Starting phenix.real_space_refine on Tue Aug 4 21:43:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhm_61487/08_2026/9jhm_61487.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhm_61487/08_2026/9jhm_61487.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/9jhm_61487/08_2026/9jhm_61487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhm_61487/08_2026/9jhm_61487.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhm_61487/08_2026/9jhm_61487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhm_61487/08_2026/9jhm_61487.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= 0.006 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 Mn 1 7.51 5 P 35 5.49 5 S 20 5.16 5 C 4244 2.51 5 N 1115 2.21 5 O 1340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s 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: 6755 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.27, per 1000 atoms: 0.19 Number of scatterers: 6755 At special positions: 0 Unit cell: (71.34, 83.64, 102.5, 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) Mn 1 24.99 S 20 16.00 P 35 15.00 O 1340 8.00 N 1115 7.00 C 4244 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: 0.35 Conformation dependent library (CDL) restraints added in 283.5 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 11 sheets defined 31.4% alpha, 17.6% beta 7 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.926A pdb=" N ASN A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.781A pdb=" N TYR A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.686A pdb=" N TYR A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.574A pdb=" N SER A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 474 through 485 removed outlier: 3.642A pdb=" N PHE A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 508 through 522 Processing helix chain 'A' and resid 583 through 603 removed outlier: 4.296A pdb=" N LEU A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.646A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.519A pdb=" N ALA A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.898A pdb=" N TYR A 175 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.834A pdb=" N GLN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 83 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.534A pdb=" N TYR A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.563A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 223 removed outlier: 7.230A pdb=" N ASN A 261 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL A 219 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 259 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.625A pdb=" N SER A 663 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 690 " --> pdb=" O LYS A 641 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS A 641 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS A 692 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU A 639 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 694 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 609 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS A 539 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS A 612 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL A 541 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA A 614 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 543 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 540 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 569 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 745 " --> pdb=" O TYR A 570 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 359 removed outlier: 4.052A pdb=" N GLY A 357 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 529 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 432 through 435 removed outlier: 6.483A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 461 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB2, first strand: chain 'A' and resid 650 through 652 224 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 0.97 Time building geometry restraints manager: 0.47 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: 1663 1.33 - 1.45: 1451 1.45 - 1.57: 3745 1.57 - 1.69: 69 1.69 - 1.81: 35 Bond restraints: 6963 Sorted by residual: bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.74e+01 bond pdb=" C1' DC E 8 " pdb=" N1 DC E 8 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" C5' DA E 3 " pdb=" C4' DA E 3 " ideal model delta sigma weight residual 1.512 1.535 -0.023 7.00e-03 2.04e+04 1.05e+01 bond pdb=" C1' DT E 12 " pdb=" N1 DT E 12 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.01e+01 bond pdb=" C3' DT E 12 " pdb=" O3' DT E 12 " ideal model delta sigma weight residual 1.435 1.475 -0.040 1.30e-02 5.92e+03 9.64e+00 ... (remaining 6958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 9102 2.29 - 4.59: 375 4.59 - 6.88: 41 6.88 - 9.17: 16 9.17 - 11.46: 2 Bond angle restraints: 9536 Sorted by residual: angle pdb=" O4' DT C 9 " pdb=" C4' DT C 9 " pdb=" C3' DT C 9 " ideal model delta sigma weight residual 106.00 102.33 3.67 6.00e-01 2.78e+00 3.74e+01 angle pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 120.82 129.75 -8.93 1.50e+00 4.44e-01 3.54e+01 angle pdb=" C GLY A 264 " pdb=" N ASN A 265 " pdb=" CA ASN A 265 " ideal model delta sigma weight residual 121.54 132.52 -10.98 1.91e+00 2.74e-01 3.31e+01 angle pdb=" C GLU A 680 " pdb=" N ASN A 681 " pdb=" CA ASN A 681 " ideal model delta sigma weight residual 123.05 131.19 -8.14 1.57e+00 4.06e-01 2.69e+01 angle pdb=" O4' DG C 4 " pdb=" C1' DG C 4 " pdb=" N9 DG C 4 " ideal model delta sigma weight residual 108.00 111.53 -3.53 7.00e-01 2.04e+00 2.55e+01 ... (remaining 9531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 3846 24.08 - 48.15: 220 48.15 - 72.23: 59 72.23 - 96.31: 6 96.31 - 120.38: 1 Dihedral angle restraints: 4132 sinusoidal: 1945 harmonic: 2187 Sorted by residual: dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -123.31 -56.69 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LYS A 63 " pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta harmonic sigma weight residual 180.00 -149.07 -30.93 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA THR A 507 " pdb=" C THR A 507 " pdb=" N ALA A 508 " pdb=" CA ALA A 508 " ideal model delta harmonic sigma weight residual 180.00 149.22 30.78 0 5.00e+00 4.00e-02 3.79e+01 ... (remaining 4129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 736 0.056 - 0.112: 221 0.112 - 0.168: 69 0.168 - 0.225: 10 0.225 - 0.281: 8 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CB ILE A 609 " pdb=" CA ILE A 609 " pdb=" CG1 ILE A 609 " pdb=" CG2 ILE A 609 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE A 712 " pdb=" CA ILE A 712 " pdb=" CG1 ILE A 712 " pdb=" CG2 ILE A 712 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU A 520 " pdb=" CB LEU A 520 " pdb=" CD1 LEU A 520 " pdb=" CD2 LEU A 520 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1041 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 470 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C GLU A 470 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU A 470 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE A 471 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 468 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C ASP A 468 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A 468 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 469 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " -0.017 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP A 623 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " -0.006 2.00e-02 2.50e+03 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 24 2.43 - 3.05: 3767 3.05 - 3.66: 10732 3.66 - 4.28: 15928 4.28 - 4.90: 25357 Nonbonded interactions: 55808 Sorted by model distance: nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.811 2.320 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.863 2.320 nonbonded pdb=" O LEU A 751 " pdb="MN MN C 801 " model vdw 1.906 2.320 nonbonded pdb=" OP1 DT C 1 " pdb="MN MN C 801 " model vdw 2.066 2.320 nonbonded pdb=" O ILE A 515 " pdb=" CG1 ILE A 519 " model vdw 2.099 3.440 ... (remaining 55803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.430 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.220 Find NCS groups from input model: 0.030 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:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 : 0.007 0.067 6963 Z= 0.394 Angle : 1.063 11.464 9536 Z= 0.667 Chirality : 0.064 0.281 1044 Planarity : 0.006 0.046 1090 Dihedral : 15.776 120.385 2738 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.48 % Rotamer: Outliers : 0.15 % Allowed : 4.19 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.83 (0.25), residues: 743 helix: -2.62 (0.26), residues: 197 sheet: -2.85 (0.36), residues: 147 loop : -2.34 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 158 TYR 0.026 0.003 TYR A 238 PHE 0.030 0.004 PHE A 154 TRP 0.034 0.004 TRP A 623 HIS 0.004 0.002 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.39 ( 6963) covalent geometry : angle 1.06324 / 0.67 ( 9536) hydrogen bonds : bond 0.20549 / 12.78 ( 241) hydrogen bonds : angle 9.69942 / 6.55 ( 661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8179 (mmt) cc_final: 0.7571 (mmt) REVERT: A 480 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8751 (pttp) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.0726 time to fit residues: 12.9982 Evaluate side-chains 76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS ** A 578 ASN ** 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 = 0.4262 r_free = 0.4262 target = 0.121082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.096600 restraints weight = 20441.101| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 5.42 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6963 Z= 0.192 Angle : 0.800 9.736 9536 Z= 0.436 Chirality : 0.052 0.279 1044 Planarity : 0.005 0.038 1090 Dihedral : 18.841 120.940 1199 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.54 % Allowed : 9.43 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.06 (0.27), residues: 743 helix: -1.55 (0.30), residues: 224 sheet: -2.38 (0.39), residues: 151 loop : -2.12 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 618 TYR 0.039 0.002 TYR A 238 PHE 0.024 0.002 PHE A 591 TRP 0.045 0.005 TRP A 623 HIS 0.007 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 ( 6963) covalent geometry : angle 0.79965 / 0.44 ( 9536) hydrogen bonds : bond 0.05721 / 3.73 ( 241) hydrogen bonds : angle 7.32726 / 4.94 ( 661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8691 (mtm) cc_final: 0.8269 (ptp) REVERT: A 98 MET cc_start: 0.7951 (mmt) cc_final: 0.7339 (mmt) REVERT: A 298 GLN cc_start: 0.8825 (mp10) cc_final: 0.8508 (mp10) REVERT: A 363 MET cc_start: 0.8944 (mmt) cc_final: 0.8531 (mmm) REVERT: A 480 LYS cc_start: 0.8983 (mtmt) cc_final: 0.8619 (pttp) REVERT: A 533 MET cc_start: 0.8254 (mmm) cc_final: 0.7793 (mmm) REVERT: A 646 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8436 (tm) outliers start: 17 outliers final: 8 residues processed: 103 average time/residue: 0.0547 time to fit residues: 7.9516 Evaluate side-chains 85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.120536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.095799 restraints weight = 20358.781| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 5.48 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6963 Z= 0.165 Angle : 0.734 9.271 9536 Z= 0.401 Chirality : 0.050 0.237 1044 Planarity : 0.004 0.031 1090 Dihedral : 18.633 120.837 1199 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.25 % Allowed : 12.28 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.64 (0.27), residues: 743 helix: -1.38 (0.30), residues: 229 sheet: -2.26 (0.45), residues: 116 loop : -1.79 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 618 TYR 0.053 0.002 TYR A 238 PHE 0.016 0.002 PHE A 432 TRP 0.066 0.005 TRP A 623 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 6963) covalent geometry : angle 0.73393 / 0.40 ( 9536) hydrogen bonds : bond 0.04837 / 3.19 ( 241) hydrogen bonds : angle 6.96833 / 4.75 ( 661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8423 (tt0) cc_final: 0.7726 (tm-30) REVERT: A 24 MET cc_start: 0.8759 (mtm) cc_final: 0.8158 (ptp) REVERT: A 51 MET cc_start: 0.9565 (ttt) cc_final: 0.9000 (tmm) REVERT: A 55 ASN cc_start: 0.9198 (p0) cc_final: 0.8632 (p0) REVERT: A 56 ARG cc_start: 0.8507 (mmp80) cc_final: 0.8260 (mmp80) REVERT: A 98 MET cc_start: 0.7894 (mmt) cc_final: 0.7316 (mmt) REVERT: A 298 GLN cc_start: 0.8871 (mp10) cc_final: 0.8497 (mp10) REVERT: A 337 VAL cc_start: 0.8550 (OUTLIER) cc_final: 0.8308 (t) REVERT: A 363 MET cc_start: 0.8904 (mmt) cc_final: 0.8188 (mmm) REVERT: A 366 PHE cc_start: 0.7825 (m-80) cc_final: 0.7622 (m-80) REVERT: A 480 LYS cc_start: 0.8954 (mtmt) cc_final: 0.8641 (pttm) REVERT: A 513 HIS cc_start: 0.7497 (m-70) cc_final: 0.7179 (m-70) REVERT: A 533 MET cc_start: 0.8317 (mmm) cc_final: 0.7886 (mmm) REVERT: A 646 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8488 (tm) REVERT: A 705 GLN cc_start: 0.9099 (mt0) cc_final: 0.8714 (mt0) outliers start: 15 outliers final: 7 residues processed: 102 average time/residue: 0.0598 time to fit residues: 8.6152 Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 703 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 0.4980 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 24 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.116371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.092573 restraints weight = 21338.683| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 5.25 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6963 Z= 0.166 Angle : 0.695 9.243 9536 Z= 0.380 Chirality : 0.048 0.220 1044 Planarity : 0.004 0.042 1090 Dihedral : 18.450 118.559 1199 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.14 % Allowed : 11.38 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.32 (0.28), residues: 743 helix: -1.05 (0.32), residues: 228 sheet: -2.19 (0.44), residues: 116 loop : -1.59 (0.28), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 618 TYR 0.035 0.002 TYR A 238 PHE 0.015 0.002 PHE A 154 TRP 0.039 0.004 TRP A 623 HIS 0.006 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 ( 6963) covalent geometry : angle 0.69550 / 0.38 ( 9536) hydrogen bonds : bond 0.04339 / 2.86 ( 241) hydrogen bonds : angle 6.59005 / 4.50 ( 661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8476 (tt0) cc_final: 0.7784 (tm-30) REVERT: A 24 MET cc_start: 0.8871 (mtm) cc_final: 0.8358 (ptp) REVERT: A 51 MET cc_start: 0.9534 (ttt) cc_final: 0.9076 (tmm) REVERT: A 55 ASN cc_start: 0.9187 (p0) cc_final: 0.8537 (p0) REVERT: A 56 ARG cc_start: 0.8497 (mmp80) cc_final: 0.8261 (mmp80) REVERT: A 98 MET cc_start: 0.7908 (mmt) cc_final: 0.7329 (mmt) REVERT: A 298 GLN cc_start: 0.8879 (mp10) cc_final: 0.8477 (mp10) REVERT: A 311 LEU cc_start: 0.8300 (mt) cc_final: 0.7675 (tp) REVERT: A 337 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8377 (t) REVERT: A 363 MET cc_start: 0.8892 (mmt) cc_final: 0.8254 (mmm) REVERT: A 466 MET cc_start: 0.8002 (ptp) cc_final: 0.7547 (pmm) REVERT: A 513 HIS cc_start: 0.7568 (m-70) cc_final: 0.7236 (m-70) REVERT: A 533 MET cc_start: 0.8247 (mmm) cc_final: 0.7730 (mmm) REVERT: A 646 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8549 (tm) outliers start: 21 outliers final: 10 residues processed: 105 average time/residue: 0.0585 time to fit residues: 8.6043 Evaluate side-chains 89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 703 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.121859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.097627 restraints weight = 20872.009| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 5.44 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6963 Z= 0.149 Angle : 0.684 9.464 9536 Z= 0.370 Chirality : 0.047 0.215 1044 Planarity : 0.004 0.034 1090 Dihedral : 18.354 119.084 1199 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.84 % Allowed : 12.87 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.12 (0.29), residues: 743 helix: -0.85 (0.32), residues: 228 sheet: -2.05 (0.44), residues: 122 loop : -1.48 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 613 TYR 0.027 0.002 TYR A 238 PHE 0.018 0.002 PHE A 432 TRP 0.035 0.004 TRP A 623 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 ( 6963) covalent geometry : angle 0.68410 / 0.37 ( 9536) hydrogen bonds : bond 0.04081 / 2.70 ( 241) hydrogen bonds : angle 6.39686 / 4.37 ( 661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8447 (tt0) cc_final: 0.7801 (tm-30) REVERT: A 24 MET cc_start: 0.8888 (mtm) cc_final: 0.8343 (ptp) REVERT: A 51 MET cc_start: 0.9490 (ttt) cc_final: 0.9127 (ptm) REVERT: A 55 ASN cc_start: 0.9122 (p0) cc_final: 0.8171 (p0) REVERT: A 56 ARG cc_start: 0.8466 (mmp80) cc_final: 0.8259 (mmp80) REVERT: A 84 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7791 (pp) REVERT: A 98 MET cc_start: 0.7919 (mmt) cc_final: 0.7359 (mmt) REVERT: A 295 GLU cc_start: 0.9300 (tp30) cc_final: 0.8975 (tp30) REVERT: A 298 GLN cc_start: 0.8902 (mp10) cc_final: 0.8454 (mp10) REVERT: A 363 MET cc_start: 0.8870 (mmt) cc_final: 0.8186 (mmt) REVERT: A 454 ASN cc_start: 0.8918 (t0) cc_final: 0.8707 (t0) REVERT: A 466 MET cc_start: 0.7981 (ptp) cc_final: 0.7545 (pmm) REVERT: A 498 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8722 (mm-30) REVERT: A 513 HIS cc_start: 0.7521 (m-70) cc_final: 0.7221 (m-70) REVERT: A 567 LEU cc_start: 0.8869 (tt) cc_final: 0.8616 (tt) REVERT: A 623 TRP cc_start: 0.5557 (t60) cc_final: 0.5082 (t60) REVERT: A 646 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8533 (tm) outliers start: 19 outliers final: 11 residues processed: 103 average time/residue: 0.0570 time to fit residues: 8.4754 Evaluate side-chains 93 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 9.9990 chunk 75 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.115771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.092084 restraints weight = 21733.538| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 5.31 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6963 Z= 0.180 Angle : 0.686 9.664 9536 Z= 0.372 Chirality : 0.048 0.217 1044 Planarity : 0.004 0.040 1090 Dihedral : 18.296 119.958 1199 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.84 % Allowed : 14.37 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.90 (0.29), residues: 743 helix: -0.74 (0.32), residues: 229 sheet: -1.79 (0.45), residues: 130 loop : -1.32 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 618 TYR 0.026 0.002 TYR A 408 PHE 0.022 0.002 PHE A 591 TRP 0.034 0.004 TRP A 528 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 ( 6963) covalent geometry : angle 0.68561 / 0.37 ( 9536) hydrogen bonds : bond 0.03981 / 2.65 ( 241) hydrogen bonds : angle 6.27444 / 4.29 ( 661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8475 (tt0) cc_final: 0.7920 (tm-30) REVERT: A 24 MET cc_start: 0.8989 (mtm) cc_final: 0.8433 (ptp) REVERT: A 51 MET cc_start: 0.9466 (ttt) cc_final: 0.9133 (ptm) REVERT: A 55 ASN cc_start: 0.9122 (p0) cc_final: 0.8150 (p0) REVERT: A 84 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7908 (pp) REVERT: A 98 MET cc_start: 0.7997 (mmt) cc_final: 0.7418 (mmt) REVERT: A 363 MET cc_start: 0.8871 (mmt) cc_final: 0.8307 (mmt) REVERT: A 454 ASN cc_start: 0.8960 (t0) cc_final: 0.8744 (t0) REVERT: A 466 MET cc_start: 0.8125 (ptp) cc_final: 0.7682 (pmm) REVERT: A 498 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8724 (mm-30) REVERT: A 513 HIS cc_start: 0.7565 (m-70) cc_final: 0.7248 (m-70) REVERT: A 567 LEU cc_start: 0.8953 (tt) cc_final: 0.8734 (tt) REVERT: A 600 GLU cc_start: 0.9445 (OUTLIER) cc_final: 0.9222 (pt0) REVERT: A 623 TRP cc_start: 0.5609 (t60) cc_final: 0.5291 (t60) REVERT: A 646 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8610 (tm) REVERT: A 709 LEU cc_start: 0.9356 (mp) cc_final: 0.9077 (mt) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.0494 time to fit residues: 7.3328 Evaluate side-chains 97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.121093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.096890 restraints weight = 20470.768| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 5.39 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6963 Z= 0.148 Angle : 0.675 8.082 9536 Z= 0.365 Chirality : 0.047 0.229 1044 Planarity : 0.004 0.045 1090 Dihedral : 18.249 119.057 1199 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.69 % Allowed : 14.52 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.75 (0.29), residues: 743 helix: -0.68 (0.32), residues: 229 sheet: -1.71 (0.45), residues: 127 loop : -1.18 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.027 0.001 TYR A 408 PHE 0.025 0.002 PHE A 147 TRP 0.040 0.004 TRP A 528 HIS 0.010 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 6963) covalent geometry : angle 0.67535 / 0.36 ( 9536) hydrogen bonds : bond 0.03777 / 2.50 ( 241) hydrogen bonds : angle 6.17312 / 4.21 ( 661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8449 (tt0) cc_final: 0.7920 (tm-30) REVERT: A 24 MET cc_start: 0.9030 (mtm) cc_final: 0.8421 (ptp) REVERT: A 51 MET cc_start: 0.9516 (ttt) cc_final: 0.9162 (ptm) REVERT: A 55 ASN cc_start: 0.9050 (p0) cc_final: 0.8509 (p0) REVERT: A 84 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7885 (pp) REVERT: A 98 MET cc_start: 0.7986 (mmt) cc_final: 0.7439 (mmt) REVERT: A 169 MET cc_start: 0.9180 (mmm) cc_final: 0.8755 (ttm) REVERT: A 283 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: A 298 GLN cc_start: 0.8950 (mp10) cc_final: 0.8533 (mp10) REVERT: A 311 LEU cc_start: 0.8266 (mt) cc_final: 0.8057 (tp) REVERT: A 363 MET cc_start: 0.8891 (mmt) cc_final: 0.8339 (mmt) REVERT: A 454 ASN cc_start: 0.8952 (t0) cc_final: 0.8738 (t0) REVERT: A 567 LEU cc_start: 0.8928 (tt) cc_final: 0.8719 (tt) REVERT: A 646 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8555 (tm) REVERT: A 734 LYS cc_start: 0.9318 (pttp) cc_final: 0.8917 (pttm) outliers start: 18 outliers final: 12 residues processed: 97 average time/residue: 0.0583 time to fit residues: 8.1477 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.109309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.085945 restraints weight = 22580.047| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 5.38 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6963 Z= 0.235 Angle : 0.726 8.196 9536 Z= 0.394 Chirality : 0.052 0.611 1044 Planarity : 0.004 0.057 1090 Dihedral : 18.302 120.785 1199 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 2.99 % Allowed : 15.12 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.82 (0.29), residues: 743 helix: -0.79 (0.31), residues: 231 sheet: -1.80 (0.44), residues: 130 loop : -1.16 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 56 TYR 0.029 0.002 TYR A 408 PHE 0.029 0.003 PHE A 591 TRP 0.080 0.007 TRP A 623 HIS 0.012 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.24 ( 6963) covalent geometry : angle 0.72629 / 0.39 ( 9536) hydrogen bonds : bond 0.04351 / 2.99 ( 241) hydrogen bonds : angle 6.33658 / 4.33 ( 661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8499 (tt0) cc_final: 0.7879 (tm-30) REVERT: A 24 MET cc_start: 0.9099 (mtm) cc_final: 0.8508 (ptp) REVERT: A 51 MET cc_start: 0.9483 (ttt) cc_final: 0.9197 (ptm) REVERT: A 84 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8038 (pp) REVERT: A 98 MET cc_start: 0.8159 (mmt) cc_final: 0.7596 (mmt) REVERT: A 298 GLN cc_start: 0.8991 (mp10) cc_final: 0.8586 (mp10) REVERT: A 311 LEU cc_start: 0.8502 (mt) cc_final: 0.8282 (tp) REVERT: A 363 MET cc_start: 0.8863 (mmt) cc_final: 0.8304 (mmt) REVERT: A 454 ASN cc_start: 0.9097 (t0) cc_final: 0.8894 (t0) REVERT: A 466 MET cc_start: 0.8368 (ptp) cc_final: 0.7890 (pmm) REVERT: A 498 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8702 (mm-30) REVERT: A 513 HIS cc_start: 0.7650 (m-70) cc_final: 0.7329 (m-70) REVERT: A 567 LEU cc_start: 0.9020 (tt) cc_final: 0.8814 (tt) REVERT: A 646 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8691 (tm) REVERT: A 734 LYS cc_start: 0.9398 (pttp) cc_final: 0.9008 (pttm) outliers start: 20 outliers final: 15 residues processed: 95 average time/residue: 0.0517 time to fit residues: 7.1538 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.116045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.091667 restraints weight = 21566.667| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 5.46 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6963 Z= 0.154 Angle : 0.709 8.387 9536 Z= 0.379 Chirality : 0.048 0.230 1044 Planarity : 0.004 0.045 1090 Dihedral : 18.273 119.041 1199 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.40 % Allowed : 15.87 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.73 (0.30), residues: 743 helix: -0.85 (0.31), residues: 231 sheet: -1.70 (0.45), residues: 130 loop : -1.02 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 721 TYR 0.025 0.002 TYR A 408 PHE 0.032 0.002 PHE A 147 TRP 0.118 0.009 TRP A 623 HIS 0.008 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 6963) covalent geometry : angle 0.70924 / 0.38 ( 9536) hydrogen bonds : bond 0.03978 / 2.68 ( 241) hydrogen bonds : angle 6.23349 / 4.25 ( 661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8484 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 24 MET cc_start: 0.9121 (mtm) cc_final: 0.8476 (ptp) REVERT: A 51 MET cc_start: 0.9500 (ttt) cc_final: 0.9153 (ptm) REVERT: A 55 ASN