Starting phenix.real_space_refine on Tue Jan 14 01:37:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xef_38288/01_2025/8xef_38288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xef_38288/01_2025/8xef_38288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xef_38288/01_2025/8xef_38288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xef_38288/01_2025/8xef_38288.map" model { file = "/net/cci-nas-00/data/ceres_data/8xef_38288/01_2025/8xef_38288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xef_38288/01_2025/8xef_38288.cif" } resolution = 4.41 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= 0.002 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3173 2.51 5 N 840 2.21 5 O 975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 5007 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1548 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 947 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 787 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain: "D" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 917 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Time building chain proxies: 3.18, per 1000 atoms: 0.64 Number of scatterers: 5007 At special positions: 0 Unit cell: (63.99, 109.35, 123.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 19 16.00 O 975 8.00 N 840 7.00 C 3173 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 594.5 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 15 sheets defined 5.9% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.799A pdb=" N ILE A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.583A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.730A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.522A pdb=" N GLN D 65 " --> pdb=" O PRO D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.627A pdb=" N ALA D 92 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 398 through 403 Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 61 removed outlier: 3.736A pdb=" N SER B 60 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR B 52 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N TRP B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ARG B 40 " --> pdb=" O TRP B 49 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 69 through 74 Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 23 removed outlier: 3.832A pdb=" N THR C 73 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.469A pdb=" N LEU C 45 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN C 36 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 47 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS C 33 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR C 35 " --> pdb=" O TYR C 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.469A pdb=" N LEU C 45 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN C 36 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 47 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS C 33 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR C 35 " --> pdb=" O TYR C 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.755A pdb=" N VAL D 18 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 45 through 51 removed outlier: 3.625A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.689A pdb=" N ARG E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.007A pdb=" N THR E 96 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 48 through 49 removed outlier: 3.593A pdb=" N ASN E 53 " --> pdb=" O PHE E 49 " (cutoff:3.500A) 108 hydrogen bonds defined for protein. 