Starting phenix.real_space_refine on Fri Jul 25 01:25:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xdn_38282/07_2025/8xdn_38282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xdn_38282/07_2025/8xdn_38282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xdn_38282/07_2025/8xdn_38282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xdn_38282/07_2025/8xdn_38282.map" model { file = "/net/cci-nas-00/data/ceres_data/8xdn_38282/07_2025/8xdn_38282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xdn_38282/07_2025/8xdn_38282.cif" } resolution = 2.93 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= 0.003 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 34 5.16 5 C 4454 2.51 5 N 1177 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6894 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2193 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain: "B" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2193 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 332 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 332 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "E" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 193 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "F" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 193 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "G" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 409 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "H" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 409 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "I" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 287 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "J" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 287 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'FUD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.74 Number of scatterers: 6894 At special positions: 0 Unit cell: (82.9026, 92.9514, 137.334, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 1 15.00 O 1228 8.00 N 1177 7.00 C 4454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.6 seconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 31.5% alpha, 35.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 83 through 86 removed outlier: 3.616A pdb=" N CYS A 86 " --> pdb=" O PHE A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 86' Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.671A pdb=" N GLU B 92 " --> pdb=" O ARG B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 96 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'D' and resid 73 through 109 removed outlier: 3.574A pdb=" N MET D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) Proline residue: D 98 - end of helix Processing helix chain 'E' and resid 42 through 60 Processing helix chain 'F' and resid 42 through 61 Processing helix chain 'G' and resid 6 through 39 removed outlier: 5.724A pdb=" N ILE G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Proline residue: G 29 - end of helix Processing helix chain 'G' and resid 49 through 53 Processing helix chain 'H' and resid 6 through 39 removed outlier: 5.259A pdb=" N ILE H 28 " --> pdb=" O ARG H 24 " (cutoff:3.500A) Proline residue: H 29 - end of helix Processing helix chain 'H' and resid 48 through 53 removed outlier: 3.617A pdb=" N LEU H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 49 Proline residue: I 42 - end of helix Processing helix chain 'J' and resid 17 through 49 Proline residue: J 42 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.625A pdb=" N LYS A 351 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS A 102 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE A 360 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 104 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLN A 181 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N PHE A 185 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 13.699A pdb=" N VAL A 186 " --> pdb=" O ASP A 209 " (cutoff:3.500A) removed outlier: 11.079A pdb=" N ASP A 209 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TRP A 188 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N SER A 214 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY A 215 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 239 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A 319 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU A 339 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 101 through 108 removed outlier: 6.338A pdb=" N GLN B 181 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHE B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 13.801A pdb=" N VAL B 186 " --> pdb=" O ASP B 209 " (cutoff:3.500A) removed outlier: 10.784A pdb=" N ASP B 209 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TRP B 188 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER B 214 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 230 " --> pdb=" O LYS B 253 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 351 " --> pdb=" O ASN B 346 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1299 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: 2.12 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1226 1.32 - 1.45: 1789 1.45 - 1.57: 3967 1.57 - 1.69: 2 1.69 - 1.82: 58 Bond restraints: 7042 Sorted by residual: bond pdb=" CG1 ILE J 28 " pdb=" CD1 ILE J 28 " ideal model delta sigma weight residual 1.513 1.434 0.079 3.90e-02 6.57e+02 4.12e+00 bond pdb=" N LYS D 105 " pdb=" CA LYS D 105 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.19e-02 7.06e+03 3.47e+00 bond pdb=" CB ARG H 11 " pdb=" CG ARG H 11 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.59e+00 bond pdb=" CB ARG D 82 " pdb=" CG ARG D 82 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.54e+00 bond pdb=" CB VAL A 324 " pdb=" CG1 VAL A 324 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.46e+00 ... (remaining 7037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 9282 2.26 - 4.53: 178 4.53 - 6.79: 30 6.79 - 9.05: 16 9.05 - 11.31: 3 Bond angle restraints: 9509 Sorted by residual: angle pdb=" N LYS D 105 " pdb=" CA LYS D 105 " pdb=" C LYS D 105 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.32e+01 angle pdb=" CA MET C 77 " pdb=" CB MET C 77 " pdb=" CG MET C 77 " ideal model delta sigma weight residual 114.10 122.42 -8.32 2.00e+00 2.50e-01 1.73e+01 angle pdb=" CA GLU C 104 " pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 114.10 122.22 -8.12 2.00e+00 2.50e-01 1.65e+01 angle pdb=" CB ARG H 11 " pdb=" CG ARG H 11 " pdb=" CD ARG H 11 " ideal model delta sigma weight residual 111.30 120.30 -9.00 2.30e+00 1.89e-01 1.53e+01 angle pdb=" CA GLN C 75 " pdb=" CB GLN C 75 " pdb=" CG GLN C 75 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 ... (remaining 9504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3477 17.95 - 35.89: 486 35.89 - 53.84: 177 53.84 - 71.78: 33 71.78 - 89.73: 14 Dihedral angle restraints: 4187 sinusoidal: 1717 harmonic: 2470 Sorted by residual: dihedral pdb=" CA ASP A 153 " pdb=" CB ASP A 153 " pdb=" CG ASP A 153 " pdb=" OD1 ASP A 153 " ideal model delta sinusoidal sigma weight residual -30.00 -89.20 59.20 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU C 109 " pdb=" CG GLU C 109 " pdb=" CD GLU C 109 " pdb=" OE1 GLU C 109 " ideal model delta sinusoidal sigma weight residual 0.00 89.73 -89.73 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP A 280 " pdb=" CB ASP A 280 " pdb=" CG ASP A 280 " pdb=" OD1 ASP A 280 " ideal model delta sinusoidal sigma weight residual -30.00 -85.94 55.94 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 4184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 646 0.037 - 0.073: 283 0.073 - 0.110: 99 0.110 - 0.147: 28 0.147 - 0.184: 6 Chirality restraints: 1062 Sorted by residual: chirality pdb=" CB THR D 103 " pdb=" CA THR D 103 " pdb=" OG1 THR D 103 " pdb=" CG2 THR D 103 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CA GLU C 104 " pdb=" N GLU C 104 " pdb=" C GLU C 104 " pdb=" CB GLU C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA LYS D 105 " pdb=" N LYS D 105 " pdb=" C LYS D 105 " pdb=" CB LYS D 105 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 1059 not shown) Planarity restraints: 1199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 109 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C GLU D 109 " -0.045 2.00e-02 2.50e+03 pdb=" O GLU D 109 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN D 110 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 226 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO B 227 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 331 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.80e+00 pdb=" C LYS B 331 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS B 331 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU B 332 " 0.011 2.00e-02 2.50e+03 ... (remaining 1196 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 535 2.74 - 3.28: 6559 3.28 - 3.82: 11204 3.82 - 4.36: 12881 4.36 - 4.90: 23298 Nonbonded interactions: 54477 Sorted by model distance: nonbonded pdb=" OE1 GLN H 10 " pdb=" NE2 GLN H 14 " model vdw 2.195 3.120 nonbonded pdb=" O ASN F 44 " pdb=" ND2 ASN F 48 " model vdw 2.199 3.120 nonbonded pdb=" O VAL C 99 " pdb=" OG1 THR C 103 " model vdw 2.201 3.040 nonbonded pdb=" O LEU I 37 " pdb=" OG1 THR I 41 " model vdw 2.205 3.040 nonbonded pdb=" O GLN B 182 " pdb=" NH2 ARG G 24 " model vdw 2.207 3.120 ... (remaining 54472 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 75 through 361) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 72 through 111) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.090 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:13.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.005 0.079 7042 Z= 0.200 Angle : 0.849 11.313 9509 Z= 0.443 Chirality : 0.048 0.184 1062 Planarity : 0.005 0.049 1199 Dihedral : 19.554 89.728 2603 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.31 % Allowed : 45.11 % Favored : 52.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.30), residues: 852 helix: 1.73 (0.33), residues: 254 sheet: -0.85 (0.27), residues: 396 loop : -0.65 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 86 HIS 0.010 0.002 HIS A 347 PHE 0.018 0.002 PHE A 356 TYR 0.029 0.002 TYR B 221 ARG 0.019 0.001 ARG I 21 Details of bonding type rmsd hydrogen bonds : bond 0.09832 ( 452) hydrogen bonds : angle 6.80757 ( 1299) covalent geometry : bond 0.00460 ( 7042) covalent geometry : angle 0.84900 ( 9509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7676 (ttm) cc_final: 0.7252 (ttm) REVERT: A 265 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7420 (mm) REVERT: A 296 ASP cc_start: 0.7659 (p0) cc_final: 0.7255 (p0) REVERT: B 249 SER cc_start: 0.6639 (m) cc_final: 0.6291 (p) REVERT: C 76 LYS cc_start: 0.7248 (mmtm) cc_final: 0.6949 (mmtt) REVERT: C 100 VAL cc_start: 0.8021 (p) cc_final: 0.7703 (m) REVERT: D 77 MET cc_start: 0.5241 (tpt) cc_final: 0.4211 (mtm) REVERT: D 82 ARG cc_start: 0.4288 (tmt-80) cc_final: 0.1508 (mtp85) REVERT: E 43 ARG cc_start: 0.6781 (ttt180) cc_final: 0.5995 (ptt-90) REVERT: E 52 PHE cc_start: 0.4945 (t80) cc_final: 0.4295 (t80) REVERT: G 44 MET cc_start: 0.4935 (ppp) cc_final: 0.4496 (pmm) REVERT: H 44 MET cc_start: 0.1728 (ppp) cc_final: 0.1280 (ppp) REVERT: J 39 ARG cc_start: 0.4715 (mmm160) cc_final: 0.4388 (mtp180) outliers start: 17 outliers final: 3 residues processed: 217 average time/residue: 1.1652 time to fit residues: 269.1938 Evaluate side-chains 178 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 174 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 265 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN F 48 ASN ** G 10 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 = 0.4676 r_free = 0.4676 target = 0.198018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.154305 restraints weight = 7700.590| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 2.61 r_work: 0.4059 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7042 Z= 0.214 Angle : 0.780 12.848 9509 Z= 0.401 Chirality : 0.047 0.151 1062 Planarity : 0.005 0.048 1199 Dihedral : 8.983 58.551 995 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 9.10 % Allowed : 37.23 % Favored : 53.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.30), residues: 852 helix: 1.74 (0.32), residues: 267 sheet: -0.97 (0.26), residues: 396 loop : -0.89 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 259 HIS 0.009 0.002 HIS A 347 PHE 0.017 0.002 PHE A 356 TYR 0.022 0.002 TYR B 221 ARG 0.010 0.001 ARG D 79 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 452) hydrogen bonds : angle 6.10841 ( 1299) covalent geometry : bond 0.00489 ( 7042) covalent geometry : angle 0.77973 ( 9509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 183 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5614 (pp20) cc_final: 0.4850 (tm-30) REVERT: A 124 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7366 (tp) REVERT: A 234 GLU cc_start: 0.7532 (pt0) cc_final: 0.7250 (pt0) REVERT: A 289 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6326 (tm-30) REVERT: A 296 ASP cc_start: 0.8016 (p0) cc_final: 0.7631 (p0) REVERT: B 114 GLN cc_start: 0.6577 (mp10) cc_final: 0.6311 (pp30) REVERT: B 248 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6326 (tmm) REVERT: B 249 SER cc_start: 0.6872 (m) cc_final: 0.6607 (p) REVERT: B 296 ASP cc_start: 0.6942 (m-30) cc_final: 0.6624 (p0) REVERT: C 76 LYS cc_start: 0.7427 (mmtm) cc_final: 0.6571 (mmpt) REVERT: D 77 MET cc_start: 0.5309 (tpt) cc_final: 0.4480 (mtm) REVERT: D 82 ARG cc_start: 0.3917 (tmt-80) cc_final: 0.1126 (mtp85) REVERT: D 108 MET cc_start: 0.6477 (ppp) cc_final: 0.6243 (ppp) REVERT: E 43 ARG cc_start: 0.6951 (ttt180) cc_final: 0.5966 (ptt180) REVERT: F 45 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.7045 (mm) REVERT: G 38 ARG cc_start: 0.6061 (OUTLIER) cc_final: 0.5291 (tmt170) REVERT: I 21 ARG cc_start: 0.8504 (tpt170) cc_final: 0.8185 (tpp80) REVERT: J 19 LYS cc_start: 0.8549 (tptt) cc_final: 0.8132 (tptm) outliers start: 67 outliers final: 35 residues processed: 226 average time/residue: 1.0936 time to fit residues: 261.3746 Evaluate side-chains 213 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 248 MET Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.0970 chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 9 optimal weight: 0.0000 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN E 48 ASN E 61 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.202147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.157857 restraints weight = 7735.461| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.69 r_work: 0.4105 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7042 Z= 0.141 Angle : 0.703 8.813 9509 Z= 0.357 Chirality : 0.044 0.148 1062 Planarity : 0.004 0.051 1199 Dihedral : 8.190 55.167 993 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 8.56 % Allowed : 36.68 % Favored : 54.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.30), residues: 852 helix: 1.98 (0.32), residues: 265 sheet: -0.96 (0.26), residues: 396 loop : -0.69 (0.47), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 259 HIS 0.005 0.001 HIS B 112 PHE 0.021 0.001 PHE G 21 TYR 0.014 0.002 TYR B 221 ARG 0.007 0.001 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 452) hydrogen bonds : angle 5.58791 ( 1299) covalent geometry : bond 0.00321 ( 7042) covalent geometry : angle 0.70257 ( 9509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5580 (pp20) cc_final: 0.4781 (tm-30) REVERT: A 180 THR cc_start: 0.7574 (OUTLIER) cc_final: 0.7373 (t) REVERT: A 193 GLU cc_start: 0.5312 (OUTLIER) cc_final: 0.5074 (tp30) REVERT: A 234 GLU cc_start: 0.7409 (pt0) cc_final: 0.7208 (pt0) REVERT: A 296 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7402 (p0) REVERT: B 114 GLN cc_start: 0.6521 (mp10) cc_final: 0.6278 (pp30) REVERT: B 234 GLU cc_start: 0.5623 (OUTLIER) cc_final: 0.5323 (pt0) REVERT: B 249 SER cc_start: 0.6910 (m) cc_final: 0.6414 (p) REVERT: B 250 LEU cc_start: 0.6960 (mp) cc_final: 0.6389 (tp) REVERT: B 296 ASP cc_start: 0.6921 (m-30) cc_final: 0.6607 (p0) REVERT: B 329 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: C 76 LYS cc_start: 0.7343 (mmtm) cc_final: 0.6673 (mmtt) REVERT: D 77 MET cc_start: 0.5173 (tpt) cc_final: 0.4420 (mtm) REVERT: D 82 ARG cc_start: 0.4113 (tmt-80) cc_final: 0.1390 (mtp85) REVERT: E 43 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6006 (ptt-90) REVERT: H 10 GLN cc_start: 0.7844 (pp30) cc_final: 0.7536 (pp30) outliers start: 63 outliers final: 24 residues processed: 230 average time/residue: 0.9804 time to fit residues: 239.8186 Evaluate side-chains 209 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 GLU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 66 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN A 346 ASN F 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.201128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156889 restraints weight = 7783.249| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 2.66 r_work: 0.4092 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7042 Z= 0.148 Angle : 0.735 15.676 9509 Z= 0.366 Chirality : 0.045 0.151 1062 Planarity : 0.005 0.051 1199 Dihedral : 7.956 56.398 991 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 8.42 % Allowed : 36.41 % Favored : 55.