cc_start: 0.9109 (p0) cc_final: 0.8591 (p0) REVERT: A 84 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8026 (pp) REVERT: A 98 MET cc_start: 0.8077 (mmt) cc_final: 0.7556 (mmt) REVERT: A 169 MET cc_start: 0.9205 (mmm) cc_final: 0.8786 (ttm) REVERT: A 197 GLU cc_start: 0.8649 (tp30) cc_final: 0.8410 (tm-30) REVERT: A 283 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8572 (tm-30) REVERT: A 298 GLN cc_start: 0.8993 (mp10) cc_final: 0.8590 (mp10) REVERT: A 311 LEU cc_start: 0.8379 (mt) cc_final: 0.8141 (tp) REVERT: A 363 MET cc_start: 0.8836 (mmt) cc_final: 0.8305 (mmt) REVERT: A 454 ASN cc_start: 0.9081 (t0) cc_final: 0.8869 (t0) REVERT: A 646 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8605 (tm) REVERT: A 734 LYS cc_start: 0.9305 (pttp) cc_final: 0.8861 (pttm) outliers start: 16 outliers final: 11 residues processed: 93 average time/residue: 0.0622 time to fit residues: 8.0587 Evaluate side-chains 90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 64 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.116212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.092543 restraints weight = 21455.632| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 5.28 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6963 Z= 0.153 Angle : 0.719 10.582 9536 Z= 0.382 Chirality : 0.049 0.244 1044 Planarity : 0.004 0.044 1090 Dihedral : 18.237 118.622 1199 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.10 % Allowed : 16.77 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.67 (0.30), residues: 743 helix: -0.87 (0.31), residues: 231 sheet: -1.68 (0.44), residues: 130 loop : -0.93 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.025 0.002 TYR A 408 PHE 0.029 0.002 PHE A 147 TRP 0.096 0.008 TRP A 623 HIS 0.009 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6963) covalent geometry : angle 0.71870 / 0.38 ( 9536) hydrogen bonds : bond 0.03912 / 2.65 ( 241) hydrogen bonds : angle 6.17088 / 4.23 ( 661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8460 (tt0) cc_final: 0.7944 (tm-30) REVERT: A 24 MET cc_start: 0.9123 (mtm) cc_final: 0.8492 (ptp) REVERT: A 51 MET cc_start: 0.9465 (ttt) cc_final: 0.9201 (ptm) REVERT: A 98 MET cc_start: 0.8103 (mmt) cc_final: 0.7512 (mmt) REVERT: A 169 MET cc_start: 0.9167 (mmm) cc_final: 0.8767 (ttm) REVERT: A 197 GLU cc_start: 0.8623 (tp30) cc_final: 0.8409 (tm-30) REVERT: A 283 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8544 (tm-30) REVERT: A 298 GLN cc_start: 0.8968 (mp10) cc_final: 0.8581 (mp10) REVERT: A 311 LEU cc_start: 0.8360 (mt) cc_final: 0.8150 (tp) REVERT: A 363 MET cc_start: 0.8839 (mmt) cc_final: 0.8333 (mmt) REVERT: A 444 LYS cc_start: 0.9295 (mmtt) cc_final: 0.9072 (mmmt) REVERT: A 454 ASN cc_start: 0.9019 (t0) cc_final: 0.8806 (t0) REVERT: A 646 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8617 (tm) REVERT: A 734 LYS cc_start: 0.9297 (pttp) cc_final: 0.8861 (pttp) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.0690 time to fit residues: 8.7198 Evaluate side-chains 86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 0.9980 chunk 1 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.777 > 50:) chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.116625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.093103 restraints weight = 21261.108| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 5.32 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6963 Z= 0.152 Angle : 0.714 8.300 9536 Z= 0.381 Chirality : 0.049 0.220 1044 Planarity : 0.004 0.044 1090 Dihedral : 18.205 118.099 1199 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.25 % Allowed : 16.77 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.69 (0.30), residues: 743 helix: -1.00 (0.31), residues: 233 sheet: -1.59 (0.44), residues: 130 loop : -0.89 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.026 0.001 TYR A 408 PHE 0.021 0.002 PHE A 147 TRP 0.081 0.007 TRP A 623 HIS 0.009 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6963) covalent geometry : angle 0.71381 / 0.38 ( 9536) hydrogen bonds : bond 0.03898 / 2.65 ( 241) hydrogen bonds : angle 6.04839 / 4.13 ( 661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1173.66 seconds wall clock time: 20 minutes 54.69 seconds (1254.69 seconds total)