243 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: 1.24 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1580 1.34 - 1.46: 1204 1.46 - 1.58: 2334 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 5140 Sorted by residual: bond pdb=" CG1 ILE B 39 " pdb=" CD1 ILE B 39 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.23e+00 bond pdb=" CB ILE B 39 " pdb=" CG2 ILE B 39 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.13e+00 bond pdb=" CA THR D 58 " pdb=" CB THR D 58 " ideal model delta sigma weight residual 1.535 1.559 -0.023 1.64e-02 3.72e+03 2.01e+00 bond pdb=" CB GLN D 1 " pdb=" CG GLN D 1 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.68e+00 bond pdb=" C ALA A 520 " pdb=" N PRO A 521 " ideal model delta sigma weight residual 1.326 1.343 -0.017 1.44e-02 4.82e+03 1.40e+00 ... (remaining 5135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 6638 1.98 - 3.96: 279 3.96 - 5.94: 68 5.94 - 7.92: 15 7.92 - 9.89: 4 Bond angle restraints: 7004 Sorted by residual: angle pdb=" CA CYS E 23 " pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " ideal model delta sigma weight residual 114.40 124.29 -9.89 2.30e+00 1.89e-01 1.85e+01 angle pdb=" C THR E 30 " pdb=" N ASN E 31 " pdb=" CA ASN E 31 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY A 476 " pdb=" N ASN A 477 " pdb=" CA ASN A 477 " ideal model delta sigma weight residual 121.54 129.18 -7.64 1.91e+00 2.74e-01 1.60e+01 angle pdb=" C ARG E 22 " pdb=" N CYS E 23 " pdb=" CA CYS E 23 " ideal model delta sigma weight residual 122.94 117.56 5.38 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C THR B 32 " pdb=" N THR B 33 " pdb=" CA THR B 33 " ideal model delta sigma weight residual 121.54 128.35 -6.81 1.91e+00 2.74e-01 1.27e+01 ... (remaining 6999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2762 17.94 - 35.89: 209 35.89 - 53.83: 31 53.83 - 71.78: 9 71.78 - 89.72: 2 Dihedral angle restraints: 3013 sinusoidal: 1147 harmonic: 1866 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 27.60 65.40 1 1.00e+01 1.00e-02 5.60e+01 dihedral pdb=" CA CYS E 23 " pdb=" C CYS E 23 " pdb=" N GLN E 24 " pdb=" CA GLN E 24 " ideal model delta harmonic sigma weight residual -180.00 -145.97 -34.03 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 87 " pdb=" CB CYS C 87 " ideal model delta sinusoidal sigma weight residual 93.00 151.09 -58.09 1 1.00e+01 1.00e-02 4.52e+01 ... (remaining 3010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 650 0.084 - 0.168: 95 0.168 - 0.251: 11 0.251 - 0.335: 0 0.335 - 0.419: 2 Chirality restraints: 758 Sorted by residual: chirality pdb=" CB ILE E 83 " pdb=" CA ILE E 83 " pdb=" CG1 ILE E 83 " pdb=" CG2 ILE E 83 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" CB ILE D 52 " pdb=" CA ILE D 52 " pdb=" CG1 ILE D 52 " pdb=" CG2 ILE D 52 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CG LEU D 108 " pdb=" CB LEU D 108 " pdb=" CD1 LEU D 108 " pdb=" CD2 LEU D 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 755 not shown) Planarity restraints: 907 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 13 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO B 14 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 37 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" CD GLN C 37 " 0.047 2.00e-02 2.50e+03 pdb=" OE1 GLN C 37 " -0.018 2.00e-02 2.50e+03 pdb=" NE2 GLN C 37 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 58 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C THR D 58 " 0.034 2.00e-02 2.50e+03 pdb=" O THR D 58 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS D 59 " -0.012 2.00e-02 2.50e+03 ... (remaining 904 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 46 2.49 - 3.09: 3507 3.09 - 3.69: 8282 3.69 - 4.30: 10984 4.30 - 4.90: 17432 Nonbonded interactions: 40251 Sorted by model distance: nonbonded pdb=" CD1 PHE A 456 " pdb=" CE LYS D 31 " model vdw 1.886 2.992 nonbonded pdb=" OH TYR A 421 " pdb=" CD LYS D 31 " model vdw 2.251 