Starting phenix.real_space_refine on Thu Jul 2 10:48:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9if5_52841/07_2026/9if5_52841.cif Found real_map, /net/cci-nas-00/data/ceres_data/9if5_52841/07_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_52841/07_2026/9if5_52841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9if5_52841/07_2026/9if5_52841.map" model { file = "/net/cci-nas-00/data/ceres_data/9if5_52841/07_2026/9if5_52841.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9if5_52841/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 1.94, per 1000 atoms: 0.24 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: 0.66 Conformation dependent library (CDL) restraints added in 336.4 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: 0.95 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: 1.08 Time building geometry restraints manager: 0.91 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: 11985 3.17 - 6.34: 39 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: 2.840 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: 0.020 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.810 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- 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 : 0.746 15.841 12037 Z= 0.557 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 0.73710 / 0.56 (12031) hydrogen bonds : bond 0.14287 / 15.57 ( 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 : 0.252 Fit side-chains revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6455 (mttt) cc_final: 0.5796 (mmmt) REVERT: A 159 LEU cc_start: 0.7023 (tp) cc_final: 0.6781 (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: 0.6067 (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: 0.3856 (ttp) REVERT: B 296 LYS cc_start: 0.7197 (ttmt) cc_final: 0.6589 (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: 0.5498 (mtp180) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.1048 time to fit residues: 14.3710 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 : 0.191 ------------------------------------------------------------------------------- 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: 9.9990 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: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.203635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.170673 restraints weight = 9708.355| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.61 r_work: 0.3530 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8562 Z= 0.174 Angle : 0.633 12.155 12037 Z= 0.354 Chirality : 0.045 0.264 1312 Planarity : 0.005 0.033 1172 Dihedral : 27.443 175.682 1929 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.37 % Allowed : 13.61 % 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: 0.81 (0.30), residues: 754 helix: 1.36 (0.29), residues: 300 sheet: -0.63 (0.51), residues: 77 loop : 0.26 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 425 TYR 0.006 0.001 TYR A 295 PHE 0.008 0.002 PHE A 553 TRP 0.010 0.001 TRP B 219 HIS 0.002 0.001 HIS B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 ( 8554) covalent geometry : angle 0.62771 / 0.35 (12031) hydrogen bonds : bond 0.04562 / 5.08 ( 393) hydrogen bonds : angle 4.14242 / 5.89 ( 1007) metal coordination : bond 0.01160 / 0.82 ( 8) metal coordination : angle 3.76821 / 7.38 ( 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 100 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.246 Fit side-chains REVERT: A 149 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7316 (ttpp) REVERT: A 152 LYS cc_start: 0.7773 (mttt) cc_final: 0.7196 (mmmt) REVERT: A 351 LEU cc_start: 0.8134 (tp) cc_final: 0.7690 (mt) REVERT: A 362 ASP cc_start: 0.7435 (p0) cc_final: 0.7152 (m-30) REVERT: B 190 MET cc_start: 0.4749 (ppp) cc_final: 0.4381 (ttp) REVERT: B 395 PRO cc_start: 0.5823 (Cg_endo) cc_final: 0.5520 (Cg_exo) outliers start: 15 outliers final: 5 residues processed: 98 average time/residue: 0.1176 time to fit residues: 14.6495 Evaluate side-chains 76 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 392 VAL 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: 0.0770 chunk 68 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 0.0010 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.0040 overall best weight: 0.2156 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.205843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.173347 restraints weight = 9627.938| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.68 