Starting phenix.real_space_refine on Wed Aug 5 03:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9if5_52841/08_2026/9if5_52841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9if5_52841/08_2026/9if5_52841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9if5_52841/08_2026/9if5_52841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9if5_52841/08_2026/9if5_52841.map" model { file = "/net/cci-nas-00/data/ceres_data/9if5_52841/08_2026/9if5_52841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9if5_52841/08_2026/9if5_52841.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 106 5.49 5 S 24 5.16 5 C 4790 2.51 5 N 1491 2.21 5 O 1738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8151 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1085 Classifications: {'DNA': 53} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 52} Chain: "F" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1090 Classifications: {'DNA': 53} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 52} Chain: "A" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2987 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 26, 'TRANS': 354} Chain breaks: 1 Chain: "B" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2987 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 26, 'TRANS': 354} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3953 SG CYS A 366 79.402 36.391 40.342 1.00 90.00 S ATOM 3968 SG CYS A 368 76.980 35.552 42.970 1.00 97.35 S ATOM 4113 SG CYS A 387 80.721 34.283 43.379 1.00 93.39 S ATOM 6940 SG CYS B 366 38.431 52.450 114.143 1.00150.68 S ATOM 6955 SG CYS B 368 39.624 50.251 111.398 1.00142.28 S ATOM 7100 SG CYS B 387 36.011 51.920 111.252 1.00148.63 S Time building chain proxies: 2.17, per 1000 atoms: 0.27 Number of scatterers: 8151 At special positions: 0 Unit cell: (120.613, 93.68, 149.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 24 16.00 P 106 15.00 O 1738 8.00 N 1491 7.00 C 4790 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: 0.78 Conformation dependent library (CDL) restraints added in 385.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" NE2 HIS A 401 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 366 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 368 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 387 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" NE2 HIS B 401 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 366 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 368 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 387 " Number of angles added : 6 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 40.4% alpha, 14.0% beta 51 base pairs and 85 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 140 through 163 Processing helix chain 'A' and resid 211 through 227 removed outlier: 3.529A pdb=" N VAL A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 331 through 346 Processing helix chain 'A' and resid 379 through 382 Processing helix chain 'A' and resid 409 through 426 removed outlier: 3.524A pdb=" N ILE A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 546 through 557 removed outlier: 3.749A pdb=" N PHE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 578 Processing helix chain 'B' and resid 141 through 163 removed outlier: 3.641A pdb=" N LEU B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 227 removed outlier: 3.588A pdb=" N VAL B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 284 through 288 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 409 through 426 Processing helix chain 'B' and resid 430 through 448 Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 540 through 545 Processing helix chain 'B' and resid 546 through 557 removed outlier: 4.045A pdb=" N PHE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 578 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 297 removed outlier: 5.463A pdb=" N LYS A 296 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 307 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 372 removed outlier: 4.290A pdb=" N VAL A 371 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 384 through 385 Processing sheet with id=AA6, first strand: chain 'B' and resid 175 through 186 Processing sheet with id=AA7, first strand: chain 'B' and resid 291 through 297 removed outlier: 5.519A pdb=" N LYS B 296 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE B 307 " --> pdb=" O LYS B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 364 through 