3.440 nonbonded pdb=" O LEU D 108 " pdb=" OH TYR E 36 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR C 17 " pdb=" NH2 ARG C 19 " model vdw 2.270 3.120 nonbonded pdb=" OH TYR B 52 " pdb=" O ASP C 95 " model vdw 2.294 3.040 ... (remaining 40246 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.070 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 5140 Z= 0.294 Angle : 0.997 9.895 7004 Z= 0.525 Chirality : 0.062 0.419 758 Planarity : 0.008 0.080 907 Dihedral : 12.948 89.720 1811 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.86 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.14 (0.31), residues: 639 helix: -3.98 (0.52), residues: 33 sheet: -1.49 (0.35), residues: 204 loop : -2.33 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 36 HIS 0.011 0.002 HIS A 339 PHE 0.022 0.003 PHE A 338 TYR 0.025 0.002 TYR B 35 ARG 0.016 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8496 (t80) cc_final: 0.7808 (t80) REVERT: A 339 HIS cc_start: 0.8418 (m170) cc_final: 0.7241 (m170) REVERT: A 354 ASN cc_start: 0.8668 (m-40) cc_final: 0.8267 (m-40) REVERT: A 368 ILE cc_start: 0.9307 (mp) cc_final: 0.9064 (mp) REVERT: A 396 TYR cc_start: 0.8505 (m-10) cc_final: 0.8302 (m-80) REVERT: B 103 TYR cc_start: 0.8318 (p90) cc_final: 0.8049 (p90) REVERT: B 108 PHE cc_start: 0.8482 (m-80) cc_final: 0.7588 (m-80) REVERT: C 16 LYS cc_start: 0.9618 (tmtt) cc_final: 0.9403 (tmtt) REVERT: C 35 TYR cc_start: 0.8536 (m-80) cc_final: 0.7686 (m-80) REVERT: C 49 TYR cc_start: 0.9200 (m-80) cc_final: 0.8943 (m-80) REVERT: C 61 PHE cc_start: 0.9103 (m-10) cc_final: 0.8838 (m-80) REVERT: D 71 THR cc_start: 0.9290 (p) cc_final: 0.8976 (p) REVERT: D 81 MET cc_start: 0.9051 (mmp) cc_final: 0.8688 (mmp) REVERT: D 83 LEU cc_start: 0.9299 (tp) cc_final: 0.9033 (tp) REVERT: D 100 GLU cc_start: 0.7745 (mp0) cc_final: 0.6465 (mp0) REVERT: E 47 LEU cc_start: 0.9515 (mm) cc_final: 0.9187 (mm) REVERT: E 71 PHE cc_start: 0.8686 (m-80) cc_final: 0.8157 (m-80) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2240 time to fit residues: 38.4261 Evaluate side-chains 102 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.0770 chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 36 optimal weight: 0.0470 chunk 57 optimal weight: 20.0000 overall best weight: 4.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.036268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.026354 restraints weight = 41202.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027806 restraints weight = 22926.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.028848 restraints weight = 15282.231| |-----------------------------------------------------------------------------| r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5140 Z= 0.312 Angle : 0.711 8.528 7004 Z= 0.375 Chirality : 0.046 0.207 758 Planarity : 0.006 0.059 907 Dihedral : 6.132 30.886 710 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.33 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.18 (0.31), residues: 639 helix: -3.96 (0.50), residues: 32 sheet: -1.68 (0.33), residues: 208 loop : -2.27 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 90 HIS 0.003 0.001 HIS C 96 PHE 0.026 0.002 PHE E 87 TYR 0.013 0.002 TYR D 32 ARG 0.005 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8478 (t80) cc_final: 0.8119 (t80) REVERT: A 396 TYR cc_start: 0.8678 (m-10) cc_final: 0.8434 (m-80) REVERT: B 56 ASN cc_start: 0.9132 (m-40) cc_final: 0.8828 (m-40) REVERT: B 57 TRP cc_start: 0.9593 (m-90) cc_final: 0.9298 (m-90) REVERT: B 100 PHE cc_start: 0.7602 (m-80) cc_final: 0.7356 (m-80) REVERT: B 103 TYR cc_start: 0.8619 (p90) cc_final: 0.8328 (p90) REVERT: B 108 PHE cc_start: 0.8739 (m-80) cc_final: 0.8423 (m-80) REVERT: B 110 PHE cc_start: 0.9175 (m-80) cc_final: 