Starting phenix.real_space_refine on Sun Apr 27 07:29:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xef_38288/04_2025/8xef_38288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xef_38288/04_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_38288/04_2025/8xef_38288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xef_38288/04_2025/8xef_38288.map" model { file = "/net/cci-nas-00/data/ceres_data/8xef_38288/04_2025/8xef_38288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xef_38288/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 3.43, per 1000 atoms: 0.69 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: 1.30 Conformation dependent library (CDL) restraints added in 636.5 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: 0.64 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: 1.18 Time building geometry restraints manager: 1.51 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.010 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.380 ------------------------------------------------------------------------------- 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 : 0.006 0.313 5147 Z= 0.482 Angle : 1.000 9.895 7016 Z= 0.527 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 Details of bonding type rmsd hydrogen bonds : bond 0.20006 ( 98) hydrogen bonds : angle 10.29185 ( 243) SS BOND : bond 0.00674 ( 6) SS BOND : angle 2.35868 ( 12) covalent geometry : bond 0.00447 ( 5140) covalent geometry : angle 0.99656 ( 7004) Misc. bond : bond 0.31308 ( 1) *********************** 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 : 0.607 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: 0.2161 time to fit residues: 37.2389 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 : 0.594 ------------------------------------------------------------------------------- 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: 1.9990 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: 4.4086 ------------------------------------------------------------------------------- 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 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 = 0.2805 r_free = 0.2805 target = 0.035699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.025729 restraints weight = 40357.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.027149 restraints weight = 22747.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2554 r_free = 0.2554 target = 0.028177 restraints weight = 15295.769| |-----------------------------------------------------------------------------| r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5147 Z= 0.243 Angle : 0.746 9.388 7016 Z= 0.392 Chirality : 0.046 0.208 758 Planarity : 0.006 0.058 907 Dihedral : 6.224 31.462 710 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 23.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.33 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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: -3.22 (0.31), residues: 639 helix: -4.01 (0.49), residues: 32 sheet: -1.73 (0.33), residues: 208 loop : -2.28 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 90 HIS 0.005 0.002 HIS C 96 PHE 0.024 0.002 PHE E 87 TYR 0.016 0.002 TYR C 85 ARG 0.006 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 98) hydrogen bonds : angle 7.50635 ( 243) SS BOND : bond 0.00782 ( 6) SS BOND : angle 2.56933 ( 12) covalent geometry : bond 0.00512 ( 5140) covalent geometry : angle 0.73870 ( 7004) Misc. bond : bond 0.00022 ( 1) *********************** 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 123 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8468 (t80) cc_final: 0.8112 (t80) REVERT: A 396 TYR cc_start: 0.8709 (m-10) cc_final: 0.8455 (m-80) REVERT: B 56 ASN cc_start: 0.9204 (m-40) cc_final: 0.8913 (m-40) REVERT: B 57 TRP cc_start: 0.9598 (m-90) cc_final: 0.9317 (m-90) REVERT: B 100 PHE cc_start: 0.7785 (m-80) cc_final: 0.7452 (m-80) REVERT: B 103 TYR cc_start: 0.8664 (p90) cc_final: 0.8378 (p90) REVERT: B 108 PHE cc_start: 0.8777 (m-80) cc_final: 0.8426 (m-80) REVERT: B 110 PHE cc_start: 0.9201 (m-80) cc_final: 0.8760 (m-80) REVERT: B 111 ASP cc_start: 0.9283 (t0) cc_final: 0.8949 (t0) REVERT: C 35 TYR cc_start: 0.8683 (m-80) cc_final: 0.7740 (m-80) REVERT: C 49 TYR cc_start: 0.9369 (m-80) cc_final: 0.8718 (m-80) REVERT: C 85 TYR cc_start: 0.9225 (m-80) cc_final: 0.8814 (m-80) REVERT: D 71 THR cc_start: 0.9284 (p) cc_final: 0.8895 (p) REVERT: D 80 TYR cc_start: 0.9316 (m-80) cc_final: 0.8958 (m-80) REVERT: D 100 GLU cc_start: 0.7977 (mp0) cc_final: 0.7641 (mp0) REVERT: D 110 TYR cc_start: 0.9489 (m-80) cc_final: 0.9232 (m-10) REVERT: E 70 ASP cc_start: 0.9519 (m-30) cc_final: 0.9300 (t0) REVERT: E 87 PHE cc_start: 0.9311 (m-80) cc_final: 0.8690 (m-10) REVERT: E 93 ASP cc_start: 0.9219 (m-30) cc_final: 0.8767 (p0) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2402 time to fit residues: 37.0632 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 : 0.658 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.9980 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 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 = 0.2778 r_free = 0.2778 target = 0.034793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.025095 restraints weight = 41510.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.026490 restraints weight = 22600.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.027503 restraints weight = 15063.820| |-----------------------------------------------------------------------------| r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5147 Z= 0.224 Angle : 0.711 7.886 7016 Z= 0.374 Chirality : 0.047 0.282 758 Planarity : 0.006 0.052 907 Dihedral : 6.129 26.706 710 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.42 % Favored : 88.42 % Rotamer: Outliers : 0.18 % Allowed : 5.84 % Favored : 93.98 % 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: -3.34 (0.31), residues: 639 helix: -3.83 (0.57), residues: 32 sheet: -1.77 (0.33), residues: 206 loop : -2.42 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 47 HIS 0.005 0.001 HIS C 96 PHE 0.015 0.002 PHE B 100 TYR 0.013 0.002 TYR D 110 ARG 0.005 0.001 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 98) hydrogen bonds : angle 7.24412 ( 243) SS BOND : bond 0.00590 ( 6) SS BOND : angle 2.06290 ( 12) covalent geometry : bond 0.00488 ( 5140) covalent geometry : angle 0.70596 ( 7004) Misc. bond : bond 0.00273 ( 1) *********************** 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 113 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8440 (t80) cc_final: 0.8099 (t80) REVERT: A 396 TYR cc_start: 0.8759 (m-10) cc_final: 0.8471 (m-80) REVERT: B 56 ASN cc_start: 0.9292 (m-40) cc_final: 0.9023 (m-40) REVERT: B 57 TRP cc_start: 0.9598 (m-90) cc_final: 0.9345 (m-90) REVERT: B 100 PHE cc_start: 0.8021 (m-80) cc_final: 0.7288 (m-80) REVERT: B 108 PHE cc_start: 0.8853 (m-80) cc_final: 0.7709 (m-80) REVERT: B 110 PHE cc_start: 0.9313 (m-80) cc_final: 0.8823 (m-80) REVERT: B 111 ASP cc_start: 0.9318 (t0) cc_final: 0.8954 (t0) REVERT: C 35 TYR cc_start: 0.8719 (m-80) cc_final: 0.7814 (m-80) REVERT: C 49 TYR cc_start: 0.9449 (m-80) cc_final: 0.9015 (m-80) REVERT: C 85 TYR cc_start: 0.9131 (m-80) cc_final: 0.8832 (m-80) REVERT: D 51 ASN cc_start: 0.9648 (t0) cc_final: 0.9374 (t0) REVERT: D 80 TYR cc_start: 0.9218 (m-80) cc_final: 0.8940 (m-80) REVERT: D 81 MET cc_start: 0.9082 (mmm) cc_final: 0.8873 (mmm) REVERT: E 47 LEU cc_start: 0.9596 (mm) cc_final: 0.9382 (mm) REVERT: E 70 ASP cc_start: 0.9510 (m-30) cc_final: 0.9291 (t0) REVERT: E 102 LYS cc_start: 0.9748 (tppt) cc_final: 0.9545 (tppt) outliers start: 1 outliers final: 1 residues processed: 113 average time/residue: 0.2209 time to fit residues: 31.6028 Evaluate side-chains 80 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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: 1.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.034262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.024316 restraints weight = 42288.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.025710 restraints weight = 23096.