366 Processing sheet with id=AA9, first strand: chain 'B' and resid 372 through 374 removed outlier: 3.623A pdb=" N VAL B 407 " --> pdb=" O TYR B 385 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 142 hydrogen bonds 284 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 85 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2061 1.33 - 1.45: 2193 1.45 - 1.58: 4054 1.58 - 1.70: 210 1.70 - 1.82: 36 Bond restraints: 8554 Sorted by residual: bond pdb=" C3' DG E 12 " pdb=" C2' DG E 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DA F 5 " pdb=" C2' DA F 5 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.91e+00 bond pdb=" C3' DC E 2 " pdb=" C2' DC E 2 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.51e+00 bond pdb=" C1' DC E 51 " pdb=" N1 DC E 51 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.37e+00 bond pdb=" C3' DA F 41 " pdb=" C2' DA F 41 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.14e+00 ... (remaining 8549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 11983 3.17 - 6.34: 41 6.34 - 9.50: 3 9.50 - 12.67: 3 12.67 - 15.84: 1 Bond angle restraints: 12031 Sorted by residual: angle pdb=" O4' DA F 31 " pdb=" C1' DA F 31 " pdb=" N9 DA F 31 " ideal model delta sigma weight residual 108.00 111.42 -3.42 7.00e-01 2.04e+00 2.38e+01 angle pdb=" O4' DG E 43 " pdb=" C4' DG E 43 " pdb=" C3' DG E 43 " ideal model delta sigma weight residual 106.00 103.23 2.77 6.00e-01 2.78e+00 2.13e+01 angle pdb=" CA LEU A 319 " pdb=" CB LEU A 319 " pdb=" CG LEU A 319 " ideal model delta sigma weight residual 116.30 132.14 -15.84 3.50e+00 8.16e-02 2.05e+01 angle pdb=" N3 DT E 23 " pdb=" C4 DT E 23 " pdb=" O4 DT E 23 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT E 13 " pdb=" C4 DT E 13 " pdb=" O4 DT E 13 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.94e+01 ... (remaining 12026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 4273 35.93 - 71.86: 529 71.86 - 107.79: 8 107.79 - 143.72: 0 143.72 - 179.65: 2 Dihedral angle restraints: 4812 sinusoidal: 2648 harmonic: 2164 Sorted by residual: dihedral pdb=" C4' DC E 2 " pdb=" C3' DC E 2 " pdb=" O3' DC E 2 " pdb=" P DG E 3 " ideal model delta sinusoidal sigma weight residual 220.00 40.35 179.65 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC E 36 " pdb=" C3' DC E 36 " pdb=" O3' DC E 36 " pdb=" P DC E 37 " ideal model delta sinusoidal sigma weight residual -140.00 34.82 -174.82 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA THR B 318 " pdb=" C THR B 318 " pdb=" N LEU B 319 " pdb=" CA LEU B 319 " ideal model delta harmonic sigma weight residual 180.00 162.46 17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 4809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 861 0.036 - 0.073: 297 0.073 - 0.109: 112 0.109 - 0.145: 36 0.145 - 0.181: 6 Chirality restraints: 1312 Sorted by residual: chirality pdb=" C3' DT E 13 " pdb=" C4' DT E 13 " pdb=" O3' DT E 13 " pdb=" C2' DT E 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA LEU A 319 " pdb=" N LEU A 319 " pdb=" C LEU A 319 " pdb=" CB LEU A 319 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" C3' DC E 36 " pdb=" C4' DC E 36 " pdb=" O3' DC E 36 " pdb=" C2' DC E 36 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.86e-01 ... (remaining 1309 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 320 " -0.213 9.50e-02 1.11e+02 9.58e-02 5.72e+00 pdb=" NE ARG B 320 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B 320 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 320 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 320 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 212 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 213 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT E 23 " 0.025 2.00e-02 2.50e+03 1.17e-02 3.43e+00 pdb=" N1 DT E 23 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DT E 23 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT E 23 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT E 23 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT E 23 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT E 23 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT E 23 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT E 23 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT E 23 " -0.006 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 3897 2.98 - 3.46: 8431 3.46 - 3.94: 15685 3.94 - 4.42: 17495 4.42 - 4.90: 24696 Nonbonded interactions: 70204 Sorted by model distance: nonbonded pdb=" O5' DC E 