0.8770 (m-80) REVERT: B 111 ASP cc_start: 0.9217 (t0) cc_final: 0.8938 (t0) REVERT: C 35 TYR cc_start: 0.8660 (m-80) cc_final: 0.7912 (m-80) REVERT: C 49 TYR cc_start: 0.9324 (m-80) cc_final: 0.8690 (m-80) REVERT: C 85 TYR cc_start: 0.9254 (m-80) cc_final: 0.8827 (m-80) REVERT: D 71 THR cc_start: 0.9290 (p) cc_final: 0.8900 (p) REVERT: D 80 TYR cc_start: 0.9357 (m-80) cc_final: 0.9015 (m-80) REVERT: D 100 GLU cc_start: 0.7949 (mp0) cc_final: 0.7247 (mp0) REVERT: D 110 TYR cc_start: 0.9484 (m-80) cc_final: 0.9147 (m-10) REVERT: E 70 ASP cc_start: 0.9519 (m-30) cc_final: 0.9311 (t0) REVERT: E 87 PHE cc_start: 0.9323 (m-80) cc_final: 0.8824 (m-10) REVERT: E 93 ASP cc_start: 0.9199 (m-30) cc_final: 0.8744 (p0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1968 time to fit residues: 30.4511 Evaluate side-chains 96 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.033434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.024010 restraints weight = 44813.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.025330 restraints weight = 24508.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.026272 restraints weight = 16404.990| |-----------------------------------------------------------------------------| r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 5140 Z= 0.427 Angle : 0.786 10.203 7004 Z= 0.418 Chirality : 0.048 0.276 758 Planarity : 0.007 0.060 907 Dihedral : 6.582 27.768 710 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 31.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.99 % Favored : 86.85 % Rotamer: Outliers : 0.18 % Allowed : 6.02 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.53 (0.30), residues: 639 helix: -4.03 (0.49), residues: 33 sheet: -1.84 (0.33), residues: 203 loop : -2.58 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 47 HIS 0.008 0.002 HIS C 96 PHE 0.022 0.003 PHE A 456 TYR 0.015 0.003 TYR D 60 ARG 0.007 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8431 (t80) cc_final: 0.8098 (t80) REVERT: A 396 TYR cc_start: 0.8826 (m-10) cc_final: 0.8551 (m-80) REVERT: B 100 PHE cc_start: 0.8246 (m-80) cc_final: 0.7329 (m-80) REVERT: B 108 PHE cc_start: 0.8874 (m-80) cc_final: 0.7680 (m-80) REVERT: B 110 PHE cc_start: 0.9309 (m-80) cc_final: 0.8854 (m-80) REVERT: B 111 ASP cc_start: 0.9303 (t0) cc_final: 0.8937 (t0) REVERT: C 35 TYR cc_start: 0.8790 (m-80) cc_final: 0.7876 (m-80) REVERT: C 49 TYR cc_start: 0.9473 (m-80) cc_final: 0.8877 (m-80) REVERT: C 85 TYR cc_start: 0.9173 (m-80) cc_final: 0.8845 (m-80) REVERT: D 51 ASN cc_start: 0.9673 (t0) cc_final: 0.9436 (t0) REVERT: D 80 TYR cc_start: 0.9208 (m-80) cc_final: 0.8958 (m-80) REVERT: E 47 LEU cc_start: 0.9674 (mm) cc_final: 0.9356 (mm) outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.1673 time to fit residues: 22.7284 Evaluate side-chains 77 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 10.0000 chunk 42 optimal weight: 0.0270 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.035554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.025504 restraints weight = 42285.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.026970 restraints weight = 22712.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.028038 restraints weight = 14987.411| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5140 Z= 0.241 Angle : 0.728 13.197 7004 Z= 0.374 Chirality : 0.048 0.237 758 Planarity : 0.005 0.052 907 Dihedral : 5.949 30.528 710 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.49 % Favored : 89.36 % Rotamer: Outliers : 0.18 % Allowed : 4.01 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.28 (0.31), residues: 639 helix: -3.61 (0.61), residues: 32 sheet: -1.71 (0.33), residues: 206 loop : -2.40 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 