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.026732 restraints weight = 15431.853| |-----------------------------------------------------------------------------| r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5147 Z= 0.232 Angle : 0.737 8.482 7016 Z= 0.386 Chirality : 0.047 0.245 758 Planarity : 0.006 0.050 907 Dihedral : 6.020 26.597 710 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.36 % Favored : 87.48 % Rotamer: Outliers : 0.18 % Allowed : 5.47 % Favored : 94.34 % 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: -3.39 (0.31), residues: 639 helix: -3.64 (0.60), residues: 32 sheet: -1.86 (0.32), residues: 206 loop : -2.44 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 49 HIS 0.004 0.001 HIS C 33 PHE 0.033 0.002 PHE A 456 TYR 0.043 0.002 TYR A 421 ARG 0.005 0.001 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 98) hydrogen bonds : angle 6.83261 ( 243) SS BOND : bond 0.00597 ( 6) SS BOND : angle 1.79606 ( 12) covalent geometry : bond 0.00505 ( 5140) covalent geometry : angle 0.73394 ( 7004) Misc. bond : bond 0.01026 ( 1) *********************** 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 108 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8520 (t80) cc_final: 0.8183 (t80) REVERT: A 396 TYR cc_start: 0.8806 (m-10) cc_final: 0.8449 (m-80) REVERT: B 100 PHE cc_start: 0.8048 (m-80) cc_final: 0.7623 (m-80) REVERT: B 108 PHE cc_start: 0.8922 (m-80) cc_final: 0.8362 (m-80) REVERT: B 110 PHE cc_start: 0.9333 (m-80) cc_final: 0.8819 (m-80) REVERT: B 111 ASP cc_start: 0.9278 (t0) cc_final: 0.9013 (t0) REVERT: C 35 TYR cc_start: 0.8800 (m-80) cc_final: 0.7936 (m-80) REVERT: C 49 TYR cc_start: 0.9447 (m-80) cc_final: 0.8998 (m-80) REVERT: C 85 TYR cc_start: 0.9218 (m-80) cc_final: 0.8977 (m-80) REVERT: C 105 VAL cc_start: 0.9560 (m) cc_final: 0.9147 (p) REVERT: D 32 TYR cc_start: 0.8698 (m-10) cc_final: 0.8473 (m-80) REVERT: D 51 ASN cc_start: 0.9659 (t0) cc_final: 0.9459 (t0) REVERT: D 80 TYR cc_start: 0.9245 (m-80) cc_final: 0.9016 (m-80) REVERT: E 34 ASN cc_start: 0.8579 (m-40) cc_final: 0.7515 (m110) REVERT: E 70 ASP cc_start: 0.9479 (m-30) cc_final: 0.9231 (t0) outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.1745 time to fit residues: 24.0233 Evaluate side-chains 80 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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: 3.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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 = 0.2788 r_free = 0.2788 target = 0.035102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.025136 restraints weight = 42301.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.026549 restraints weight = 22890.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.027569 restraints weight = 15225.786| |-----------------------------------------------------------------------------| r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5147 Z= 0.179 Angle : 0.721 9.183 7016 Z= 0.375 Chirality : 0.048 0.202 758 Planarity : 0.005 0.048 907 Dihedral : 5.919 29.651 710 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.42 % Favored : 88.42 % Rotamer: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: -3.39 (0.31), residues: 639 helix: -3.45 (0.64), residues: 32 sheet: -1.90 (0.32), residues: 210 loop : -2.42 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 49 HIS 0.003 0.001 HIS B 42 PHE 0.037 0.002 PHE A 456 TYR 0.045 0.002 TYR A 421 ARG 0.013 0.001 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 98) hydrogen bonds : angle 6.77459 ( 243) SS BOND : bond 0.00826 ( 6) SS BOND : angle 2.29017 ( 12) covalent geometry : bond 0.00400 ( 5140) covalent geometry : angle 0.71518 ( 7004) Misc. bond : bond 0.00738 ( 1) *********************** 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 115 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.666 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: 0.8498 (t80) cc_final: 0.8142 (t80) REVERT: A 396 TYR cc_start: 0.8801 (m-10) cc_final: 0.8443 (m-80) REVERT: B 52 TYR cc_start: 0.9455 (p90) cc_final: 0.8871 (p90) REVERT: B 100 PHE cc_start: 0.8033 (m-80) cc_final: 0.7274 (m-80) REVERT: B 102 ASP cc_start: 0.9032 (t0) cc_final: 0.8738 (t0) REVERT: B 108 PHE cc_start: 0.8940 (m-80) cc_final: 0.8355 (m-80) REVERT: B 110 PHE cc_start: 0.9342 (m-80) cc_final: 0.8877 (m-80) REVERT: B 111 ASP cc_start: 