50 " pdb=" O4' DC E 50 " model vdw 2.505 2.432 nonbonded pdb=" O MET A 361 " pdb=" OD1 ASP A 362 " model vdw 2.512 3.040 nonbonded pdb=" O5' DG E 40 " pdb=" O4' DG E 40 " model vdw 2.522 2.432 nonbonded pdb=" O TRP A 526 " pdb=" CA PHE A 527 " model vdw 2.532 2.776 nonbonded pdb=" O5' DA E 47 " pdb=" O4' DA E 47 " model vdw 2.545 2.432 ... (remaining 70199 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.720 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 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 0.054 8562 Z= 0.444 Angle : 0.748 15.841 12037 Z= 0.559 Chirality : 0.046 0.181 1312 Planarity : 0.005 0.096 1172 Dihedral : 23.486 179.648 3420 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.32 % Allowed : 15.03 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.30), residues: 754 helix: 1.17 (0.30), residues: 293 sheet: -0.34 (0.54), residues: 77 loop : 0.26 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 425 TYR 0.009 0.001 TYR B 385 PHE 0.009 0.001 PHE A 553 TRP 0.014 0.001 TRP B 219 HIS 0.002 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.44 ( 8554) covalent geometry : angle 0.73981 / 0.56 (12031) hydrogen bonds : bond 0.14287 / 15.59 ( 393) hydrogen bonds : angle 5.25636 / 7.28 ( 1007) metal coordination : bond 0.01499 / 1.09 ( 8) metal coordination : angle 5.13012 / 9.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 106 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6455 (mttt) cc_final: 0.5772 (mmmt) REVERT: A 159 LEU cc_start: 0.7023 (tp) cc_final: 0.6780 (tp) REVERT: A 197 LYS cc_start: 0.8204 (mmtp) cc_final: 0.7689 (mmtt) REVERT: A 224 LYS cc_start: 0.7761 (tttt) cc_final: 0.7521 (ttpt) REVERT: A 267 THR cc_start: 0.7412 (p) cc_final: 0.7109 (p) REVERT: A 292 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7799 (tt0) REVERT: A 296 LYS cc_start: 0.7400 (tttt) cc_final: 0.7104 (ttmt) REVERT: A 347 ARG cc_start: 0.6837 (mtt180) cc_final: 0.6616 (ttm170) REVERT: A 351 LEU cc_start: 0.7036 (tp) cc_final: 0.6245 (mt) REVERT: A 362 ASP cc_start: 0.7569 (p0) cc_final: 0.6877 (m-30) REVERT: A 367 GLU cc_start: 0.7518 (pt0) cc_final: 0.7269 (pt0) REVERT: A 390 ARG cc_start: 0.6636 (ppt170) cc_final: 0.6068 (tpm170) REVERT: A 414 LYS cc_start: 0.7440 (tttt) cc_final: 0.6971 (ttpp) REVERT: A 544 ARG cc_start: 0.6412 (mtt180) cc_final: 0.6135 (mtm110) REVERT: A 559 ASP cc_start: 0.8200 (m-30) cc_final: 0.7781 (m-30) REVERT: A 578 LYS cc_start: 0.7622 (mttt) cc_final: 0.7361 (mtmt) REVERT: A 583 THR cc_start: 0.8138 (m) cc_final: 0.7906 (p) REVERT: B 176 GLU cc_start: 0.6520 (pt0) cc_final: 0.6275 (tp30) REVERT: B 190 MET cc_start: 0.4454 (ppp) cc_final: 0.3857 (ttp) REVERT: B 296 LYS cc_start: 0.7197 (ttmt) cc_final: 0.6590 (mtpp) REVERT: B 297 LYS cc_start: 0.6983 (mmtp) cc_final: 0.6695 (ttmm) REVERT: B 306 LYS cc_start: 0.7053 (tttm) cc_final: 0.5757 (mmtt) REVERT: B 313 GLN cc_start: 0.7045 (mt0) cc_final: 0.6733 (mt0) REVERT: B 323 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6393 (mm-30) REVERT: B 349 LYS cc_start: 0.5835 (mttt) cc_final: 0.5632 (ptpt) REVERT: B 395 PRO cc_start: 0.5518 (Cg_endo) cc_final: 0.5262 (Cg_exo) REVERT: B 579 ARG cc_start: 0.5915 (mtp180) cc_final: 0.5516 (mtp180) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.1377 time to fit residues: 18.6791 Evaluate side-chains 79 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 407 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.204272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170721 restraints weight = 9714.959| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.66 r_work: 0.3567 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8562 Z= 0.165 Angle : 0.633 12.267 12037 Z= 0.351 Chirality : 0.045 0.295 1312 Planarity : 0.005 0.034 1172 Dihedral : 27.409 175.916 1929 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.74 % Allowed : 14.08 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.30), residues: 754 helix: 1.41 (0.29), residues: 300 sheet: -0.63 (0.50), residues: 77 loop : 0.27 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 425 TYR 0.006 0.001 TYR A 295 PHE 0.008 0.002 PHE A 553 TRP 0.009 0.001 TRP B 219 HIS 0.003 0.001 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 ( 8554) covalent geometry : angle 0.62723 / 0.35 (12031) hydrogen bonds : bond 0.04450 / 4.98 ( 393) hydrogen bonds : angle 4.13524 / 5.88 ( 1007) metal coordination : bond 0.01142 / 0.82 ( 8) metal coordination : angle 3.70540 / 7.