt0) cc_final: 0.6857 (tm-30) REVERT: A 152 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7799 (t) REVERT: A 306 THR cc_start: 0.7448 (p) cc_final: 0.7075 (m) REVERT: A 363 SER cc_start: 0.7439 (OUTLIER) cc_final: 0.7207 (m) REVERT: A 408 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 444 SER cc_start: 0.6163 (OUTLIER) cc_final: 0.5889 (p) REVERT: B 34 GLN cc_start: 0.7530 (tt0) cc_final: 0.6855 (tm-30) REVERT: B 152 VAL cc_start: 0.8112 (OUTLIER) cc_final: 0.7787 (t) REVERT: B 306 THR cc_start: 0.7463 (p) cc_final: 0.7093 (m) REVERT: B 363 SER cc_start: 0.7421 (OUTLIER) cc_final: 0.7201 (m) REVERT: B 408 SER cc_start: 0.7998 (OUTLIER) cc_final: 0.7573 (p) REVERT: B 444 SER cc_start: 0.6149 (OUTLIER) cc_final: 0.5888 (p) outliers start: 23 outliers final: 9 residues processed: 96 average time/residue: 2.0057 time to fit residues: 203.6437 Evaluate side-chains 96 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 444 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.167639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.144645 restraints weight = 13815.075| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 0.93 r_work: 0.3234 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5830 Z= 0.206 Angle : 0.497 4.555 7946 Z= 0.266 Chirality : 0.037 0.141 978 Planarity : 0.004 0.039 974 Dihedral : 4.628 41.207 782 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.07 % Allowed : 17.80 % Favored : 79.13 % 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: 2.63 (0.31), residues: 726 helix: 2.32 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -1.27 (0.57), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.019 0.002 PHE B 99 TYR 0.014 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5210.74 seconds wall clock time: 99 minutes 8.05 seconds (5948.05 seconds total)