0.9323 (t0) cc_final: 0.8104 (p0) REVERT: C 35 TYR cc_start: 0.8824 (m-80) cc_final: 0.8051 (m-80) REVERT: C 49 TYR cc_start: 0.9438 (m-80) cc_final: 0.9005 (m-80) REVERT: C 85 TYR cc_start: 0.9213 (m-80) cc_final: 0.8958 (m-80) REVERT: C 105 VAL cc_start: 0.9578 (m) cc_final: 0.9196 (p) REVERT: D 32 TYR cc_start: 0.8431 (m-10) cc_final: 0.8192 (m-80) REVERT: D 51 ASN cc_start: 0.9697 (t0) cc_final: 0.9440 (t0) REVERT: D 81 MET cc_start: 0.8390 (mmp) cc_final: 0.8054 (mmp) REVERT: D 83 LEU cc_start: 0.9276 (tp) cc_final: 0.9057 (tp) REVERT: E 31 ASN cc_start: 0.9330 (p0) cc_final: 0.9120 (p0) REVERT: E 71 PHE cc_start: 0.8615 (m-80) cc_final: 0.8319 (m-10) REVERT: E 93 ASP cc_start: 0.9221 (m-30) cc_final: 0.8685 (m-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.2079 time to fit residues: 31.0608 Evaluate side-chains 85 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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: 10.0000 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** ** 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 = 0.2817 r_free = 0.2817 target = 0.035876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.025727 restraints weight = 40338.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.027163 restraints weight = 22012.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.028227 restraints weight = 14743.302| |-----------------------------------------------------------------------------| r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5147 Z= 0.134 Angle : 0.661 5.876 7016 Z= 0.344 Chirality : 0.048 0.336 758 Planarity : 0.005 0.044 907 Dihedral : 5.566 24.824 710 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.49 % Favored : 89.36 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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 (0.31), residues: 639 helix: -3.30 (0.72), residues: 33 sheet: -1.60 (0.33), residues: 203 loop : -2.35 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 49 HIS 0.002 0.001 HIS A 505 PHE 0.023 0.002 PHE A 456 TYR 0.035 0.001 TYR A 421 ARG 0.011 0.001 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 98) hydrogen bonds : angle 6.42397 ( 243) SS BOND : bond 0.00339 ( 6) SS BOND : angle 1.83913 ( 12) covalent geometry : bond 0.00309 ( 5140) covalent geometry : angle 0.65697 ( 7004) Misc. bond : bond 0.00404 ( 1) *********************** 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 114 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.965 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: 0.8499 (t80) cc_final: 0.8162 (t80) REVERT: A 396 TYR cc_start: 0.8747 (m-10) cc_final: 0.8433 (m-80) REVERT: B 52 TYR cc_start: 0.9394 (p90) cc_final: 0.8821 (p90) REVERT: B 72 SER cc_start: 0.9480 (t) cc_final: 0.9251 (p) REVERT: B 100 PHE cc_start: 0.7990 (m-80) cc_final: 0.7628 (m-80) REVERT: B 108 PHE cc_start: 0.8915 (m-80) cc_final: 0.8273 (m-80) REVERT: B 110 PHE cc_start: 0.9331 (m-80) cc_final: 0.8580 (m-80) REVERT: B 111 ASP cc_start: 0.9217 (t0) cc_final: 0.8321 (m-30) REVERT: C 35 TYR cc_start: 0.8889 (m-80) cc_final: 0.7734 (m-80) REVERT: C 49 TYR cc_start: 0.9405 (m-80) cc_final: 0.8990 (m-80) REVERT: D 71 THR cc_start: 0.9093 (p) cc_final: 0.8831 (p) REVERT: D 80 TYR cc_start: 0.9164 (m-80) cc_final: 0.8941 (m-80) REVERT: D 81 MET cc_start: 0.8294 (mmp) cc_final: 0.7705 (mmp) REVERT: E 11 LEU cc_start: 0.9087 (mm) cc_final: 0.8769 (mm) REVERT: E 50 ASP cc_start: 0.9748 (m-30) cc_final: 0.9389 (t0) REVERT: E 70 ASP cc_start: 0.9464 (m-30) cc_final: 0.9219 (t0) REVERT: E 90 GLN cc_start: 0.9510 (tm-30) cc_final: 0.9296 (mp10) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1773 time to fit residues: 25.9914 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 : 0.601 ------------------------------------------------------------------------------- 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: 7.9990 chunk 14 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 26 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.9584 ------------------------------------------------------------------------------- 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 = 0.2794 r_free = 0.2794 target = 0.035040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2447 r_free = 0.2447 target = 0.025080 restraints weight = 41872.