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.263 Fit side-chains REVERT: A 149 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7191 (ttpp) REVERT: A 152 LYS cc_start: 0.7747 (mttt) cc_final: 0.7192 (mmmt) REVERT: A 351 LEU cc_start: 0.8118 (tp) cc_final: 0.7673 (mt) REVERT: A 362 ASP cc_start: 0.7295 (p0) cc_final: 0.7063 (m-30) REVERT: A 414 LYS cc_start: 0.8353 (tttt) cc_final: 0.8147 (ttpp) REVERT: B 190 MET cc_start: 0.4748 (ppp) cc_final: 0.4372 (ttp) REVERT: B 306 LYS cc_start: 0.7959 (tttm) cc_final: 0.7609 (mmtt) REVERT: B 351 LEU cc_start: 0.6934 (tp) cc_final: 0.6733 (tp) REVERT: B 395 PRO cc_start: 0.5809 (Cg_endo) cc_final: 0.5517 (Cg_exo) outliers start: 11 outliers final: 3 residues processed: 94 average time/residue: 0.1281 time to fit residues: 15.0910 Evaluate side-chains 76 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 407 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 26 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN B 313 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.203554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.171246 restraints weight = 9612.676| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.61 r_work: 0.3547 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8562 Z= 0.154 Angle : 0.598 9.678 12037 Z= 0.335 Chirality : 0.044 0.292 1312 Planarity : 0.004 0.031 1172 Dihedral : 27.495 178.799 1929 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.90 % Allowed : 14.08 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.30), residues: 754 helix: 1.48 (0.29), residues: 300 sheet: -0.62 (0.49), residues: 77 loop : 0.25 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 425 TYR 0.006 0.001 TYR B 365 PHE 0.022 0.002 PHE A 557 TRP 0.014 0.001 TRP B 541 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 8554) covalent geometry : angle 0.59285 / 0.33 (12031) hydrogen bonds : bond 0.03974 / 4.42 ( 393) hydrogen bonds : angle 3.78734 / 5.35 ( 1007) metal coordination : bond 0.01192 / 0.82 ( 8) metal coordination : angle 3.54347 / 6.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 149 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7203 (ttpp) REVERT: A 152 LYS cc_start: 0.7698 (mttt) cc_final: 0.7085 (mmmt) REVERT: A 320 ARG cc_start: 0.7363 (mmm-85) cc_final: 0.7083 (mmm160) REVERT: A 351 LEU cc_start: 0.8150 (tp) cc_final: 0.7716 (mt) REVERT: A 362 ASP cc_start: 0.7319 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: B 190 MET cc_start: 0.4590 (ppp) cc_final: 0.4203 (ttp) REVERT: B 351 LEU cc_start: 0.6652 (tp) cc_final: 0.6397 (tp) REVERT: B 409 MET cc_start: 0.7282 (mtp) cc_final: 0.6894 (mtp) outliers start: 12 outliers final: 6 residues processed: 82 average time/residue: 0.1094 time to fit residues: 11.6965 Evaluate side-chains 77 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 52 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 313 GLN ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.203240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.169245 restraints weight = 9780.892| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.64 r_work: 0.3529 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8562 Z= 0.154 Angle : 0.590 9.482 12037 Z= 0.329 Chirality : 0.044 0.305 1312 Planarity : 0.004 0.031 1172 Dihedral : 27.593 179.019 1928 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.22 % Allowed : 14.56 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.30), residues: 754 helix: 1.52 (0.30), residues: 301 sheet: -0.60 (0.48), residues: 77 loop : 0.25 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.007 0.001 TYR B 385 PHE 0.013 0.001 PHE A 557 TRP 0.010 0.001 TRP A 220 HIS 0.002 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 ( 8554) covalent geometry : angle 0.58150 / 0.33 (12031) hydrogen bonds : bond 0.03791 / 4.20 ( 393) hydrogen bonds : angle 3.61988 / 5.08 ( 1007) metal coordination : bond 0.01456 / 1.05 ( 8) metal coordination : angle 4.51714 / 7.