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.30), residues: 852 helix: 1.95 (0.32), residues: 263 sheet: -0.92 (0.26), residues: 398 loop : -0.51 (0.49), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 259 HIS 0.006 0.001 HIS A 347 PHE 0.015 0.001 PHE G 21 TYR 0.014 0.002 TYR J 34 ARG 0.006 0.001 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 452) hydrogen bonds : angle 5.52386 ( 1299) covalent geometry : bond 0.00338 ( 7042) covalent geometry : angle 0.73451 ( 9509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.5620 (pp20) cc_final: 0.4846 (tm-30) REVERT: A 265 LEU cc_start: 0.8266 (mm) cc_final: 0.7831 (mm) REVERT: B 114 GLN cc_start: 0.6529 (mp10) cc_final: 0.6308 (pp30) REVERT: B 234 GLU cc_start: 0.5549 (OUTLIER) cc_final: 0.4958 (pt0) REVERT: B 249 SER cc_start: 0.6850 (m) cc_final: 0.6195 (p) REVERT: B 250 LEU cc_start: 0.6940 (mp) cc_final: 0.6418 (tp) REVERT: B 254 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6024 (m-80) REVERT: B 296 ASP cc_start: 0.6872 (m-30) cc_final: 0.6537 (p0) REVERT: C 76 LYS cc_start: 0.7293 (mmtm) cc_final: 0.6636 (mmpt) REVERT: D 77 MET cc_start: 0.5327 (tpt) cc_final: 0.4536 (mtm) REVERT: D 82 ARG cc_start: 0.4295 (tmt-80) cc_final: 0.1496 (mtp85) REVERT: E 43 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.5930 (ptt180) REVERT: H 12 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7935 (mt) REVERT: H 14 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6943 (pm20) outliers start: 62 outliers final: 33 residues processed: 224 average time/residue: 1.0005 time to fit residues: 238.3468 Evaluate side-chains 215 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 234 GLU Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 14 GLN Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain I residue 27 SER Chi-restraints excluded: chain I residue 40 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN E 48 ASN F 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.200688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.156950 restraints weight = 7679.730| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.63 r_work: 0.4091 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7042 Z= 0.154 Angle : 0.746 12.470 9509 Z= 0.373 Chirality : 0.045 0.142 1062 Planarity : 0.004 0.051 1199 Dihedral : 7.823 58.921 991 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 8.15 % Allowed : 37.09 % Favored : 54.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 852 helix: 1.95 (0.32), residues: 263 sheet: -0.84 (0.26), residues: 400 loop : -0.50 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 259 HIS 0.011 0.001 HIS A 220 PHE 0.023 0.001 PHE G 27 TYR 0.016 0.002 TYR H 33 ARG 0.010 0.001 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.03480 ( 452) hydrogen bonds : angle 5.41613 ( 1299) covalent geometry : bond 0.00356 ( 7042) covalent geometry : angle 0.74621 ( 9509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7356 (tp) REVERT: A 160 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7227 (tp) REVERT: A 182 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.5930 (mp-120) REVERT: A 265 LEU cc_start: 0.8217 (mm) cc_final: 0.7812 (mm) REVERT: B 249 SER cc_start: 0.6918 (m) cc_final: 0.6553 (p) REVERT: B 250 LEU cc_start: 0.6892 (mp) cc_final: 0.6373 (tp) REVERT: B 254 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: B 296 ASP cc_start: 0.6876 (m-30) cc_final: 0.6540 (p0) REVERT: C 76 LYS cc_start: 0.7309 (mmtm) cc_final: 0.6662 (mmpt) REVERT: D 76 LYS cc_start: 0.6060 (mmtm) cc_final: 0.5359 (tptt) REVERT: D 77 MET cc_start: 0.5356 (tpt) cc_final: 0.4605 (mtm) REVERT: D 82 ARG cc_start: 0.4400 (tmt-80) cc_final: 0.1573 (mtp85) REVERT: E 43 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.5912 (ptt180) REVERT: E 57 TRP cc_start: 0.6713 (t60) cc_final: 0.6320 (t60) REVERT: G 44 MET cc_start: 0.3727 (pp-130) cc_final: 0.2761 (pmm) outliers start: 60 outliers final: 37 residues processed: 217 average time/residue: 0.9329 time to fit residues: 215.4603 Evaluate side-chains 217 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 38 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.200658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.156734 restraints weight = 7783.957| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 2.66 r_work: 0.4095 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 7042 Z= 0.154 Angle : 0.748 13.853 9509 Z= 0.372 Chirality : 0.045 0.194 1062 Planarity : 0.004 0.051 1199 Dihedral : 7.741 58.570 991 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 7.61 % Allowed : 37.50 % Favored : 54.