Starting phenix.real_space_refine on Thu Mar 6 05:04:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xef_38288/03_2025/8xef_38288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xef_38288/03_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_38288/03_2025/8xef_38288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xef_38288/03_2025/8xef_38288.map" model { file = "/net/cci-nas-00/data/ceres_data/8xef_38288/03_2025/8xef_38288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xef_38288/03_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-5624/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: 3.84, per 1000 atoms: 0.77 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 630.6 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: 0.63 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: 1.20 Time building geometry restraints manager: 1.52 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: 1.830 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.900 Find NCS groups from input model: 0.060 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.110 ------------------------------------------------------------------------------- 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 : 0.570 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: 0.2190 time to fit residues: 37.8341 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 : 0.988 ------------------------------------------------------------------------------- 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 = 24)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.027807 restraints weight = 22928.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.028854 restraints weight = 15280.346| |-----------------------------------------------------------------------------| r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8479 (t80) cc_final: 0.8118 (t80) REVERT: A 396 TYR cc_start: 0.8678 (m-10) cc_final: 0.8434 (m-80) REVERT: B 56 ASN cc_start: 0.9131 (m-40) cc_final: 0.8827 (m-40) REVERT: B 57 TRP cc_start: 0.9593 (m-90) cc_final: 0.9299 (m-90) REVERT: B 100 PHE cc_start: 0.7598 (m-80) cc_final: 0.7354 (m-80) REVERT: B 103 TYR cc_start: 0.8620 (p90) cc_final: 0.8329 (p90) REVERT: B 108 PHE cc_start: 0.8737 (m-80) cc_final: 0.8422 (m-80) REVERT: B 110 PHE cc_start: 0.9174 (m-80) cc_final: 0.8770 (m-80) REVERT: B 111 ASP cc_start: 0.9215 (t0) cc_final: 0.8936 (t0) REVERT: C 35 TYR cc_start: 0.8658 (m-80) cc_final: 0.7912 (m-80) REVERT: C 49 TYR cc_start: 0.9322 (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: 0.8899 (p) REVERT: D 80 TYR cc_start: 0.9357 (m-80) cc_final: 0.9015 (m-80) REVERT: D 100 GLU cc_start: 0.7948 (mp0) cc_final: 0.7245 (mp0) REVERT: D 110 TYR cc_start: 0.9485 (m-80) cc_final: 0.9148 (m-10) REVERT: E 70 ASP cc_start: 0.9519 (m-30) cc_final: 0.9312 (t0) REVERT: E 87 PHE cc_start: 0.9323 (m-80) cc_final: 0.8824 (m-10) REVERT: E 93 ASP cc_start: 0.9198 (m-30) cc_final: 0.8743 (p0) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2209 time to fit residues: 34.3438 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 : 0.689 ------------------------------------------------------------------------------- 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: 9.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.034321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.024644 restraints weight = 43489.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.026017 restraints weight = 23874.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.026986 restraints weight = 15969.135| |-----------------------------------------------------------------------------| r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5140 Z= 0.363 Angle : 0.730 8.492 7004 Z= 0.387 Chirality : 0.047 0.277 758 Planarity : 0.006 0.051 907 Dihedral : 6.265 25.431 710 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 27.