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.026494 restraints weight = 22998.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.027526 restraints weight = 15445.082| |-----------------------------------------------------------------------------| r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5147 Z= 0.176 Angle : 0.758 19.799 7016 Z= 0.384 Chirality : 0.049 0.271 758 Planarity : 0.005 0.059 907 Dihedral : 5.839 27.985 710 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.80 % Favored : 89.05 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -3.16 (0.32), residues: 639 helix: -3.19 (0.74), residues: 32 sheet: -1.76 (0.33), residues: 204 loop : -2.27 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 47 HIS 0.003 0.001 HIS C 96 PHE 0.045 0.002 PHE A 456 TYR 0.033 0.002 TYR A 421 ARG 0.007 0.001 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 98) hydrogen bonds : angle 6.71917 ( 243) SS BOND : bond 0.00941 ( 6) SS BOND : angle 1.99155 ( 12) covalent geometry : bond 0.00395 ( 5140) covalent geometry : angle 0.75367 ( 7004) Misc. bond : bond 0.00892 ( 1) *********************** 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 113 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.544 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: 0.8469 (t80) cc_final: 0.8112 (t80) REVERT: A 396 TYR cc_start: 0.8780 (m-10) cc_final: 0.8454 (m-80) REVERT: B 52 TYR cc_start: 0.9472 (p90) cc_final: 0.8850 (p90) REVERT: B 72 SER cc_start: 0.9507 (t) cc_final: 0.9267 (p) REVERT: B 100 PHE cc_start: 0.8329 (m-80) cc_final: 0.7477 (m-80) REVERT: B 102 ASP cc_start: 0.9038 (t70) cc_final: 0.8794 (t0) REVERT: B 108 PHE cc_start: 0.8961 (m-80) cc_final: 0.8342 (m-80) REVERT: B 110 PHE cc_start: 0.9425 (m-80) cc_final: 0.8922 (m-80) REVERT: B 111 ASP cc_start: 0.9366 (t0) cc_final: 0.8014 (p0) REVERT: C 35 TYR cc_start: 0.8976 (m-80) cc_final: 0.8082 (m-80) REVERT: C 49 TYR cc_start: 0.9481 (m-80) cc_final: 0.9048 (m-80) REVERT: C 85 TYR cc_start: 0.9360 (m-10) cc_final: 0.8792 (m-80) REVERT: D 51 ASN cc_start: 0.9692 (t0) cc_final: 0.9438 (t0) REVERT: D 71 THR cc_start: 0.9080 (p) cc_final: 0.8828 (p) REVERT: D 80 TYR cc_start: 0.9108 (m-80) cc_final: 0.8849 (m-80) REVERT: E 11 LEU cc_start: 0.9121 (mm) cc_final: 0.8812 (mm) REVERT: E 34 ASN cc_start: 0.8932 (m-40) cc_final: 0.8044 (m110) outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1857 time to fit residues: 27.0268 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 : 0.663 ------------------------------------------------------------------------------- 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: 3.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.2835 r_free = 0.2835 target = 0.036218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.026397 restraints weight = 41102.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.027850 restraints weight = 22162.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.028912 restraints weight = 14718.459| |-----------------------------------------------------------------------------| r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5147 Z= 0.135 Angle : 0.698 8.998 7016 Z= 0.357 Chirality : 0.048 0.278 758 Planarity : 0.005 0.056 907 Dihedral : 5.615 27.564 710 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.17 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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: -3.14 (0.77), residues: 33 sheet: -1.54 (0.34), residues: 199 loop : -2.20 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 47 HIS 0.003 0.001 HIS A 505 PHE 0.025 0.002 PHE A 456 TYR 0.019 0.001 TYR A 421 ARG 0.007 0.001 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 98) hydrogen bonds : angle 6.11897 ( 243) SS BOND : bond 0.00535 ( 6) SS BOND : angle 1.67148 ( 12) covalent geometry : bond 0.00318 ( 5140) covalent geometry : angle 0.69539 ( 7004) Misc. bond : bond 0.00710 ( 1) *********************** 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 117 