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.30), residues: 852 helix: 1.90 (0.33), residues: 263 sheet: -0.80 (0.26), residues: 400 loop : -0.47 (0.49), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 259 HIS 0.008 0.001 HIS B 112 PHE 0.015 0.001 PHE G 27 TYR 0.013 0.001 TYR J 34 ARG 0.005 0.001 ARG G 38 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 452) hydrogen bonds : angle 5.38592 ( 1299) covalent geometry : bond 0.00356 ( 7042) covalent geometry : angle 0.74752 ( 9509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 179 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7394 (tp) REVERT: A 265 LEU cc_start: 0.8291 (mm) cc_final: 0.7878 (mm) REVERT: B 112 HIS cc_start: 0.6101 (p-80) cc_final: 0.5642 (p-80) REVERT: B 249 SER cc_start: 0.6989 (m) cc_final: 0.6603 (p) REVERT: B 250 LEU cc_start: 0.6942 (mp) cc_final: 0.6414 (tp) REVERT: B 254 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6138 (m-80) REVERT: C 76 LYS cc_start: 0.7378 (mmtm) cc_final: 0.6767 (mmpt) REVERT: D 76 LYS cc_start: 0.5980 (mmtm) cc_final: 0.5328 (tptt) REVERT: D 77 MET cc_start: 0.5306 (tpt) cc_final: 0.4563 (mtm) REVERT: D 82 ARG cc_start: 0.4412 (tmt-80) cc_final: 0.1560 (mtp85) REVERT: E 43 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.5956 (ptt180) REVERT: E 57 TRP cc_start: 0.6730 (t60) cc_final: 0.6327 (t60) REVERT: G 44 MET cc_start: 0.3618 (pp-130) cc_final: 0.2700 (pmm) outliers start: 56 outliers final: 35 residues processed: 216 average time/residue: 1.0765 time to fit residues: 246.4045 Evaluate side-chains 210 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 172 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain H residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 321 ASN E 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.199385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.156094 restraints weight = 7741.119| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 3.05 r_work: 0.4076 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7042 Z= 0.166 Angle : 0.778 13.993 9509 Z= 0.390 Chirality : 0.047 0.239 1062 Planarity : 0.005 0.051 1199 Dihedral : 7.769 58.883 991 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 7.88 % Allowed : 38.32 % Favored : 53.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.30), residues: 852 helix: 1.74 (0.33), residues: 264 sheet: -0.71 (0.26), residues: 396 loop : -0.55 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 259 HIS 0.006 0.001 HIS A 347 PHE 0.027 0.002 PHE G 27 TYR 0.015 0.002 TYR H 33 ARG 0.014 0.001 ARG I 21 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 452) hydrogen bonds : angle 5.40373 ( 1299) covalent geometry : bond 0.00384 ( 7042) covalent geometry : angle 0.77765 ( 9509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7392 (tp) REVERT: A 265 LEU cc_start: 0.8289 (mm) cc_final: 0.7916 (mm) REVERT: B 249 SER cc_start: 0.7028 (m) cc_final: 0.6684 (p) REVERT: B 250 LEU cc_start: 0.6942 (mp) cc_final: 0.6423 (tp) REVERT: B 254 TYR cc_start: 0.7217 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: C 76 LYS cc_start: 0.7417 (mmtm) cc_final: 0.7024 (mmpt) REVERT: D 76 LYS cc_start: 0.6072 (mmtm) cc_final: 0.5395 (tptt) REVERT: D 77 MET cc_start: 0.5376 (tpt) cc_final: 0.4656 (mtm) REVERT: D 82 ARG cc_start: 0.4351 (tmt-80) cc_final: 0.1435 (mtp85) REVERT: E 43 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.5915 (ptt180) REVERT: E 57 TRP cc_start: 0.6755 (t60) cc_final: 0.6348 (t60) REVERT: E 60 ARG cc_start: 0.6023 (mtt90) cc_final: 0.5528 (mtt90) REVERT: G 44 MET cc_start: 0.3669 (pp-130) cc_final: 0.2659 (pmm) REVERT: H 11 ARG cc_start: 0.8807 (ppt170) cc_final: 0.8562 (ppt170) REVERT: I 18 ARG cc_start: 0.8107 (pmm-80) cc_final: 0.7882 (pmm150) outliers start: 58 outliers final: 39 residues processed: 214 average time/residue: 0.9775 time to fit residues: 222.2341 Evaluate side-chains 209 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 321 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 10 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 = 0.4715 r_free = 0.4715 target = 0.202486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.159848 restraints weight = 7612.354| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 2.81 r_work: 0.4100 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 7042 Z= 0.159 Angle : 0.798 12.564 9509 Z= 0.401 Chirality : 0.047 0.226 1062 Planarity : 0.005 0.061 1199 Dihedral : 7.681 59.624 991 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.79 % Allowed : 39.54 % Favored : 53.