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 149 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7189 (ttpp) REVERT: A 152 LYS cc_start: 0.7650 (mttt) cc_final: 0.7045 (mmmt) REVERT: A 320 ARG cc_start: 0.7473 (mmm-85) cc_final: 0.7143 (mmm160) REVERT: A 351 LEU cc_start: 0.8173 (tp) cc_final: 0.7722 (mt) REVERT: A 362 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7017 (m-30) REVERT: B 190 MET cc_start: 0.4454 (ppp) cc_final: 0.3989 (ttp) REVERT: B 351 LEU cc_start: 0.6786 (tp) cc_final: 0.6518 (tp) REVERT: B 539 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.4997 (pptt) outliers start: 14 outliers final: 7 residues processed: 83 average time/residue: 0.1155 time to fit residues: 12.4634 Evaluate side-chains 78 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 406 ASN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 539 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 0.0870 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 26 optimal weight: 0.2980 chunk 75 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN B 313 GLN ** B 401 HIS ** 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 = 0.4275 r_free = 0.4275 target = 0.202845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170247 restraints weight = 9782.607| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.71 r_work: 0.3532 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 8562 Z= 0.151 Angle : 0.579 9.049 12037 Z= 0.322 Chirality : 0.044 0.303 1312 Planarity : 0.004 0.032 1172 Dihedral : 27.605 179.279 1928 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.37 % Allowed : 14.24 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.30), residues: 754 helix: 1.50 (0.30), residues: 299 sheet: -0.61 (0.49), residues: 77 loop : 0.25 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.006 0.001 TYR A 385 PHE 0.016 0.001 PHE A 557 TRP 0.016 0.001 TRP A 526 HIS 0.002 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 8554) covalent geometry : angle 0.57102 / 0.32 (12031) hydrogen bonds : bond 0.03653 / 4.07 ( 393) hydrogen bonds : angle 3.53421 / 4.91 ( 1007) metal coordination : bond 0.01167 / 0.75 ( 8) metal coordination : angle 4.19616 / 7.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.161 Fit side-chains REVERT: A 149 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7138 (ttpp) REVERT: A 152 LYS cc_start: 0.7726 (mttt) cc_final: 0.7161 (mmmt) REVERT: A 320 ARG cc_start: 0.7452 (mmm-85) cc_final: 0.7132 (mmm160) REVERT: A 351 LEU cc_start: 0.8173 (tp) cc_final: 0.7716 (mt) REVERT: A 362 ASP cc_start: 0.7295 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: B 190 MET cc_start: 0.4333 (ppp) cc_final: 0.4083 (ttm) REVERT: B 351 LEU cc_start: 0.6810 (tp) cc_final: 0.6542 (tp) REVERT: B 409 MET cc_start: 0.7295 (mtp) cc_final: 0.6784 (mtp) REVERT: B 539 LYS cc_start: 0.5743 (OUTLIER) cc_final: 0.5095 (pptt) outliers start: 15 outliers final: 9 residues processed: 79 average time/residue: 0.1117 time to fit residues: 11.5882 Evaluate side-chains 78 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 539 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 76 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 406 ASN ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.202685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.169889 restraints weight = 9607.004| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 1.61 r_work: 0.3546 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8562 Z= 0.154 Angle : 0.585 8.768 12037 Z= 0.325 Chirality : 0.044 0.305 1312 Planarity : 0.005 0.100 1172 Dihedral : 27.611 178.460 1928 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.85 % Allowed : 14.72 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.30), residues: 754 helix: 1.61 (0.30), residues: 295 sheet: -0.48 (0.50), residues: 84 loop : 0.30 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 285 TYR 0.007 0.001 TYR B 385 PHE 0.019 0.002 PHE A 557 TRP 0.014 0.001 TRP A 526 HIS 0.002 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 8554) covalent geometry : angle 0.57775 / 0.32 (12031) hydrogen bonds : bond 0.03648 / 4.04 ( 393) hydrogen bonds : angle 3.50768 / 4.87 ( 1007) metal coordination : bond 0.01094 / 0.74 ( 8) metal coordination : angle 4.04781 / 6.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.242 Fit side-chains REVERT: A 149 LYS cc_start: 0.7352 (OUTLIER) cc_final: 0.7137 (ttpp) REVERT: A 152 LYS cc_start: 0.7707 (mttt) cc_final: 0.7153 (mmmt) REVERT: A 320 ARG cc_start: 0.7409 (mmm-85) cc_final: 0.7088 (mmm160) REVERT: A 351 LEU cc_start: 0.8137 (tp) cc_final: 0.7709 (mt) REVERT: A 362 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: B 190 MET cc_start: 0.4340 (ppp) cc_final: 0.4092 (ttm) REVERT: B 351 LEU cc_start: 0.6809 (tp) cc_final: 0.6566 (tp) REVERT: B 539 LYS cc_start: 0.5824 (OUTLIER) cc_final: 0.5105 (pptt) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.1046 time to fit residues: 10.7993 Evaluate side-chains 80 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 