49 HIS 0.002 0.001 HIS C 33 PHE 0.028 0.002 PHE A 456 TYR 0.031 0.002 TYR A 421 ARG 0.005 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8469 (t80) cc_final: 0.8141 (t80) REVERT: A 396 TYR cc_start: 0.8771 (m-10) cc_final: 0.8468 (m-80) REVERT: B 100 PHE cc_start: 0.7826 (m-80) cc_final: 0.7340 (m-80) REVERT: B 110 PHE cc_start: 0.9290 (m-80) cc_final: 0.8764 (m-80) REVERT: B 111 ASP cc_start: 0.9214 (t0) cc_final: 0.8894 (t0) REVERT: C 35 TYR cc_start: 0.8739 (m-80) cc_final: 0.8013 (m-80) REVERT: C 49 TYR cc_start: 0.9385 (m-80) cc_final: 0.8993 (m-80) REVERT: D 51 ASN cc_start: 0.9662 (t0) cc_final: 0.9411 (t0) REVERT: D 80 TYR cc_start: 0.9273 (m-80) cc_final: 0.9026 (m-80) REVERT: E 34 ASN cc_start: 0.8845 (m-40) cc_final: 0.7656 (m110) REVERT: E 71 PHE cc_start: 0.8518 (m-80) cc_final: 0.8198 (m-10) REVERT: E 93 ASP cc_start: 0.9388 (m-30) cc_final: 0.8904 (p0) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.1782 time to fit residues: 24.9259 Evaluate side-chains 84 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 46 optimal weight: 0.0370 overall best weight: 3.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.034384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.024817 restraints weight = 44027.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.026177 restraints weight = 23681.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.027152 restraints weight = 15730.031| |-----------------------------------------------------------------------------| r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5140 Z= 0.311 Angle : 0.737 8.763 7004 Z= 0.384 Chirality : 0.048 0.201 758 Planarity : 0.006 0.050 907 Dihedral : 6.030 23.966 710 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.99 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.46 (0.30), residues: 639 helix: -3.62 (0.58), residues: 33 sheet: -1.89 (0.32), residues: 210 loop : -2.51 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 49 HIS 0.004 0.002 HIS B 42 PHE 0.029 0.002 PHE A 456 TYR 0.039 0.002 TYR A 421 ARG 0.012 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8498 (t80) cc_final: 0.8142 (t80) REVERT: A 396 TYR cc_start: 0.8810 (m-10) cc_final: 0.8457 (m-80) REVERT: B 100 PHE cc_start: 0.8023 (m-80) cc_final: 0.7601 (m-80) REVERT: B 108 PHE cc_start: 0.8939 (m-80) cc_final: 0.8337 (m-80) REVERT: B 110 PHE cc_start: 0.9374 (m-80) cc_final: 0.8811 (m-80) REVERT: C 35 TYR cc_start: 0.8886 (m-80) cc_final: 0.7968 (m-80) REVERT: C 49 TYR cc_start: 0.9446 (m-80) cc_final: 0.9058 (m-80) REVERT: D 51 ASN cc_start: 0.9677 (t0) cc_final: 0.9432 (t0) REVERT: D 80 TYR cc_start: 0.9202 (m-80) cc_final: 0.8952 (m-80) REVERT: E 70 ASP cc_start: 0.9498 (m-30) cc_final: 0.9251 (t0) REVERT: E 93 ASP cc_start: 0.9391 (m-30) cc_final: 0.8947 (p0) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1877 time to fit residues: 25.3244 Evaluate side-chains 79 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.035330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.025345 restraints weight = 42335.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.026787 restraints weight = 22802.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.027827 restraints weight = 15119.783| |-----------------------------------------------------------------------------| r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5140 Z= 0.226 Angle : 0.691 8.171 7004 Z= 0.360 Chirality : 0.048 0.323 758 Planarity : 0.005 0.046 907 Dihedral : 5.708 30.196 710 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.95 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.35 (0.31), residues: 639 helix: -3.31 (0.68), residues: 32 sheet: -1.66 (0.34), residues: 196 loop : -2.54 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 