Starting phenix.real_space_refine on Tue Jul 29 20:57:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wc9_21603/07_2025/6wc9_21603.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wc9_21603/07_2025/6wc9_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/cci-nas-00/data/ceres_data/6wc9_21603/07_2025/6wc9_21603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wc9_21603/07_2025/6wc9_21603.map" model { file = "/net/cci-nas-00/data/ceres_data/6wc9_21603/07_2025/6wc9_21603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wc9_21603/07_2025/6wc9_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.94, 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: 3.39 Conformation dependent library (CDL) restraints added in 995.5 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 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: 1.02 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: 4.43 Time building geometry restraints manager: 4.09 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: 12.680 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: 0.220 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.710 Find NCS groups from input model: 0.280 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:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.270 ------------------------------------------------------------------------------- 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= 0.346 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 Details of bonding type rmsd hydrogen bonds : bond 0.12139 ( 466) hydrogen bonds : angle 4.86041 ( 1368) covalent geometry : bond 0.00592 ( 5830) covalent geometry : angle 0.53684 ( 7946) *********************** 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 to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.834 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: 2.2470 time to fit residues: 253.3029 Evaluate side-chains 87 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.168222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.147039 restraints weight = 13805.739| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 0.87 r_work: 0.3162 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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= 0.174 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 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 466) hydrogen bonds : angle 3.87916 ( 1368) covalent geometry : bond 0.00385 ( 5830) covalent geometry : angle 0.54690 ( 7946) *********************** 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 to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.353 Fit side-chains REVERT: A 34 GLN cc_start: 0.8326 (tt0) cc_final: 0.7663 (tm-30) REVERT: A 408 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7869 (p) REVERT: A 415 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7446 (mm-30) REVERT: B 34 GLN cc_start: 0.8313 (tt0) cc_final: 0.7655 (tm-30) REVERT: B 306 THR cc_start: 0.7750 (p) cc_final: 0.7390 (m) REVERT: B 408 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7863 (p) REVERT: B 415 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7433 (mm-30) outliers start: 15 outliers final: 4 residues processed: 99 average time/residue: 2.7308 time to fit residues: 287.0058 Evaluate side-chains 82 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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 37 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 40 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN B 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.169348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.151677 restraints weight = 13760.330| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 0.83 r_work: 0.3261 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2314 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= 0.128 Angle : 0.480 4.390 7946 Z= 0.255 Chirality : 0.036 0.132 978 Planarity : 0.004 0.038 974 Dihedral : 4.606 31.591 784 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.40 % Allowed : 16.02 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.32), residues: 726 helix: 2.08 (0.21), residues: 597 sheet: None (None), residues: 0 loop : -1.90 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.017 0.001 PHE B 99 TYR 0.012 0.002 TYR A 359 ARG 0.001 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 466) hydrogen bonds : angle 3.71105 ( 1368) covalent geometry : bond 0.00279 ( 5830) covalent geometry : angle 0.47980 ( 7946) *********************** 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 to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.953 Fit side-chains REVERT: A 34 GLN cc_start: 0.8511 (tt0) cc_final: 0.7681 (tm-30) REVERT: A 152 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7950 (t) REVERT: A 306 THR cc_start: 0.7732 (p) cc_final: 0.7412 (m) REVERT: A 415 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7497 (mm-30) REVERT: A 444 SER cc_start: 0.6366 (OUTLIER) cc_final: 0.6121 (p) REVERT: A 460 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7944 (tt) REVERT: B 34 GLN cc_start: 0.8509 (tt0) cc_final: 0.7680 (tm-30) REVERT: B 152 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7938 (t) REVERT: B 306 THR cc_start: 0.7721 (p) cc_final: 0.7411 (m) REVERT: B 460 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7986 (tt) outliers start: 21 outliers final: 6 residues processed: 95 average time/residue: 2.3560 time to fit residues: 235.6354 Evaluate side-chains 91 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 460 