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.30), residues: 852 helix: 1.54 (0.33), residues: 264 sheet: -0.62 (0.26), residues: 396 loop : -0.47 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 259 HIS 0.005 0.001 HIS A 347 PHE 0.024 0.001 PHE D 101 TYR 0.009 0.001 TYR I 34 ARG 0.012 0.001 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.03466 ( 452) hydrogen bonds : angle 5.33513 ( 1299) covalent geometry : bond 0.00375 ( 7042) covalent geometry : angle 0.79828 ( 9509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7311 (ttm) REVERT: A 124 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7360 (tp) REVERT: A 265 LEU cc_start: 0.8271 (mm) cc_final: 0.7881 (mm) REVERT: B 249 SER cc_start: 0.7040 (m) cc_final: 0.6652 (t) REVERT: B 250 LEU cc_start: 0.6906 (mp) cc_final: 0.6327 (tp) REVERT: B 254 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: C 72 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6856 (t80) REVERT: C 76 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7173 (mmpt) REVERT: D 76 LYS cc_start: 0.6115 (mmtm) cc_final: 0.5426 (tptt) REVERT: D 77 MET cc_start: 0.5374 (tpt) cc_final: 0.4668 (mtm) REVERT: D 82 ARG cc_start: 0.4330 (tmt-80) cc_final: 0.1483 (mtp85) REVERT: E 43 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.5912 (ptt-90) REVERT: E 57 TRP cc_start: 0.6725 (t60) cc_final: 0.6349 (t60) REVERT: G 44 MET cc_start: 0.3398 (pp-130) cc_final: 0.2565 (pmm) outliers start: 50 outliers final: 33 residues processed: 206 average time/residue: 1.4115 time to fit residues: 311.0625 Evaluate side-chains 201 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 321 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** H 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.203525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.161855 restraints weight = 7851.395| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 2.75 r_work: 0.4107 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 7042 Z= 0.163 Angle : 0.837 13.793 9509 Z= 0.421 Chirality : 0.048 0.304 1062 Planarity : 0.005 0.063 1199 Dihedral : 7.703 59.625 991 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 6.66 % Allowed : 40.08 % Favored : 53.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.30), residues: 852 helix: 1.29 (0.32), residues: 264 sheet: -0.57 (0.26), residues: 396 loop : -0.42 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 259 HIS 0.007 0.001 HIS B 112 PHE 0.030 0.001 PHE D 101 TYR 0.015 0.001 TYR H 33 ARG 0.009 0.001 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.03564 ( 452) hydrogen bonds : angle 5.39080 ( 1299) covalent geometry : bond 0.00389 ( 7042) covalent geometry : angle 0.83653 ( 9509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7316 (ttm) REVERT: A 124 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7327 (tp) REVERT: A 265 LEU cc_start: 0.8286 (mm) cc_final: 0.7906 (mm) REVERT: A 329 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5163 (mm-30) REVERT: B 249 SER cc_start: 0.7146 (m) cc_final: 0.6876 (p) REVERT: B 250 LEU cc_start: 0.6847 (mp) cc_final: 0.6421 (tp) REVERT: B 254 TYR cc_start: 0.7167 (OUTLIER) cc_final: 0.6096 (m-80) REVERT: C 72 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6888 (t80) REVERT: C 76 LYS cc_start: 0.7598 (mmtm) cc_final: 0.7170 (mmpt) REVERT: D 76 LYS cc_start: 0.6151 (mmtm) cc_final: 0.5461 (tptt) REVERT: D 77 MET cc_start: 0.5412 (tpt) cc_final: 0.4680 (mtm) REVERT: D 82 ARG cc_start: 0.4279 (tmt-80) cc_final: 0.1486 (mtp85) REVERT: E 43 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.5905 (ptt-90) REVERT: E 57 TRP cc_start: 0.6738 (t60) cc_final: 0.6356 (t60) REVERT: G 44 MET cc_start: 0.3399 (pp-130) cc_final: 0.2482 (pmm) REVERT: J 28 ILE cc_start: 0.9055 (tp) cc_final: 0.8780 (tp) outliers start: 49 outliers final: 32 residues processed: 199 average time/residue: 1.1124 time to fit residues: 235.0512 Evaluate side-chains 204 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.0570 