49 HIS 0.003 0.001 HIS C 33 PHE 0.032 0.002 PHE A 456 TYR 0.029 0.002 TYR A 421 ARG 0.010 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8505 (t80) cc_final: 0.8174 (t80) REVERT: A 396 TYR cc_start: 0.8774 (m-10) cc_final: 0.8471 (m-80) REVERT: B 100 PHE cc_start: 0.7941 (m-80) cc_final: 0.7711 (m-80) REVERT: B 108 PHE cc_start: 0.8927 (m-80) cc_final: 0.8307 (m-80) REVERT: B 110 PHE cc_start: 0.9372 (m-80) cc_final: 0.8754 (m-80) REVERT: C 35 TYR cc_start: 0.8897 (m-80) cc_final: 0.8016 (m-80) REVERT: C 49 TYR cc_start: 0.9421 (m-80) cc_final: 0.9030 (m-80) REVERT: C 85 TYR cc_start: 0.9224 (m-80) cc_final: 0.9015 (m-80) REVERT: C 105 VAL cc_start: 0.9586 (m) cc_final: 0.9308 (p) REVERT: D 51 ASN cc_start: 0.9667 (t0) cc_final: 0.9390 (t0) REVERT: D 80 TYR cc_start: 0.9237 (m-80) cc_final: 0.9034 (m-80) REVERT: E 31 ASN cc_start: 0.9328 (p0) cc_final: 0.9104 (p0) REVERT: E 34 ASN cc_start: 0.8827 (m-40) cc_final: 0.7703 (m110) REVERT: E 71 PHE cc_start: 0.8550 (m-80) cc_final: 0.8232 (m-10) REVERT: E 93 ASP cc_start: 0.9372 (m-30) cc_final: 0.8849 (p0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1968 time to fit residues: 28.8704 Evaluate side-chains 90 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 35 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 0.0020 chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 8 optimal weight: 0.2980 chunk 61 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.025518 restraints weight = 40137.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.026931 restraints weight = 22375.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.027963 restraints weight = 15153.010| |-----------------------------------------------------------------------------| r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5140 Z= 0.213 Angle : 0.701 10.027 7004 Z= 0.362 Chirality : 0.048 0.277 758 Planarity : 0.005 0.058 907 Dihedral : 5.510 23.667 710 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.80 % Favored : 89.05 % Rotamer: Outliers : 0.18 % Allowed : 2.37 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.15 (0.32), residues: 639 helix: -3.07 (0.77), residues: 32 sheet: -1.68 (0.33), residues: 207 loop : -2.32 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 49 HIS 0.002 0.001 HIS A 505 PHE 0.026 0.001 PHE A 456 TYR 0.025 0.001 TYR A 421 ARG 0.008 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8477 (t80) cc_final: 0.8132 (t80) REVERT: A 396 TYR cc_start: 0.8784 (m-10) cc_final: 0.8469 (m-80) REVERT: B 52 TYR cc_start: 0.9763 (p90) cc_final: 0.9237 (p90) REVERT: B 72 SER cc_start: 0.9524 (t) cc_final: 0.9290 (p) REVERT: B 100 PHE cc_start: 0.8077 (m-80) cc_final: 0.7728 (m-80) REVERT: B 108 PHE cc_start: 0.8939 (m-80) cc_final: 0.8262 (m-80) REVERT: B 110 PHE cc_start: 0.9422 (m-80) cc_final: 0.8887 (m-80) REVERT: B 111 ASP cc_start: 0.9185 (t0) cc_final: 0.8965 (t0) REVERT: C 35 TYR cc_start: 0.8908 (m-80) cc_final: 0.8149 (m-80) REVERT: C 49 TYR cc_start: 0.9436 (m-80) cc_final: 0.9021 (m-80) REVERT: D 51 ASN cc_start: 0.9631 (t0) cc_final: 0.9417 (t0) REVERT: D 71 THR cc_start: 0.9112 (p) cc_final: 0.8824 (p) REVERT: D 81 MET cc_start: 0.8553 (mmp) cc_final: 0.8143 (mmp) REVERT: D 83 LEU cc_start: 0.9304 (tp) cc_final: 0.9093 (tp) REVERT: E 34 ASN cc_start: 0.8533 (m-40) cc_final: 0.7204 (m110) REVERT: E 50 ASP cc_start: 0.9763 (m-30) cc_final: 0.9279 (t0) REVERT: E 70 ASP cc_start: 0.9427 (m-30) cc_final: 0.9184 (t0) REVERT: E 87 PHE cc_start: 0.9388 (m-80) cc_final: 0.9185 (m-80) REVERT: E 93 ASP cc_start: 0.9366 (m-30) cc_final: 0.8965 (m-30) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.2015 time to fit residues: 30.2552 Evaluate side-chains 90 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 40 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.025621 restraints weight = 41704.