405 CYS Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 539 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 78 optimal weight: 7.9990 chunk 84 optimal weight: 0.0570 chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 82 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 GLN ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.203713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.171316 restraints weight = 9736.928| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.62 r_work: 0.3567 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8562 Z= 0.136 Angle : 0.565 8.421 12037 Z= 0.315 Chirality : 0.043 0.305 1312 Planarity : 0.004 0.032 1172 Dihedral : 27.562 176.545 1928 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.69 % Allowed : 15.35 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.30), residues: 754 helix: 1.71 (0.30), residues: 295 sheet: -0.46 (0.50), residues: 84 loop : 0.25 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 419 TYR 0.007 0.001 TYR A 385 PHE 0.012 0.001 PHE A 553 TRP 0.014 0.001 TRP A 526 HIS 0.002 0.000 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 ( 8554) covalent geometry : angle 0.55799 / 0.31 (12031) hydrogen bonds : bond 0.03476 / 3.86 ( 393) hydrogen bonds : angle 3.44518 / 4.77 ( 1007) metal coordination : bond 0.00982 / 0.64 ( 8) metal coordination : angle 3.90588 / 6.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.241 Fit side-chains REVERT: A 152 LYS cc_start: 0.7686 (mttt) cc_final: 0.7153 (mmmt) REVERT: A 320 ARG cc_start: 0.7143 (mmm-85) cc_final: 0.6808 (mmm160) REVERT: A 351 LEU cc_start: 0.8195 (tp) cc_final: 0.7739 (mt) REVERT: A 362 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6904 (m-30) REVERT: B 409 MET cc_start: 0.7096 (mtp) cc_final: 0.6790 (mtp) REVERT: B 539 LYS cc_start: 0.5755 (OUTLIER) cc_final: 0.5009 (pptt) outliers start: 17 outliers final: 11 residues processed: 79 average time/residue: 0.0983 time to fit residues: 10.2428 Evaluate side-chains 78 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 402 GLU Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 405 CYS Chi-restraints excluded: chain B residue 539 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 28 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.201227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.169044 restraints weight = 9595.064| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.59 r_work: 0.3532 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8562 Z= 0.176 Angle : 0.609 8.417 12037 Z= 0.335 Chirality : 0.044 0.315 1312 Planarity : 0.004 0.032 1172 Dihedral : 27.545 175.323 1928 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.69 % Allowed : 15.51 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.30), residues: 754 helix: 1.61 (0.30), residues: 295 sheet: -0.52 (0.50), residues: 84 loop : 0.20 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 221 TYR 0.007 0.001 TYR B 385 PHE 0.017 0.002 PHE A 553 TRP 0.012 0.001 TRP A 526 HIS 0.003 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 ( 8554) covalent geometry : angle 0.60106 / 0.33 (12031) hydrogen bonds : bond 0.03868 / 4.28 ( 393) hydrogen bonds : angle 3.52609 / 4.83 ( 1007) metal coordination : bond 0.01268 / 0.89 ( 8) metal coordination : angle 4.46260 / 7.35 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.244 Fit side-chains REVERT: A 152 LYS cc_start: 0.7702 (mttt) cc_final: 0.7130 (mmmt) REVERT: A 320 ARG cc_start: 0.7390 (mmm-85) cc_final: 0.7090 (mmm160) REVERT: A 351 LEU cc_start: 0.8154 (tp) cc_final: 0.7730 (mt) REVERT: B 539 LYS cc_start: 0.5828 (OUTLIER) cc_final: 0.5037 (pptt) outliers start: 17 outliers final: 12 residues processed: 81 average time/residue: 0.0932 time to fit residues: 10.0111 Evaluate side-chains 80 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 539 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.201820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.168372 restraints weight = 9645.916| |-----------------------------------------------------------------------------| r_work (start): 0.3916 rms_B_bonded: 1.64 r_work: 0.3518 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8562 Z= 0.160 Angle : 0.600 8.263 12037 Z= 0.330 Chirality : 0.044 0.304 1312 Planarity : 0.004 0.032 1172 Dihedral : 27.467 174.298 1928 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.06 % Allowed : 15.82 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.30), residues: 754 helix: 1.63 (0.30), residues: 295 sheet: -0.58 (0.50), residues: 84 loop : 0.17 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 221 TYR 0.007 0.001 TYR A 385 PHE 0.023 0.002 PHE A 557 TRP 0.020 0.001 TRP B 584 HIS 0.002 0.000 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 ( 8554) covalent geometry : angle 0.59217 / 0.33 (12031) hydrogen bonds : bond 0.03678 / 4.11 ( 393) hydrogen bonds : angle 3.52602 / 4.81 ( 1007) metal coordination : bond 0.01181 / 0.76 ( 8) metal coordination : angle 4.46074 / 7.