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.21 % Favored : 87.64 % 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: -3.43 (0.30), residues: 639 helix: -3.94 (0.53), residues: 33 sheet: -1.81 (0.33), residues: 208 loop : -2.48 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 47 HIS 0.007 0.002 HIS C 96 PHE 0.017 0.003 PHE A 456 TYR 0.013 0.002 TYR A 473 ARG 0.006 0.001 ARG C 76 *********************** 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 114 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8434 (t80) cc_final: 0.8105 (t80) REVERT: A 396 TYR cc_start: 0.8794 (m-10) cc_final: 0.8526 (m-80) REVERT: B 100 PHE cc_start: 0.8099 (m-80) cc_final: 0.7311 (m-80) REVERT: B 108 PHE cc_start: 0.8835 (m-80) cc_final: 0.7686 (m-80) REVERT: B 110 PHE cc_start: 0.9303 (m-80) cc_final: 0.8845 (m-80) REVERT: B 111 ASP cc_start: 0.9276 (t0) cc_final: 0.8827 (t0) REVERT: C 35 TYR cc_start: 0.8751 (m-80) cc_final: 0.7838 (m-80) REVERT: C 49 TYR cc_start: 0.9437 (m-80) cc_final: 0.8830 (m-80) REVERT: C 85 TYR cc_start: 0.9160 (m-80) cc_final: 0.8855 (m-80) REVERT: D 51 ASN cc_start: 0.9658 (t0) cc_final: 0.9397 (t0) REVERT: D 80 TYR cc_start: 0.9218 (m-80) cc_final: 0.8936 (m-80) REVERT: E 47 LEU cc_start: 0.9635 (mm) cc_final: 0.9364 (mm) REVERT: E 70 ASP cc_start: 0.9538 (m-30) cc_final: 0.9315 (t0) REVERT: E 87 PHE cc_start: 0.9322 (m-80) cc_final: 0.8765 (m-10) REVERT: E 93 ASP cc_start: 0.9359 (m-30) cc_final: 0.8918 (p0) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.1653 time to fit residues: 24.1574 Evaluate side-chains 82 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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: 0.7980 chunk 35 optimal weight: 9.9990 chunk 36 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 = 0.2764 r_free = 0.2764 target = 0.034601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.024720 restraints weight = 42071.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.026134 restraints weight = 22566.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.027167 restraints weight = 14943.893| |-----------------------------------------------------------------------------| r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5140 Z= 0.288 Angle : 0.739 15.833 7004 Z= 0.378 Chirality : 0.048 0.245 758 Planarity : 0.005 0.051 907 Dihedral : 6.008 30.880 710 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.42 % Favored : 88.42 % Rotamer: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % 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: -3.36 (0.31), residues: 639 helix: -3.77 (0.56), residues: 32 sheet: -1.81 (0.33), residues: 206 loop : -2.42 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 49 HIS 0.003 0.001 HIS C 33 PHE 0.022 0.002 PHE A 456 TYR 0.027 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 110 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 PHE cc_start: 0.8523 (t80) cc_final: 0.8197 (t80) REVERT: A 396 TYR cc_start: 0.8791 (m-10) cc_final: 0.8439 (m-80) REVERT: B 100 PHE cc_start: 0.8025 (m-80) cc_final: 0.7578 (m-80) REVERT: B 108 PHE cc_start: 0.8929 (m-80) cc_final: 0.8348 (m-80) REVERT: B 110 PHE cc_start: 0.9328 (m-80) cc_final: 0.8745 (m-80) REVERT: C 35 TYR cc_start: 0.8780 (m-80) cc_final: 0.7882 (m-80) REVERT: C 49 TYR cc_start: 0.9413 (m-80) cc_final: 0.9011 (m-80) REVERT: C 105 VAL cc_start: 0.9579 (m) cc_final: 0.9219 (p) REVERT: D 51 ASN cc_start: 0.9697 (t0) cc_final: 0.9443 (t0) REVERT: D 80 TYR cc_start: 0.9263 (m-80) cc_final: 0.9042 (m-80) REVERT: E 34 ASN cc_start: 0.8798 (m-40) cc_final: 0.7654 (m110) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.1733 time to fit residues: 24.3011 Evaluate side-chains 80 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 20 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** E 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.033965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.024407 restraints weight = 43765.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.025763 restraints weight = 23494.