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.027043 restraints weight = 22726.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.028092 restraints weight = 15206.256| |-----------------------------------------------------------------------------| r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5140 Z= 0.257 Angle : 0.722 11.450 7004 Z= 0.373 Chirality : 0.048 0.274 758 Planarity : 0.005 0.055 907 Dihedral : 5.785 30.404 710 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.42 % Favored : 88.42 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.13 (0.31), residues: 639 helix: -3.03 (0.79), residues: 32 sheet: -1.65 (0.34), residues: 200 loop : -2.32 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 47 HIS 0.002 0.001 HIS C 33 PHE 0.027 0.002 PHE A 456 TYR 0.021 0.002 TYR C 85 ARG 0.007 0.001 ARG C 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8491 (t80) cc_final: 0.8149 (t80) REVERT: A 396 TYR cc_start: 0.8809 (m-10) cc_final: 0.8479 (m-80) REVERT: B 72 SER cc_start: 0.9476 (t) cc_final: 0.9254 (p) REVERT: B 100 PHE cc_start: 0.8208 (m-80) cc_final: 0.7706 (m-80) REVERT: B 108 PHE cc_start: 0.8920 (m-80) cc_final: 0.8266 (m-80) REVERT: B 110 PHE cc_start: 0.9380 (m-80) cc_final: 0.8811 (m-80) REVERT: B 111 ASP cc_start: 0.9201 (t0) cc_final: 0.8900 (t0) REVERT: C 35 TYR cc_start: 0.9018 (m-80) cc_final: 0.8166 (m-80) REVERT: C 49 TYR cc_start: 0.9434 (m-80) cc_final: 0.9040 (m-80) REVERT: C 85 TYR cc_start: 0.9373 (m-10) cc_final: 0.9165 (m-80) REVERT: D 32 TYR cc_start: 0.8220 (m-10) cc_final: 0.7896 (m-80) REVERT: D 71 THR cc_start: 0.9074 (p) cc_final: 0.8811 (p) REVERT: D 80 TYR cc_start: 0.9138 (m-80) cc_final: 0.8923 (m-80) REVERT: D 81 MET cc_start: 0.8470 (mmp) cc_final: 0.7863 (mmp) REVERT: E 34 ASN cc_start: 0.9079 (m-40) cc_final: 0.8531 (m-40) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1954 time to fit residues: 28.5421 Evaluate side-chains 92 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 27 optimal weight: 8.9990 chunk 31 optimal weight: 30.0000 chunk 29 optimal weight: 8.9990 chunk 13 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.036099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.025776 restraints weight = 40657.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.027248 restraints weight = 22701.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2564 r_free = 0.2564 target = 0.028315 restraints weight = 15282.269| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5140 Z= 0.214 Angle : 0.769 17.419 7004 Z= 0.387 Chirality : 0.050 0.232 758 Planarity : 0.005 0.058 907 Dihedral : 5.526 31.114 710 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.33 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -3.06 (0.32), residues: 639 helix: -3.03 (0.79), residues: 32 sheet: -1.68 (0.34), residues: 198 loop : -2.21 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 47 HIS 0.002 0.001 HIS C 33 PHE 0.035 0.002 PHE A 456 TYR 0.029 0.002 TYR A 421 ARG 0.007 0.001 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8514 (t80) cc_final: 0.8184 (t80) REVERT: A 396 TYR cc_start: 0.8777 (m-10) cc_final: 0.8397 (m-80) REVERT: B 72 SER cc_start: 0.9516 (t) cc_final: 0.9290 (p) REVERT: B 100 PHE cc_start: 0.8084 (m-80) cc_final: 0.7676 (m-80) REVERT: B 108 PHE cc_start: 0.8966 (m-80) cc_final: 0.8281 (m-80) REVERT: B 110 PHE cc_start: 0.9433 (m-80) cc_final: 0.8880 (m-80) REVERT: B 111 ASP cc_start: 0.9227 (t0) cc_final: 0.8991 (t0) REVERT: C 35 TYR cc_start: 0.9010 (m-80) cc_final: 0.8228 (m-80) REVERT: C 49 TYR cc_start: 0.9447 (m-80) cc_final: 0.9026 (m-80) REVERT: C 61 PHE cc_start: 0.9112 (m-10) cc_final: 