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.167378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.142289 restraints weight = 13916.468| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 0.97 r_work: 0.3117 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5830 Z= 0.154 Angle : 0.514 4.696 7946 Z= 0.276 Chirality : 0.037 0.144 978 Planarity : 0.004 0.039 974 Dihedral : 4.635 34.103 782 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.56 % Allowed : 16.18 % 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: 2.24 (0.31), residues: 726 helix: 2.11 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.67 (0.56), 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 B 99 TYR 0.014 0.002 TYR A 359 ARG 0.002 0.000 ARG B 474 Details of bonding type rmsd hydrogen bonds : bond 0.05315 ( 466) hydrogen bonds : angle 3.73388 ( 1368) covalent geometry : bond 0.00348 ( 5830) covalent geometry : angle 0.51376 ( 7946) *********************** 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 98 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.831 Fit side-chains REVERT: A 34 GLN cc_start: 0.8413 (tt0) cc_final: 0.7663 (tm-30) REVERT: A 152 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8003 (t) REVERT: A 306 THR cc_start: 0.7795 (p) cc_final: 0.7396 (m) REVERT: A 415 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 444 SER cc_start: 0.6379 (OUTLIER) cc_final: 0.6160 (p) REVERT: A 460 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8069 (tt) REVERT: B 34 GLN cc_start: 0.8388 (tt0) cc_final: 0.7658 (tm-30) REVERT: B 152 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.7996 (t) REVERT: B 306 THR cc_start: 0.7790 (p) cc_final: 0.7411 (m) REVERT: B 444 SER cc_start: 0.6360 (OUTLIER) cc_final: 0.6148 (p) REVERT: B 460 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8087 (tt) outliers start: 22 outliers final: 10 residues processed: 92 average time/residue: 2.2003 time to fit residues: 214.1136 Evaluate side-chains 91 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 426 TYR Chi-restraints excluded: chain B residue 444 SER 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 23 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 53 optimal weight: 0.2980 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.168356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.141736 restraints weight = 13864.494| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.04 r_work: 0.3099 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5830 Z= 0.129 Angle : 0.480 4.424 7946 Z= 0.255 Chirality : 0.036 0.134 978 Planarity : 0.004 0.038 974 Dihedral : 4.524 35.257 782 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.88 % Allowed : 16.50 % Favored : 79.61 % 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: 2.58 (0.32), residues: 726 helix: 2.36 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.62 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 324 HIS 0.005 0.001 HIS A 328 PHE 0.017 0.001 PHE B 99 TYR 0.013 0.002 TYR A 359 ARG 0.001 0.000 ARG A 442 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 466) hydrogen bonds : angle 3.65413 ( 1368) covalent geometry : bond 0.00281 ( 5830) covalent geometry : angle 0.47991 ( 7946) *********************** 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 107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.919 Fit side-chains REVERT: A 34 GLN cc_start: 0.8459 (tt0) cc_final: 0.7689 (tm-30) REVERT: A 152 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.7999 (t) REVERT: A 306 THR cc_start: 0.7781 (p) cc_final: 0.7381 (m) REVERT: A 444 SER cc_start: 0.6376 (OUTLIER) cc_final: 0.6153 (p) REVERT: A 460 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8064 (tt) REVERT: B 34 GLN cc_start: 0.8448 (tt0) cc_final: 0.7649 (tm-30) REVERT: B 152 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.7993 (t) REVERT: B 306 THR cc_start: 0.7782 (p) cc_final: 0.7385 (m) REVERT: B 444 SER cc_start: 0.6348 (OUTLIER) cc_final: 0.6135 (p) REVERT: B 460 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8083 (tt) outliers start: 24 outliers final: 12 residues processed: 99 average time/residue: 2.0514 time to fit residues: 215.0397 Evaluate side-chains 98 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 362 THR 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 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.167684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.140962 restraints weight = 14027.036| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.04 r_work: 0.3094 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2778 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= 0.145 Angle : 0.499 4.452 7946 Z= 0.267 Chirality : 0.037 0.141 978 Planarity : 0.004 0.038 974 Dihedral : 4.606 36.434 782 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.53 % Allowed : 16.34 % 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: 2.35 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.53 (0.54), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 324 HIS 0.006 0.001 HIS A 328 PHE 0.020 0.002 PHE B 99 TYR 0.013 0.002 TYR B 359 ARG 0.002 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.05099 ( 466) hydrogen bonds : angle 3.68188 ( 1368) covalent geometry : bond 0.00323 ( 5830) covalent geometry : angle 0.49937 ( 7946) *********************** 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 107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.922 Fit side-chains REVERT: A 34 GLN cc_start: 0.8450 (tt0) cc_final: 0.7681 (tm-30) REVERT: A 152 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8017 (t) REVERT: A 306 THR cc_start: 0.7814 (p) cc_final: 0.7401 (m) REVERT: A 408 SER cc_start: 0.8206 (OUTLIER) cc_final: 0.7902 (p) REVERT: A 444 SER cc_start: 0.6402 (OUTLIER) cc_final: 0.6172 (p) REVERT: B 34 GLN cc_start: 0.8434 (tt0) cc_final: 0.7675 (tm-30) REVERT: B 152 VAL cc_start: 0.8330 (OUTLIER) cc_final: 0.8008 (t) REVERT: B 306 THR cc_start: 0.7789 (p) cc_final: 0.7388 (m) REVERT: B 408 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7910 (p) REVERT: B 444 SER cc_start: 0.6377 (OUTLIER) cc_final: 0.6158 (p) REVERT: B 460 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8125 (tt) outliers start: 28 outliers final: 12 residues processed: 97 average time/residue: 2.0256 time to fit residues: 208.4201 Evaluate side-chains 99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 362 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.167324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.142512 restraints weight = 14042.152| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.00 r_work: 0.3113 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2867 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= 0.152 Angle : 0.506 4.487 7946 Z= 0.271 Chirality : 0.037 0.145 978 Planarity : 0.004 0.038 974 Dihedral : 4.654 37.982 782 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.37 % Allowed : 16.02 % Favored : 79.61 % 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: 2.54 (0.31), residues: 726 helix: 2.31 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.49 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 324 HIS 0.006 0.001 HIS A 328 PHE 0.020 0.002 PHE A 99 TYR 0.014 0.002 TYR A 359 ARG 0.001 0.000 ARG B 474 Details of bonding type rmsd hydrogen bonds : bond 0.05211 ( 466) hydrogen bonds : angle 3.72114 ( 1368) covalent geometry : bond 0.00343 ( 5830) covalent geometry : angle 0.50631 ( 7946) *********************** 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 107 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.893 Fit side-chains REVERT: A 34 GLN cc_start: 0.8392 (tt0) cc_final: 0.7687 (tm-30) REVERT: A 152 VAL cc_start: 0.8341 (OUTLIER) cc_final: 0.8017 (t) REVERT: A 306 THR cc_start: 0.7832 (p) cc_final: 0.7418 (m) REVERT: A 363 SER cc_start: 0.7749 (OUTLIER) cc_final: 0.7427 (m) REVERT: A 408 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7913 (p) REVERT: A 444 SER cc_start: 0.6417 (OUTLIER) cc_final: 0.6166 (p) REVERT: B 34 GLN cc_start: 0.8349 (tt0) cc_final: 0.7681 (tm-30) REVERT: B 152 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8011 (t) REVERT: B 306 THR cc_start: 0.7812 (p) cc_final: 0.7399 (m) REVERT: B 408 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7915 (p) REVERT: B 444 SER cc_start: 0.6404 (OUTLIER) cc_final: 0.6172 (p) outliers start: 27 outliers final: 12 residues processed: 96 average time/residue: 2.0518 time to fit residues: 208.7919 Evaluate side-chains 97 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL 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 362 THR 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 51 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.166668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.140391 restraints weight = 14067.090| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.08 r_work: 0.3105 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2926 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= 0.166 Angle : 0.520 4.765 7946 Z= 0.280 Chirality : 0.038 0.150 978 Planarity : 0.004 0.038 974 Dihedral : 4.741 39.438 782 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.72 % Allowed : 16.99 % 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: 2.41 (0.31), residues: 726 helix: 2.21 (0.21), residues: 599 sheet: None (None), residues: 0 loop : -1.50 (0.55), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 324 HIS 0.006 0.001 HIS A 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 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 466) hydrogen bonds : angle 3.75606 ( 1368) covalent geometry : bond 0.00379 ( 5830) covalent geometry : angle 0.52049 ( 7946) *********************** 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 101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.979 Fit side-chains REVERT: A 34 GLN cc_start: 0.8514 (tt0) cc_final: 0.7737 (tm-30) REVERT: A 152 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8032 (t) REVERT: A 306 THR cc_start: 0.7846 (p) cc_final: 0.7422 (m) REVERT: A 363 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7471 (m) REVERT: A 408 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7945 (p) REVERT: A 444 SER cc_start: 0.6426 (OUTLIER) cc_final: 0.6199 (p) REVERT: B 34 GLN cc_start: 0.8484 (tt0) cc_final: 0.7729 (tm-30) REVERT: B 152 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8021 (t) REVERT: B 306 THR cc_start: 0.7852 (p) cc_final: 0.7437 (m) REVERT: B 408 SER cc_start: 0.8242 (OUTLIER) cc_final: 0.7931 (p) REVERT: B 444 SER cc_start: 0.6427 (OUTLIER) cc_final: 0.6217 (p) outliers start: 23 outliers final: 11 residues processed: 93 average time/residue: 2.1301 time to fit residues: 210.6335 Evaluate side-chains 96 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 362 THR 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 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 42 optimal weight: 0.3980 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 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 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.167451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.142746 restraints weight = 13981.928| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.01 r_work: 