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.026737 restraints weight = 15570.614| |-----------------------------------------------------------------------------| r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 5140 Z= 0.348 Angle : 0.758 10.312 7004 Z= 0.393 Chirality : 0.048 0.204 758 Planarity : 0.006 0.058 907 Dihedral : 6.215 31.810 710 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.83 % Favored : 87.01 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % 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: -3.53 (0.30), residues: 639 helix: -3.61 (0.60), residues: 32 sheet: -1.96 (0.32), residues: 212 loop : -2.55 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 47 HIS 0.004 0.001 HIS C 33 PHE 0.039 0.003 PHE A 456 TYR 0.046 0.002 TYR A 421 ARG 0.008 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 106 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.759 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: 0.8488 (t80) cc_final: 0.8147 (t80) REVERT: A 396 TYR cc_start: 0.8828 (m-10) cc_final: 0.8495 (m-80) REVERT: B 57 TRP cc_start: 0.9571 (m-90) cc_final: 0.9368 (m-90) REVERT: B 100 PHE cc_start: 0.8067 (m-80) cc_final: 0.7661 (m-80) REVERT: B 108 PHE cc_start: 0.8972 (m-80) cc_final: 0.8376 (m-80) REVERT: B 110 PHE cc_start: 0.9367 (m-80) cc_final: 0.8833 (m-80) REVERT: C 35 TYR cc_start: 0.8926 (m-80) cc_final: 0.8023 (m-80) REVERT: C 49 TYR cc_start: 0.9458 (m-80) cc_final: 0.9089 (m-80) REVERT: C 85 TYR cc_start: 0.9369 (m-10) cc_final: 0.8808 (m-80) REVERT: C 105 VAL cc_start: 0.9543 (m) cc_final: 0.9000 (p) REVERT: D 51 ASN cc_start: 0.9713 (t0) cc_final: 0.9442 (t0) REVERT: D 80 TYR cc_start: 0.9219 (m-80) cc_final: 0.8969 (m-80) REVERT: E 70 ASP cc_start: 0.9493 (m-30) cc_final: 0.9244 (t0) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1899 time to fit residues: 25.8343 Evaluate side-chains 86 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 5.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 54 optimal weight: 0.0570 chunk 58 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.6902 ------------------------------------------------------------------------------- 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 = 0.2803 r_free = 0.2803 target = 0.035567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.025670 restraints weight = 41901.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.027125 restraints weight = 22568.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.028168 restraints weight = 14874.646| |-----------------------------------------------------------------------------| r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5140 Z= 0.213 Angle : 0.703 18.415 7004 Z= 0.353 Chirality : 0.048 0.328 758 Planarity : 0.005 0.045 907 Dihedral : 5.679 26.456 710 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.49 % Favored : 89.36 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: -3.25 (0.31), residues: 639 helix: -3.41 (0.66), residues: 33 sheet: -1.71 (0.33), residues: 209 loop : -2.38 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 49 HIS 0.002 0.001 HIS A 505 PHE 0.032 0.002 PHE A 456 TYR 0.039 0.002 TYR A 421 ARG 0.007 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 : 1.088 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: 0.8531 (t80) cc_final: 0.8196 (t80) REVERT: A 396 TYR cc_start: 0.8766 (m-10) cc_final: 0.8465 (m-80) REVERT: B 72 SER cc_start: 0.9452 (t) cc_final: 0.9224 (p) REVERT: B 100 PHE cc_start: 0.7905 (m-80) cc_final: 0.7590 (m-80) REVERT: B 108 PHE cc_start: 0.8922 (m-80) cc_final: 0.8276 (m-80) REVERT: B 110 PHE cc_start: 0.9356 (m-80) cc_final: 0.8760 (m-80) REVERT: B 111 ASP cc_start: 0.9273 (t0) cc_final: 0.9006 (t0) REVERT: C 35 TYR cc_start: 0.8909 (m-80) cc_final: 0.8172 (m-80) REVERT: C 49 TYR cc_start: 0.9410 (m-80) cc_final: 0.9035 (m-80) REVERT: C 85 TYR cc_start: 0.9312 (m-10) cc_final: 0.8788 (m-80) REVERT: C 105 VAL cc_start: 0.9545 (m) cc_final: 0.9090 (p) REVERT: D 51 ASN cc_start: 0.9691 (t0) cc_final: 0.9341 (t0) REVERT: D 80 TYR cc_start: 0.9244 (m-80) cc_final: 0.9037 (m-80) REVERT: E 34 ASN cc_start: 0.8530 (m-40) cc_final: 0.7626 (m110) REVERT: E 70 ASP cc_start: 0.9448 (m-30) cc_final: 0.9196 (t0) REVERT: E 93 ASP cc_start: 0.9402 (m-30) cc_final: 0.8853 (p0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2109 time to fit residues: 31.0910 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 : 0.806 ------------------------------------------------------------------------------- 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: 7.9990 chunk 54 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 422 ASN ** 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 = 0.2785 r_free = 0.2785 target = 0.034613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.024664 restraints weight = 41772.