0.8866 (m-10) REVERT: C 85 TYR cc_start: 0.9296 (m-10) cc_final: 0.8907 (m-80) REVERT: D 71 THR cc_start: 0.9066 (p) cc_final: 0.8809 (p) REVERT: D 80 TYR cc_start: 0.9127 (m-80) cc_final: 0.8858 (m-80) REVERT: E 11 LEU cc_start: 0.9110 (mm) cc_final: 0.8812 (mm) REVERT: E 34 ASN cc_start: 0.8992 (m-40) cc_final: 0.8341 (m-40) REVERT: E 71 PHE cc_start: 0.8877 (m-10) cc_final: 0.8620 (m-10) REVERT: E 93 ASP cc_start: 0.9111 (m-30) cc_final: 0.8836 (p0) REVERT: E 101 THR cc_start: 0.8904 (p) cc_final: 0.7872 (p) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1618 time to fit residues: 23.7324 Evaluate side-chains 88 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.036133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.026071 restraints weight = 40568.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2535 r_free = 0.2535 target = 0.027530 restraints weight = 22132.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.028591 restraints weight = 14804.898| |-----------------------------------------------------------------------------| r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5140 Z= 0.217 Angle : 0.707 10.904 7004 Z= 0.365 Chirality : 0.049 0.255 758 Planarity : 0.005 0.059 907 Dihedral : 5.474 28.184 710 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.95 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.96 (0.32), residues: 639 helix: -3.03 (0.78), residues: 32 sheet: -1.48 (0.35), residues: 190 loop : -2.21 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 47 HIS 0.002 0.001 HIS C 33 PHE 0.055 0.002 PHE A 456 TYR 0.031 0.002 TYR A 421 ARG 0.012 0.001 ARG D 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8443 (t80) cc_final: 0.8123 (t80) REVERT: A 396 TYR cc_start: 0.8789 (m-10) cc_final: 0.8449 (m-80) REVERT: B 72 SER cc_start: 0.9493 (t) cc_final: 0.9269 (p) REVERT: B 100 PHE cc_start: 0.8178 (m-80) cc_final: 0.7751 (m-80) REVERT: B 108 PHE cc_start: 0.8967 (m-80) cc_final: 0.8272 (m-80) REVERT: B 110 PHE cc_start: 0.9422 (m-80) cc_final: 0.8857 (m-80) REVERT: B 111 ASP cc_start: 0.9254 (t0) cc_final: 0.9013 (t0) REVERT: C 35 TYR cc_start: 0.9034 (m-80) cc_final: 0.8209 (m-80) REVERT: C 49 TYR cc_start: 0.9441 (m-80) cc_final: 0.9026 (m-80) REVERT: D 71 THR cc_start: 0.9016 (p) cc_final: 0.8757 (p) REVERT: D 80 TYR cc_start: 0.9102 (m-80) cc_final: 0.8865 (m-80) REVERT: D 81 MET cc_start: 0.8640 (mmp) cc_final: 0.8239 (mmp) REVERT: E 34 ASN cc_start: 0.8804 (m-40) cc_final: 0.8134 (m-40) REVERT: E 70 ASP cc_start: 0.9397 (m-30) cc_final: 0.9124 (t0) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1789 time to fit residues: 25.3318 Evaluate side-chains 89 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.035256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.025261 restraints weight = 42232.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.026702 restraints weight = 23087.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.027735 restraints weight = 15398.041| |-----------------------------------------------------------------------------| r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5140 Z= 0.255 Angle : 0.715 14.242 7004 Z= 0.365 Chirality : 0.048 0.261 758 Planarity : 0.005 0.059 907 Dihedral : 5.608 27.634 710 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.64 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.99 (0.32), residues: 639 helix: -2.96 (0.81), residues: 32 sheet: -1.54 (0.35), residues: 190 loop : -2.22 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 47 HIS 0.003 0.001 HIS C 33 PHE 0.032 0.002 PHE A 456 TYR 0.023 0.002 TYR C 85 ARG 0.008 0.001 ARG C 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.31 seconds wall clock time: 35 minutes 54.55 seconds (2154.55 seconds total)