r_work: 0.3573 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8562 Z= 0.138 Angle : 0.579 10.057 12037 Z= 0.328 Chirality : 0.043 0.260 1312 Planarity : 0.004 0.031 1172 Dihedral : 27.455 177.358 1929 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.90 % Allowed : 13.92 % 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: 0.95 (0.30), residues: 754 helix: 1.59 (0.30), residues: 300 sheet: -0.68 (0.48), residues: 87 loop : 0.29 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 425 TYR 0.006 0.001 TYR A 385 PHE 0.020 0.001 PHE A 557 TRP 0.013 0.001 TRP B 541 HIS 0.002 0.000 HIS B 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 ( 8554) covalent geometry : angle 0.57443 / 0.33 (12031) hydrogen bonds : bond 0.03919 / 4.35 ( 393) hydrogen bonds : angle 3.81833 / 5.42 ( 1007) metal coordination : bond 0.01041 / 0.80 ( 8) metal coordination : angle 3.39640 / 6.51 ( 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 89 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.217 Fit side-chains REVERT: A 149 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7071 (ttpp) REVERT: A 152 LYS cc_start: 0.7674 (mttt) cc_final: 0.7016 (mmmt) REVERT: A 320 ARG cc_start: 0.7312 (mmm-85) cc_final: 0.7037 (mmm160) REVERT: A 351 LEU cc_start: 0.8136 (tp) cc_final: 0.7679 (mt) REVERT: A 362 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6936 (m-30) REVERT: A 557 PHE cc_start: 0.7915 (m-80) cc_final: 0.7687 (m-10) REVERT: B 190 MET cc_start: 0.4613 (ppp) cc_final: 0.4224 (ttp) REVERT: B 214 ASP cc_start: 0.6836 (t0) cc_final: 0.6612 (t0) REVERT: B 395 PRO cc_start: 0.5867 (Cg_endo) cc_final: 0.5565 (Cg_exo) REVERT: B 409 MET cc_start: 0.7234 (mtp) cc_final: 0.6851 (mtp) outliers start: 12 outliers final: 5 residues processed: 85 average time/residue: 0.1078 time to fit residues: 11.9183 Evaluate side-chains 78 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 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: 0.0370 chunk 11 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 GLN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4243 r_free = 0.4243 target = 0.199285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.161871 restraints weight = 9742.014| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.96 r_work: 0.3440 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 8562 Z= 0.217 Angle : 0.660 9.423 12037 Z= 0.364 Chirality : 0.046 0.295 1312 Planarity : 0.005 0.043 1172 Dihedral : 27.654 178.518 1928 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.06 % Allowed : 15.03 % Favored : 82.91 % 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: 0.68 (0.30), residues: 754 helix: 1.21 (0.29), residues: 301 sheet: -0.56 (0.52), residues: 77 loop : 0.17 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 285 TYR 0.011 0.002 TYR B 385 PHE 0.013 0.002 PHE A 553 TRP 0.014 0.002 TRP A 526 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 ( 8554) covalent geometry : angle 0.65153 / 0.36 (12031) hydrogen bonds : bond 0.04542 / 5.00 ( 393) hydrogen bonds : angle 3.72083 / 5.25 ( 1007) metal coordination : bond 0.01698 / 1.13 ( 8) metal coordination : angle 4.78770 / 7.68 ( 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 80 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.190 Fit side-chains REVERT: A 149 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7295 (ttpp) REVERT: A 152 LYS cc_start: 0.7748 (mttt) cc_final: 0.7154 (mmmt) REVERT: A 320 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.7215 (mmm160) REVERT: A 351 LEU cc_start: 0.8184 (tp) cc_final: 0.7703 (mt) REVERT: A 362 ASP cc_start: 0.7519 (p0) cc_final: 0.7180 (m-30) REVERT: B 190 MET cc_start: 0.4427 (ppp) cc_final: 0.3950 (ttp) REVERT: B 214 ASP cc_start: 0.7005 (t0) cc_final: 0.6637 (t0) REVERT: B 409 MET cc_start: 0.7370 (mtp) cc_final: 0.6903 (mtp) REVERT: B 539 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5152 (pptt) outliers start: 13 outliers final: 7 residues processed: 78 average time/residue: 0.0975 time to fit residues: 9.9720 Evaluate side-chains 73 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 552 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4271 r_free = 0.4271 target = 0.202368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.169857 restraints weight = 9749.754| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.55 r_work: 0.3534 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8562 Z= 0.155 Angle : 0.587 8.853 12037 Z= 0.329 Chirality : 0.043 0.270 1312 Planarity : 0.004 0.042 1172 Dihedral : 27.659 179.372 1928 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 0.75 (0.30), residues: 754 helix: 1.36 (0.30), residues: 301 sheet: -0.59 (0.51), residues: 77 loop : 0.14 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 221 TYR 0.008 0.001 TYR B 385 PHE 0.013 0.001 PHE A 557 TRP 0.010 0.001 TRP A 220 HIS 0.002 0.000 HIS B 226 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 8554) covalent geometry : angle 0.57949 / 0.33 (12031) hydrogen bonds : bond 0.03772 / 4.16 ( 393) hydrogen bonds : angle 3.59661 / 5.04 ( 1007) metal coordination : bond 0.01266 / 0.75 ( 8) metal coordination : angle 4.31253 / 7.28 ( 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 78 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.226 Fit side-chains REVERT: A 149 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7282 (ttpp) REVERT: A 152 LYS cc_start: 0.7762 (mttt) cc_final: 0.7190 (mmmt) REVERT: A 320 ARG cc_start: 0.7463 (mmm-85) cc_final: 0.7125 (mmm160) REVERT: A 351 LEU cc_start: 0.8131 (tp) cc_final: 0.7718 (mt) REVERT: A 362 ASP cc_start: 0.7277 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: B 190 MET cc_start: 0.4378 (ppp) cc_final: 0.4145 (ttm) REVERT: B 539 LYS cc_start: 0.5743 (OUTLIER) cc_final: 0.5050 (pptt) outliers start: 12 outliers final: 8 residues processed: 74 average time/residue: 0.0910 time to fit residues: 9.0650 Evaluate side-chains 75 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 229 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 387 CYS 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 405 CYS 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: 7.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.199390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.165213 restraints weight = 9492.925| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.65 r_work: 0.3481 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8562 Z= 0.202 Angle : 0.627 8.525 12037 Z= 0.347 Chirality : 0.045 0.291 1312 Planarity : 0.005 0.032 1172 Dihedral : 27.708 179.020 1928 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.69 % Allowed : 15.19 % 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: 0.63 (0.30), residues: 754 helix: 1.20 (0.29), residues: 295 sheet: -0.55 (0.52), residues: 84 loop : 0.14 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 285 TYR 0.009 0.001 TYR B 385 PHE 0.015 0.002 PHE A 553 TRP 0.022 0.002 TRP A 526 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 ( 8554) covalent geometry : angle 0.61685 / 0.35 (12031) hydrogen bonds : bond 0.04228 / 4.66 ( 393) hydrogen bonds : angle 3.64086 / 5.03 ( 1007) metal coordination : bond 0.01417 / 1.00 ( 8) metal coordination : angle 5.15926 / 8.20 ( 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 85 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.241 Fit side-chains REVERT: A 149 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.7260 (ttpp) REVERT: A 152 LYS cc_start: 0.7773 (mttt) cc_final: 0.7147 (mmmt) REVERT: A 320 ARG cc_start: 0.7509 (mmm-85) cc_final: 0.7174 (mmm160) REVERT: A 351 LEU cc_start: 0.8208 (tp) cc_final: 0.7783 (mt) REVERT: A 362 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7148 (m-30) REVERT: A 423 LYS cc_start: 0.6969 (mmtt) cc_final: 0.6701 (tmtt) REVERT: B 190 MET cc_start: 0.4306 (ppp) cc_final: 0.4048 (ttm) REVERT: B 409 MET cc_start: 0.7340 (mtp) cc_final: 0.7040 (mtp) REVERT: B 539 LYS cc_start: 0.5846 (OUTLIER) cc_final: 0.5072 (pptt) outliers start: 17 outliers final: 10 residues processed: 81 average time/residue: 0.1012 time to fit residues: 10.6632 Evaluate side-chains 76 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 381 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 78 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.200304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.166341 restraints weight = 9705.986| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.66 r_work: 0.3505 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8562 Z= 0.172 Angle : 0.605 8.258 12037 Z= 0.336 Chirality : 0.044 0.280 1312 Planarity : 0.004 0.034 1172 Dihedral : 27.685 178.111 1928 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.85 % Allowed : 15.03 % 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: 0.71 (0.30), residues: 754 helix: 1.36 (0.30), residues: 295 sheet: -0.53 (0.53), residues: 84 loop : 0.10 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 419 TYR 0.008 0.001 TYR B 385 PHE 0.017 