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.026041 restraints weight = 23149.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.027028 restraints weight = 15584.860| |-----------------------------------------------------------------------------| r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5140 Z= 0.248 Angle : 0.768 24.583 7004 Z= 0.382 Chirality : 0.049 0.270 758 Planarity : 0.005 0.058 907 Dihedral : 5.860 31.566 710 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.95 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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: -3.27 (0.31), residues: 639 helix: -3.21 (0.73), residues: 33 sheet: -1.89 (0.33), residues: 206 loop : -2.31 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 49 HIS 0.002 0.001 HIS A 505 PHE 0.090 0.003 PHE A 456 TYR 0.046 0.002 TYR A 421 ARG 0.007 0.001 ARG C 76 *********************** 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 111 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.830 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: 0.8483 (t80) cc_final: 0.8133 (t80) REVERT: A 396 TYR cc_start: 0.8796 (m-10) cc_final: 0.8488 (m-80) REVERT: B 72 SER cc_start: 0.9514 (t) cc_final: 0.9273 (p) REVERT: B 100 PHE cc_start: 0.8141 (m-80) cc_final: 0.7729 (m-80) REVERT: B 108 PHE cc_start: 0.8981 (m-80) cc_final: 0.8354 (m-80) REVERT: B 110 PHE cc_start: 0.9443 (m-80) cc_final: 0.8849 (m-80) REVERT: B 111 ASP cc_start: 0.9392 (t0) cc_final: 0.9134 (t0) REVERT: C 35 TYR cc_start: 0.8930 (m-80) cc_final: 0.8137 (m-80) REVERT: C 49 TYR cc_start: 0.9474 (m-80) cc_final: 0.9064 (m-80) REVERT: C 85 TYR cc_start: 0.9304 (m-10) cc_final: 0.8752 (m-80) REVERT: C 105 VAL cc_start: 0.9540 (m) cc_final: 0.9134 (p) REVERT: D 51 ASN cc_start: 0.9759 (t0) cc_final: 0.9461 (t0) REVERT: D 80 TYR cc_start: 0.9134 (m-80) cc_final: 0.8929 (m-80) REVERT: E 34 ASN cc_start: 0.8850 (m-40) cc_final: 0.7766 (m110) REVERT: E 71 PHE cc_start: 0.9126 (m-10) cc_final: 0.8827 (m-10) REVERT: E 93 ASP cc_start: 0.9429 (m-30) cc_final: 0.8940 (p0) REVERT: E 101 THR cc_start: 0.8336 (p) cc_final: 0.7955 (p) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.2376 time to fit residues: 34.1741 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 : 0.858 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 58 optimal weight: 0.0870 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 2 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 0.0570 chunk 35 optimal weight: 4.9990 overall best weight: 0.6076 ------------------------------------------------------------------------------- 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 = 0.2848 r_free = 0.2848 target = 0.036956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.026642 restraints weight = 40528.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.028167 restraints weight = 21842.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.029277 restraints weight = 14431.972| |-----------------------------------------------------------------------------| r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5140 Z= 0.209 Angle : 0.763 15.189 7004 Z= 0.386 Chirality : 0.050 0.369 758 Planarity : 0.005 0.056 907 Dihedral : 5.705 28.823 710 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.08 % Favored : 90.77 % 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: -3.05 (0.32), residues: 639 helix: -2.98 (0.81), residues: 33 sheet: -1.66 (0.34), residues: 206 loop : -2.21 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 HIS 0.003 0.001 HIS A 505 PHE 0.078 0.002 PHE A 456 TYR 0.019 0.001 TYR D 32 ARG 0.006 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 119 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.600 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: 0.8494 (t80) cc_final: 0.8156 (t80) REVERT: A 396 TYR cc_start: 0.8764 (m-10) cc_final: 0.8476 (m-80) REVERT: A 465 GLU cc_start: 0.8072 (pt0) cc_final: 