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.048 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: 0.8509 (t80) cc_final: 0.8187 (t80) REVERT: A 396 TYR cc_start: 0.8791 (m-10) cc_final: 0.8478 (m-80) REVERT: A 465 GLU cc_start: 0.8092 (pt0) cc_final: 0.7777 (pt0) REVERT: B 52 TYR cc_start: 0.9329 (p90) cc_final: 0.8755 (p90) REVERT: B 72 SER cc_start: 0.9432 (t) cc_final: 0.9213 (p) REVERT: B 100 PHE cc_start: 0.8028 (m-80) cc_final: 0.7621 (m-80) REVERT: B 108 PHE cc_start: 0.8906 (m-80) cc_final: 0.8221 (m-80) REVERT: B 110 PHE cc_start: 0.9356 (m-80) cc_final: 0.8812 (m-80) REVERT: B 111 ASP cc_start: 0.9254 (t0) cc_final: 0.9052 (t0) REVERT: C 35 TYR cc_start: 0.8935 (m-80) cc_final: 0.8187 (m-80) REVERT: C 49 TYR cc_start: 0.9393 (m-80) cc_final: 0.8996 (m-80) REVERT: D 51 ASN cc_start: 0.9699 (t0) cc_final: 0.9402 (t0) REVERT: D 71 THR cc_start: 0.9062 (p) cc_final: 0.8807 (p) REVERT: D 80 TYR cc_start: 0.9158 (m-80) cc_final: 0.8940 (m-80) REVERT: D 81 MET cc_start: 0.8366 (mmp) cc_final: 0.8004 (mmp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2641 time to fit residues: 40.4110 Evaluate side-chains 94 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 0.1980 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 overall best weight: 1.2322 ------------------------------------------------------------------------------- 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 = 0.2852 r_free = 0.2852 target = 0.036568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.026508 restraints weight = 40140.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.027991 restraints weight = 21984.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.029061 restraints weight = 14712.048| |-----------------------------------------------------------------------------| r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.765 5147 Z= 0.607 Angle : 1.193 48.543 7016 Z= 0.645 Chirality : 0.049 0.238 758 Planarity : 0.006 0.113 907 Dihedral : 5.462 26.208 710 Min Nonbonded Distance : 1.657 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.49 % Favored : 89.36 % 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 : 0.00 % 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: -2.97 (0.32), residues: 639 helix: -3.10 (0.76), residues: 33 sheet: -1.49 (0.34), residues: 199 loop : -2.21 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 47 HIS 0.002 0.001 HIS C 33 PHE 0.174 0.005 PHE A 456 TYR 0.020 0.001 TYR A 421 ARG 0.007 0.001 ARG C 76 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 98) hydrogen bonds : angle 5.89159 ( 243) SS BOND : bond 0.00448 ( 6) SS BOND : angle 1.68680 ( 12) covalent geometry : bond 0.01740 ( 5140) covalent geometry : angle 1.19230 ( 7004) Misc. bond : bond 0.02107 ( 1) *********************** 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 117 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.704 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: 0.8430 (t80) cc_final: 0.8109 (t80) REVERT: A 396 TYR cc_start: 0.8772 (m-10) cc_final: 0.8422 (m-80) REVERT: A 465 GLU cc_start: 0.8286 (pt0) cc_final: 0.7926 (pt0) REVERT: B 52 TYR cc_start: 0.9387 (p90) cc_final: 0.8788 (p90) REVERT: B 72 SER cc_start: 0.9493 (t) cc_final: 0.9259 (p) REVERT: B 100 PHE cc_start: 0.8063 (m-80) cc_final: 0.7702 (m-80) REVERT: B 103 TYR cc_start: 0.8683 (p90) cc_final: 0.8421 (p90) REVERT: B 108 PHE cc_start: 0.8962 (m-80) cc_final: 0.8281 (m-80) REVERT: B 110 PHE cc_start: 0.9427 (m-80) cc_final: 0.8864 (m-80) REVERT: C 35 TYR cc_start: 0.8928 (m-80) cc_final: 0.8131 (m-80) REVERT: C 49 TYR cc_start: 0.9450 (m-80) cc_final: 0.9012 (m-80) REVERT: D 71 THR cc_start: 0.9041 (p) cc_final: 0.8764 (p) REVERT: D 80 TYR cc_start: 0.9105 (m-80) cc_final: 0.8829 (m-80) REVERT: D 110 TYR cc_start: 0.9526 (m-80) cc_final: 0.9046 (m-80) REVERT: E 4 MET cc_start: 0.8146 (tpp) cc_final: 0.7775 (tpp) REVERT: E 46 LEU cc_start: 0.8895 (tt) cc_final: 0.8620 (tt) REVERT: E 50 ASP cc_start: 0.9772 (m-30) cc_final: 0.9305 (t0) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2345 time to fit residues: 35.3828 Evaluate side-chains 95 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 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** A 493 GLN B 58 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.033105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.023768 restraints weight = 44585.