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 321 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.202962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.160234 restraints weight = 7797.299| |-----------------------------------------------------------------------------| r_work (start): 0.4280 rms_B_bonded: 2.79 r_work: 0.4111 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.4111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7042 Z= 0.164 Angle : 0.882 14.938 9509 Z= 0.446 Chirality : 0.049 0.264 1062 Planarity : 0.005 0.057 1199 Dihedral : 7.692 59.425 991 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.57 % Allowed : 41.71 % Favored : 52.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.30), residues: 852 helix: 1.20 (0.32), residues: 264 sheet: -0.54 (0.26), residues: 396 loop : -0.39 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 259 HIS 0.004 0.001 HIS A 347 PHE 0.047 0.002 PHE D 101 TYR 0.010 0.001 TYR I 34 ARG 0.018 0.001 ARG I 21 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 452) hydrogen bonds : angle 5.44039 ( 1299) covalent geometry : bond 0.00386 ( 7042) covalent geometry : angle 0.88240 ( 9509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7313 (ttm) REVERT: A 124 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7292 (tp) REVERT: A 265 LEU cc_start: 0.8255 (mm) cc_final: 0.7890 (mm) REVERT: A 270 MET cc_start: 0.7093 (ttm) cc_final: 0.6891 (ttt) REVERT: A 329 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.5194 (mm-30) REVERT: B 234 GLU cc_start: 0.5694 (pt0) cc_final: 0.5370 (pt0) REVERT: B 249 SER cc_start: 0.7091 (m) cc_final: 0.6789 (p) REVERT: B 250 LEU cc_start: 0.6776 (mp) cc_final: 0.6368 (tp) REVERT: B 254 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6072 (m-80) REVERT: C 72 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6780 (t80) REVERT: C 76 LYS cc_start: 0.7608 (mmtm) cc_final: 0.7187 (mmpt) REVERT: D 76 LYS cc_start: 0.6134 (mmtm) cc_final: 0.5441 (tptt) REVERT: D 77 MET cc_start: 0.5416 (tpt) cc_final: 0.4655 (mtm) REVERT: D 82 ARG cc_start: 0.4276 (tmt-80) cc_final: 0.1468 (mmt180) REVERT: E 43 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.5872 (ptt-90) REVERT: E 57 TRP cc_start: 0.6726 (t60) cc_final: 0.6348 (t60) REVERT: G 44 MET cc_start: 0.3427 (pp-130) cc_final: 0.2505 (pmm) REVERT: I 20 MET cc_start: 0.8272 (pmm) cc_final: 0.7995 (pmm) REVERT: J 28 ILE cc_start: 0.9055 (tp) cc_final: 0.8779 (tp) outliers start: 41 outliers final: 32 residues processed: 192 average time/residue: 1.0329 time to fit residues: 211.7202 Evaluate side-chains 203 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 98 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 191 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 329 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 90 CYS Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 254 TYR Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 72 PHE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 43 ARG Chi-restraints excluded: chain E residue 62 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 238 HIS A 321 ASN ** B 167 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 = 0.4720 r_free = 0.4720 target = 0.202987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.160995 restraints weight = 7746.571| |-----------------------------------------------------------------------------| r_work (start): 0.4273 rms_B_bonded: 2.74 r_work: 0.4113 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7042 Z= 0.171 Angle : 0.886 16.006 9509 Z= 0.452 Chirality : 0.049 0.233 1062 Planarity : 0.005 0.053 1199 Dihedral : 7.750 57.880 991 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.98 % Allowed : 41.17 % Favored : 52.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.30), residues: 852 helix: 1.13 (0.32), residues: 264 sheet: -0.54 (0.26), residues: 396 loop : -0.40 (0.49), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 259 HIS 0.006 0.001 HIS B 112 PHE 0.055 0.002 PHE D 101 TYR 0.017 0.002 TYR H 33 ARG 0.007 0.001 ARG H 11 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 452) hydrogen bonds : angle 5.51058 ( 1299) covalent geometry : bond 0.00403 ( 7042) covalent geometry : angle 0.88553 ( 9509) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7457.65 seconds wall clock time: 135 minutes 5.70 seconds (8105.70 seconds total)