0.002 PHE A 553 TRP 0.015 0.002 TRP B 584 HIS 0.002 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 ( 8554) covalent geometry : angle 0.59508 / 0.34 (12031) hydrogen bonds : bond 0.03831 / 4.26 ( 393) hydrogen bonds : angle 3.57369 / 4.96 ( 1007) metal coordination : bond 0.01609 / 0.97 ( 8) metal coordination : angle 4.88589 / 7.76 ( 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 87 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.157 Fit side-chains REVERT: A 149 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7283 (ttpp) REVERT: A 152 LYS cc_start: 0.7789 (mttt) cc_final: 0.7185 (mmmt) REVERT: A 320 ARG cc_start: 0.7397 (mmm-85) cc_final: 0.7062 (mmm160) REVERT: A 351 LEU cc_start: 0.8204 (tp) cc_final: 0.7813 (mt) REVERT: A 362 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: A 423 LYS cc_start: 0.6976 (mmtt) cc_final: 0.6774 (tmtt) REVERT: B 190 MET cc_start: 0.4334 (ppp) cc_final: 0.4099 (ttm) REVERT: B 345 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.4483 (mtp-110) REVERT: B 409 MET cc_start: 0.7396 (mtp) cc_final: 0.6686 (mtp) REVERT: B 539 LYS cc_start: 0.5907 (OUTLIER) cc_final: 0.5035 (pptt) outliers start: 18 outliers final: 11 residues processed: 83 average time/residue: 0.0987 time to fit residues: 10.6732 Evaluate side-chains 80 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 381 ILE Chi-restraints excluded: chain A residue 387 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 23 optimal weight: 0.5980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.196607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.163557 restraints weight = 9562.303| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.53 r_work: 0.3446 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 8562 Z= 0.250 Angle : 0.688 9.515 12037 Z= 0.377 Chirality : 0.048 0.310 1312 Planarity : 0.005 0.037 1172 Dihedral : 27.748 176.215 1928 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.53 % Allowed : 15.19 % 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: 0.44 (0.30), residues: 754 helix: 1.00 (0.29), residues: 295 sheet: -0.49 (0.54), residues: 84 loop : 0.03 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 285 TYR 0.013 0.002 TYR B 385 PHE 0.024 0.002 PHE A 553 TRP 0.019 0.002 TRP A 526 HIS 0.004 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 ( 8554) covalent geometry : angle 0.67497 / 0.38 (12031) hydrogen bonds : bond 0.04607 / 5.06 ( 393) hydrogen bonds : angle 3.75414 / 5.15 ( 1007) metal coordination : bond 0.01744 / 1.17 ( 8) metal coordination : angle 5.99512 / 9.29 ( 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 84 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.173 Fit side-chains REVERT: A 149 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7439 (ttpp) REVERT: A 152 LYS cc_start: 0.7881 (mttt) cc_final: 0.7259 (mmmt) REVERT: A 320 ARG cc_start: 0.7453 (mmm-85) cc_final: 0.7116 (mmm160) REVERT: A 351 LEU cc_start: 0.8208 (tp) cc_final: 0.7858 (mt) REVERT: A 362 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7233 (m-30) REVERT: B 154 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7656 (mt) REVERT: B 345 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.4361 (mtp-110) REVERT: B 539 LYS cc_start: 0.6091 (OUTLIER) cc_final: 0.5112 (pptt) outliers start: 16 outliers final: 10 residues processed: 81 average time/residue: 0.0951 time to fit residues: 10.0016 Evaluate side-chains 80 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 345 ARG 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: 0.9980 chunk 47 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4237 r_free = 0.4237 target = 0.198747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.165348 restraints weight = 9617.025| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.58 r_work: 0.3490 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8562 Z= 0.184 Angle : 0.624 8.056 12037 Z= 0.346 Chirality : 0.045 0.287 1312 Planarity : 0.004 0.036 1172 Dihedral : 27.685 175.753 1928 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.37 % Allowed : 15.51 % 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: 0.61 (0.30), residues: 754 helix: 1.18 (0.30), residues: 295 sheet: -0.35 (0.60), residues: 72 loop : 0.05 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 189 TYR 0.009 0.001 TYR A 295 PHE 0.017 0.002 PHE A 553 TRP 0.014 0.002 TRP A 526 HIS 0.002 0.001 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 ( 8554) covalent geometry : angle 0.61366 / 