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.246 Fit side-chains REVERT: A 152 LYS cc_start: 0.7738 (mttt) cc_final: 0.7162 (mmmt) REVERT: A 320 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7096 (mmm160) REVERT: A 351 LEU cc_start: 0.8161 (tp) cc_final: 0.7743 (mt) REVERT: B 345 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.4558 (mtp-110) REVERT: B 539 LYS cc_start: 0.5854 (OUTLIER) cc_final: 0.5022 (pptt) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.0806 time to fit residues: 8.3192 Evaluate side-chains 76 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 345 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 539 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.0020 chunk 71 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.3106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 HIS ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.204003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.171662 restraints weight = 9650.989| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.57 r_work: 0.3572 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8562 Z= 0.132 Angle : 0.579 8.506 12037 Z= 0.322 Chirality : 0.042 0.300 1312 Planarity : 0.004 0.033 1172 Dihedral : 27.360 173.133 1928 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.22 % Allowed : 15.82 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.30), residues: 754 helix: 1.88 (0.31), residues: 293 sheet: -0.62 (0.49), residues: 84 loop : 0.16 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 221 TYR 0.008 0.001 TYR A 385 PHE 0.013 0.001 PHE A 557 TRP 0.009 0.001 TRP A 526 HIS 0.006 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 ( 8554) covalent geometry : angle 0.57232 / 0.32 (12031) hydrogen bonds : bond 0.03467 / 3.88 ( 393) hydrogen bonds : angle 3.49049 / 4.76 ( 1007) metal coordination : bond 0.00968 / 0.61 ( 8) metal coordination : angle 3.93153 / 6.87 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.146 Fit side-chains revert: symmetry clash REVERT: A 152 LYS cc_start: 0.7677 (mttt) cc_final: 0.7117 (mmmt) REVERT: A 320 ARG cc_start: 0.7276 (mmm-85) cc_final: 0.6942 (mmm160) REVERT: A 351 LEU cc_start: 0.8165 (tp) cc_final: 0.7749 (mt) REVERT: B 345 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.4523 (mtp-110) REVERT: B 539 LYS cc_start: 0.5788 (OUTLIER) cc_final: 0.4903 (pptt) outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.1065 time to fit residues: 10.1998 Evaluate side-chains 74 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 345 ARG Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 539 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 51 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 16 optimal weight: 0.1980 chunk 62 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.202897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.171669 restraints weight = 9735.980| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.43 r_work: 0.3584 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8562 Z= 0.146 Angle : 0.580 8.526 12037 Z= 0.321 Chirality : 0.043 0.302 1312 Planarity : 0.004 0.032 1172 Dihedral : 27.264 171.276 1928 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.90 % Allowed : 15.82 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.31), residues: 754 helix: 1.84 (0.30), residues: 295 sheet: -0.58 (0.51), residues: 84 loop : 0.14 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 221 TYR 0.008 0.001 TYR A 385 PHE 0.013 0.001 PHE A 553 TRP 0.010 0.001 TRP A 526 HIS 0.002 0.001 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 ( 8554) covalent geometry : angle 0.57255 / 0.32 (12031) hydrogen bonds : bond 0.03582 / 3.98 ( 393) hydrogen bonds : angle 3.48447 / 4.74 ( 1007) metal coordination : bond 0.01055 / 0.73 ( 8) metal coordination : angle 4.23849 / 7.12 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1830.41 seconds wall clock time: 32 minutes 1.71 seconds (1921.71 seconds total)