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.025096 restraints weight = 24594.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.026044 restraints weight = 16468.510| |-----------------------------------------------------------------------------| r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.787 5147 Z= 0.678 Angle : 1.240 48.742 7016 Z= 0.689 Chirality : 0.052 0.277 758 Planarity : 0.007 0.065 907 Dihedral : 6.355 25.625 710 Min Nonbonded Distance : 1.633 Molprobity Statistics. All-atom Clashscore : 34.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.24 % Favored : 85.60 % 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 : 0.00 % 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: -3.32 (0.31), residues: 639 helix: -3.27 (0.69), residues: 32 sheet: -1.93 (0.32), residues: 206 loop : -2.34 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 36 HIS 0.009 0.002 HIS C 96 PHE 0.061 0.004 PHE A 456 TYR 0.037 0.003 TYR D 32 ARG 0.011 0.002 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 98) hydrogen bonds : angle 7.04932 ( 243) SS BOND : bond 0.00518 ( 6) SS BOND : angle 2.10924 ( 12) covalent geometry : bond 0.01856 ( 5140) covalent geometry : angle 1.23781 ( 7004) Misc. bond : bond 0.01488 ( 1) ********************** 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 102 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.831 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: 0.8392 (t80) cc_final: 0.8099 (t80) REVERT: B 72 SER cc_start: 0.9536 (t) cc_final: 0.9266 (p) REVERT: B 100 PHE cc_start: 0.8782 (m-80) cc_final: 0.7546 (m-80) REVERT: B 108 PHE cc_start: 0.9087 (m-80) cc_final: 0.7908 (m-80) REVERT: B 110 PHE cc_start: 0.9525 (m-80) cc_final: 0.8991 (m-80) REVERT: B 111 ASP cc_start: 0.9557 (t0) cc_final: 0.8291 (p0) REVERT: C 35 TYR cc_start: 0.8992 (m-80) cc_final: 0.8049 (m-80) REVERT: C 49 TYR cc_start: 0.9571 (m-80) cc_final: 0.9170 (m-80) REVERT: C 85 TYR cc_start: 0.9365 (m-80) cc_final: 0.9161 (m-80) REVERT: D 80 TYR cc_start: 0.9096 (m-80) cc_final: 0.8894 (m-80) REVERT: E 34 ASN cc_start: 0.8405 (m-40) cc_final: 0.7413 (m-40) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2001 time to fit residues: 26.3447 Evaluate side-chains 81 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 5.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 3 optimal weight: 0.4980 chunk 26 optimal weight: 0.0170 chunk 7 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- 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 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.035915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.025781 restraints weight = 40882.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.027224 restraints weight = 22138.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2566 r_free = 0.2566 target = 0.028291 restraints weight = 14799.037| |-----------------------------------------------------------------------------| r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.834 5147 Z= 0.623 Angle : 1.170 49.109 7016 Z= 0.652 Chirality : 0.050 0.254 758 Planarity : 0.005 0.052 907 Dihedral : 5.934 30.264 710 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.55 % Favored : 90.30 % 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: -3.07 (0.32), residues: 639 helix: -3.00 (0.78), residues: 33 sheet: -1.70 (0.34), residues: 198 loop : -2.21 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 47 HIS 0.001 0.000 HIS D 59 PHE 0.074 0.002 PHE A 456 TYR 0.014 0.001 TYR C 85 ARG 0.010 0.001 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 98) hydrogen bonds : angle 6.32143 ( 243) SS BOND : bond 0.00774 ( 6) SS BOND : angle 1.88455 ( 12) covalent geometry : bond 0.01783 ( 5140) covalent geometry : angle 1.16860 ( 7004) Misc. bond : bond 0.02053 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2449.56 seconds wall clock time: 45 minutes 5.27 seconds (2705.27 seconds total)