0.35 (12031) hydrogen bonds : bond 0.03940 / 4.37 ( 393) hydrogen bonds : angle 3.67205 / 5.05 ( 1007) metal coordination : bond 0.01547 / 0.94 ( 8) metal coordination : angle 5.19349 / 8.12 ( 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: 15 poor density : 67 time to evaluate : 0.160 Fit side-chains REVERT: A 149 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7416 (ttpp) REVERT: A 152 LYS cc_start: 0.7846 (mttt) cc_final: 0.7252 (mmmt) REVERT: A 278 MET cc_start: 0.8565 (mmm) cc_final: 0.8362 (mmm) REVERT: A 320 ARG cc_start: 0.7386 (mmm-85) cc_final: 0.7043 (mmm160) REVERT: A 351 LEU cc_start: 0.8211 (tp) cc_final: 0.7853 (mt) REVERT: A 362 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: B 345 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.4489 (mtp-110) REVERT: B 539 LYS cc_start: 0.6108 (OUTLIER) cc_final: 0.4981 (pptt) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.0988 time to fit residues: 9.8823 Evaluate side-chains 80 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 263 ILE Chi-restraints excluded: chain A residue 362 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 552 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.0000 chunk 71 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.201698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.171265 restraints weight = 9616.920| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.49 r_work: 0.3554 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8562 Z= 0.147 Angle : 0.588 8.070 12037 Z= 0.328 Chirality : 0.043 0.282 1312 Planarity : 0.004 0.033 1172 Dihedral : 27.524 174.099 1928 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: 0.77 (0.31), residues: 754 helix: 1.49 (0.30), residues: 294 sheet: -0.49 (0.59), residues: 72 loop : 0.04 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 189 TYR 0.008 0.001 TYR A 385 PHE 0.012 0.001 PHE A 553 TRP 0.013 0.001 TRP A 526 HIS 0.002 0.001 HIS B 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 ( 8554) covalent geometry : angle 0.57960 / 0.33 (12031) hydrogen bonds : bond 0.03614 / 4.00 ( 393) hydrogen bonds : angle 3.58342 / 4.91 ( 1007) metal coordination : bond 0.01239 / 0.75 ( 8) metal coordination : angle 4.53234 / 7.58 ( 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 84 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.242 Fit side-chains REVERT: A 149 LYS cc_start: 0.7510 (OUTLIER) cc_final: 0.7274 (ttpp) REVERT: A 152 LYS cc_start: 0.7786 (mttt) cc_final: 0.7228 (mmmt) REVERT: A 320 ARG cc_start: 0.7249 (mmm-85) cc_final: 0.6924 (mmm160) REVERT: A 351 LEU cc_start: 0.8206 (tp) cc_final: 0.7850 (mt) REVERT: A 362 ASP cc_start: 0.7183 (OUTLIER) cc_final: 0.6952 (m-30) REVERT: B 345 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.4553 (mtp-110) REVERT: B 539 LYS cc_start: 0.6094 (OUTLIER) cc_final: 0.4892 (pptt) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.1080 time to fit residues: 11.0273 Evaluate side-chains 77 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 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 583 THR Chi-restraints excluded: chain B residue 345 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.0070 chunk 62 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.4260 r_free = 0.4260 target = 0.201296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.167647 restraints weight = 9715.328| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.62 r_work: 0.3524 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2969 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= 0.152 Angle : 0.584 7.926 12037 Z= 0.326 Chirality : 0.043 0.280 1312 Planarity : 0.004 0.032 1172 Dihedral : 27.420 172.778 1928 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.37 % Allowed : 15.82 % 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: 0.80 (0.31), residues: 754 helix: 1.51 (0.30), residues: 294 sheet: -0.33 (0.60), residues: 72 loop : 0.03 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 221 TYR 0.012 0.001 TYR B 365 PHE 0.013 0.001 PHE A 553 TRP 0.011 0.001 TRP A 526 HIS 0.002 0.000 HIS A 401 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 8554) covalent geometry : angle 0.57609 / 0.32 (12031) hydrogen bonds : bond 0.03645 / 4.05 ( 393) hydrogen bonds : angle 3.55533 / 4.85 ( 1007) metal coordination : bond 0.01218 / 0.77 ( 8) metal coordination : angle 4.42970 / 7.23 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.48 seconds wall clock time: 31 minutes 22.95 seconds (1882.95 seconds total)