0.3106 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2933 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= 0.145 Angle : 0.499 4.471 7946 Z= 0.267 Chirality : 0.037 0.143 978 Planarity : 0.004 0.039 974 Dihedral : 4.667 40.005 782 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.24 % Allowed : 17.64 % 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: 2.55 (0.31), residues: 726 helix: 2.28 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -1.39 (0.56), 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 0.013 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.05102 ( 466) hydrogen bonds : angle 3.73094 ( 1368) covalent geometry : bond 0.00323 ( 5830) covalent geometry : angle 0.49904 ( 7946) *********************** 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 99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.893 Fit side-chains REVERT: A 34 GLN cc_start: 0.8446 (tt0) cc_final: 0.7693 (tm-30) REVERT: A 152 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8013 (t) REVERT: A 306 THR cc_start: 0.7818 (p) cc_final: 0.7410 (m) REVERT: A 363 SER cc_start: 0.7728 (OUTLIER) cc_final: 0.7429 (m) REVERT: A 408 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7902 (p) REVERT: A 444 SER cc_start: 0.6405 (OUTLIER) cc_final: 0.6158 (p) REVERT: B 34 GLN cc_start: 0.8396 (tt0) cc_final: 0.7691 (tm-30) REVERT: B 152 VAL cc_start: 0.8340 (OUTLIER) cc_final: 0.8007 (t) REVERT: B 306 THR cc_start: 0.7825 (p) cc_final: 0.7418 (m) REVERT: B 408 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.7893 (p) REVERT: B 444 SER cc_start: 0.6391 (OUTLIER) cc_final: 0.6156 (p) outliers start: 20 outliers final: 11 residues processed: 94 average time/residue: 2.1496 time to fit residues: 214.1582 Evaluate side-chains 96 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 362 THR 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 25 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 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 360 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.167340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.142783 restraints weight = 13955.025| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.00 r_work: 0.3110 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2960 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= 0.146 Angle : 0.500 4.557 7946 Z= 0.268 Chirality : 0.037 0.142 978 Planarity : 0.004 0.039 974 Dihedral : 4.670 40.747 782 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: 2.57 (0.31), residues: 726 helix: 2.29 (0.21), residues: 601 sheet: None (None), residues: 0 loop : -1.35 (0.56), 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 0.020 0.002 PHE A 99 TYR 0.014 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.05114 ( 466) hydrogen bonds : angle 3.71902 ( 1368) covalent geometry : bond 0.00328 ( 5830) covalent geometry : angle 0.50037 ( 7946) ********************** 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 to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 1.232 Fit side-chains REVERT: A 34 GLN cc_start: 0.8428 (tt0) cc_final: 0.7689 (tm-30) REVERT: A 152 VAL cc_start: 0.8347 (OUTLIER) cc_final: 0.8011 (t) REVERT: A 306 THR cc_start: 0.7817 (p) cc_final: 0.7406 (m) REVERT: A 363 SER cc_start: 0.7711 (OUTLIER) cc_final: 0.7420 (m) REVERT: A 408 SER cc_start: 0.8218 (OUTLIER) cc_final: 0.7898 (p) REVERT: A 444 SER cc_start: 0.6398 (OUTLIER) cc_final: 0.6147 (p) REVERT: B 34 GLN cc_start: 0.8392 (tt0) cc_final: 0.7693 (tm-30) REVERT: B 152 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8004 (t) REVERT: B 306 THR cc_start: 0.7817 (p) cc_final: 0.7412 (m) REVERT: B 363 SER cc_start: 0.7707 (OUTLIER) cc_final: 0.7410 (m) REVERT: B 408 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.7887 (p) REVERT: B 444 SER cc_start: 0.6382 (OUTLIER) cc_final: 0.6140 (p) outliers start: 23 outliers final: 12 residues processed: 95 average time/residue: 2.6283 time to fit residues: 264.1833 Evaluate side-chains 98 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL 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 362 THR 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 15 optimal weight: 0.9990 chunk 66 optimal weight: 0.2980 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 19 optimal weight: 0.0970 chunk 67 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.2378 ------------------------------------------------------------------------------- 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 = 0.3765 r_free = 0.3765 target = 0.170661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.147496 restraints weight = 13883.714| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 0.96 r_work: 0.3174 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5830 Z= 0.101 Angle : 0.449 4.765 7946 Z= 0.237 Chirality : 0.035 0.129 978 Planarity : 0.004 0.040 974 Dihedral : 4.390 40.401 782 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.27 % Allowed : 18.61 % 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: 3.20 (0.32), residues: 726 helix: 2.76 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.29 (0.56), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 394 HIS 0.002 0.000 HIS A 328 PHE 0.014 0.001 PHE B 99 TYR 0.011 0.002 TYR B 359 ARG 0.001 0.000 ARG A 506 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 466) hydrogen bonds : angle 3.57666 ( 1368) covalent geometry : bond 0.00206 ( 5830) covalent geometry : angle 0.44928 ( 7946) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8726.11 seconds wall clock time: 155 minutes 6.84 seconds (9306.84 seconds total)