0.7767 (pt0) REVERT: B 72 SER cc_start: 0.9429 (t) cc_final: 0.9213 (p) REVERT: B 100 PHE cc_start: 0.7794 (m-80) cc_final: 0.7543 (m-80) REVERT: B 103 TYR cc_start: 0.8708 (p90) cc_final: 0.8320 (p90) REVERT: B 108 PHE cc_start: 0.8913 (m-80) cc_final: 0.8220 (m-80) REVERT: B 110 PHE cc_start: 0.9363 (m-80) cc_final: 0.8570 (m-80) REVERT: B 111 ASP cc_start: 0.9269 (t0) cc_final: 0.8403 (m-30) REVERT: C 35 TYR cc_start: 0.8932 (m-80) cc_final: 0.7850 (m-80) REVERT: C 49 TYR cc_start: 0.9377 (m-80) cc_final: 0.8993 (m-80) REVERT: D 51 ASN cc_start: 0.9629 (t0) cc_final: 0.9328 (t0) REVERT: D 71 THR cc_start: 0.9116 (p) cc_final: 0.8823 (p) REVERT: D 81 MET cc_start: 0.8504 (mmp) cc_final: 0.8097 (mmp) REVERT: D 110 TYR cc_start: 0.9544 (m-80) cc_final: 0.9057 (m-80) REVERT: E 34 ASN cc_start: 0.8523 (m-40) cc_final: 0.7523 (m110) REVERT: E 50 ASP cc_start: 0.9762 (m-30) cc_final: 0.9278 (t0) REVERT: E 70 ASP cc_start: 0.9447 (m-30) cc_final: 0.9206 (t0) REVERT: E 71 PHE cc_start: 0.8991 (m-10) cc_final: 0.8752 (m-10) REVERT: E 87 PHE cc_start: 0.9119 (m-80) cc_final: 0.8858 (m-80) REVERT: E 93 ASP cc_start: 0.9410 (m-30) cc_final: 0.8899 (p0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1794 time to fit residues: 27.0818 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 : 0.584 ------------------------------------------------------------------------------- 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: 9.9990 chunk 31 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.0670 chunk 46 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 34 optimal weight: 0.0270 chunk 53 optimal weight: 6.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 422 ASN ** 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 = 0.2866 r_free = 0.2866 target = 0.037391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.026891 restraints weight = 38706.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.028418 restraints weight = 21590.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.029485 restraints weight = 14487.427| |-----------------------------------------------------------------------------| r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5140 Z= 0.197 Angle : 0.759 11.873 7004 Z= 0.393 Chirality : 0.051 0.310 758 Planarity : 0.005 0.059 907 Dihedral : 5.329 26.107 710 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.55 % Favored : 90.30 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Cbeta Deviations : 0.17 % 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: -2.88 (0.32), residues: 639 helix: -3.07 (0.81), residues: 33 sheet: -1.46 (0.34), residues: 205 loop : -2.14 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 36 HIS 0.003 0.001 HIS A 505 PHE 0.027 0.001 PHE A 456 TYR 0.037 0.002 TYR A 421 ARG 0.008 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 119 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.580 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: 0.8461 (t80) cc_final: 0.8107 (t80) REVERT: A 396 TYR cc_start: 0.8753 (m-10) cc_final: 0.8446 (m-80) REVERT: A 465 GLU cc_start: 0.8189 (pt0) cc_final: 0.7800 (pt0) REVERT: B 72 SER cc_start: 0.9473 (t) cc_final: 0.9254 (p) REVERT: B 100 PHE cc_start: 0.7823 (m-80) cc_final: 0.7370 (m-80) REVERT: B 103 TYR cc_start: 0.8675 (p90) cc_final: 0.8167 (p90) REVERT: B 108 PHE cc_start: 0.8935 (m-80) cc_final: 0.7676 (m-80) REVERT: B 110 PHE cc_start: 0.9405 (m-80) cc_final: 0.8607 (m-80) REVERT: B 111 ASP cc_start: 0.9320 (t0) cc_final: 0.8457 (m-30) REVERT: C 35 TYR cc_start: 0.8952 (m-80) cc_final: 0.7849 (m-80) REVERT: C 49 TYR cc_start: 0.9401 (m-80) cc_final: 0.8987 (m-80) REVERT: D 81 MET cc_start: 0.8598 (mmp) cc_final: 0.8049 (mmp) REVERT: D 83 LEU cc_start: 0.9287 (tp) cc_final: 0.9072 (tp) REVERT: D 110 TYR cc_start: 0.9551 (m-80) cc_final: 0.9053 (m-80) REVERT: E 4 MET cc_start: 0.8123 (tpp) cc_final: 0.7467 (tpp) REVERT: E 34 ASN cc_start: 0.8711 (m-40) cc_final: 0.7713 (m-40) REVERT: E 50 ASP cc_start: 0.9753 (m-30) cc_final: 0.9236 (t0) REVERT: E 70 ASP cc_start: 0.9353 (m-30) cc_final: 0.9085 (t0) REVERT: E 93 ASP cc_start: 0.9372 (m-30) cc_final: 0.8878 (p0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.2100 time to fit residues: 31.7642 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 : 1.399 ------------------------------------------------------------------------------- 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: 5.9990 chunk 17 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 1 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 422 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** E 90 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 = 0.2799 r_free = 0.2799 target = 0.035086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.025057 restraints weight = 42000.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.026446 restraints weight = 23582.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.027455 restraints weight = 15956.586| |-----------------------------------------------------------------------------| r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5140 Z= 0.294 Angle : 0.913 41.358 7004 Z= 0.429 Chirality : 0.050 0.360 758 Planarity : 0.006 0.060 907 Dihedral : 5.709 32.659 710 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 23.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.11 % Favored : 88.73 % 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: -3.01 (0.32), residues: 639 helix: -2.85 (0.81), residues: 34 sheet: -1.72 (0.33), residues: 206 loop : -2.14 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 90 HIS 0.004 0.001 HIS C 96 PHE 0.073 0.003 PHE A 456 TYR 0.013 0.002 TYR A 421 ARG 0.010 0.002 ARG C 76 ********************** 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 114 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.833 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: 0.8424 (t80) cc_final: 0.8135 (t80) REVERT: A 396 TYR cc_start: 0.8808 (m-10) cc_final: 0.8411 (m-80) REVERT: B 57 TRP cc_start: 0.9558 (m-90) cc_final: 0.9311 (m-90) REVERT: B 72 SER cc_start: 0.9500 (t) cc_final: 0.9241 (p) REVERT: B 100 PHE cc_start: 0.8413 (m-80) cc_final: 0.7742 (m-80) REVERT: B 108 PHE cc_start: 0.9002 (m-80) cc_final: 0.8303 (m-80) REVERT: B 110 PHE cc_start: 0.9478 (m-80) cc_final: 0.8858 (m-80) REVERT: B 111 ASP cc_start: 0.9461 (t0) cc_final: 0.9194 (t0) REVERT: C 35 TYR cc_start: 0.8932 (m-80) cc_final: 0.7986 (m-80) REVERT: C 49 TYR cc_start: 0.9495 (m-80) cc_final: 0.9077 (m-80) REVERT: D 32 TYR cc_start: 0.8246 (m-10) cc_final: 0.7870 (m-80) REVERT: D 71 THR cc_start: 0.8977 (p) cc_final: 0.8678 (p) REVERT: D 83 LEU cc_start: 0.9338 (tp) cc_final: 0.9137 (tp) REVERT: E 34 ASN cc_start: 0.8664 (m-40) cc_final: 0.7963 (m-40) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1973 time to fit residues: 28.9709 Evaluate side-chains 87 residues out of total 548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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: 6.9990 chunk 32 optimal weight: 9.9990 chunk 3 optimal weight: 0.0050 chunk 26 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- 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 = 0.2815 r_free = 0.2815 target = 0.035810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.025551 restraints weight = 40518.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.027008 restraints weight = 22202.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.028054 restraints weight = 14872.735| |-----------------------------------------------------------------------------| r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 5140 Z= 0.262 Angle : 0.764 12.737 7004 Z= 0.394 Chirality : 0.051 0.387 758 Planarity : 0.005 0.058 907 Dihedral : 5.920 41.966 710 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.49 % Favored : 89.20 % 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 : 0.49 % 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: -2.98 (0.32), residues: 639 helix: -2.64 (0.83), residues: 33 sheet: -1.62 (0.34), residues: 197 loop : -2.19 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 34 HIS 0.004 0.001 HIS D 59 PHE 0.096 0.003 PHE A 456 TYR 0.014 0.002 TYR C 85 ARG 0.009 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.05 seconds wall clock time: 41 minutes 54.43 seconds (2514.43 seconds total)