Starting phenix.real_space_refine on Thu Jul 2 06:55:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ld0_62998/07_2026/9ld0_62998_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ld0_62998/07_2026/9ld0_62998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ld0_62998/07_2026/9ld0_62998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ld0_62998/07_2026/9ld0_62998.map" model { file = "/net/cci-nas-00/data/ceres_data/9ld0_62998/07_2026/9ld0_62998_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ld0_62998/07_2026/9ld0_62998_neut.cif" } resolution = 3.17 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= 0.107 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 1 6.06 5 P 54 5.49 5 S 21 5.16 5 C 4359 2.51 5 N 1313 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s 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: 7232 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 558 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 6124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6124 Classifications: {'peptide': 832} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 785} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" 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 6957 SG CYS A 845 33.009 52.323 26.451 1.00 47.15 S Time building chain proxies: 1.54, per 1000 atoms: 0.21 Number of scatterers: 7232 At special positions: 0 Unit cell: (81.8748, 84.0294, 129.276, 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 1 29.99 S 21 16.00 P 54 15.00 O 1484 8.00 N 1313 7.00 C 4359 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: 0.60 Conformation dependent library (CDL) restraints added in 360.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 845 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 814 " 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1508 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 1 sheets defined 75.0% alpha, 2.2% beta 27 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.921A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 3.722A pdb=" N MET A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 97 through 113 removed outlier: 5.256A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.800A pdb=" N THR A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 166 through 184 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 219 removed outlier: 3.652A pdb=" N ALA A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 213 - end of helix removed outlier: 3.568A pdb=" N HIS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 234 through 252 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 268 through 286 Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 302 through 320 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 336 through 354 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 370 through 390 Proline residue: A 383 - end of helix Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 404 through 422 Proline residue: A 417 - end of helix Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 438 through 456 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 472 through 490 Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 506 through 525 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 540 through 558 removed outlier: 3.644A pdb=" N ALA A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Proline residue: A 553 - end of helix Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 574 through 592 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 608 through 626 Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 642 through 660 Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 664 through 673 Processing helix chain 'A' and resid 676 through 690 removed outlier: 3.804A pdb=" N ALA A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 703 removed outlier: 3.719A pdb=" N LEU A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 733 removed outlier: 3.733A pdb=" N ILE A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 752 removed outlier: 4.055A pdb=" N ASP A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 742 " --> pdb=" O SER A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 807 Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 844 through 853 removed outlier: 4.301A pdb=" N ALA A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 794 through 798 removed outlier: 6.856A pdb=" N ALA A 831 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N VAL A 862 " --> pdb=" O ALA A 831 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 833 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 861 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 879 " --> pdb=" O VAL A 861 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2199 1.34 - 1.46: 1188 1.46 - 1.58: 3942 1.58 - 1.70: 106 1.70 - 1.82: 25 Bond restraints: 7460 Sorted by residual: bond pdb=" C3' DG C 10 " pdb=" C2' DG C 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DA C 17 " pdb=" C2' DA C 17 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.16e+00 bond pdb=" N ILE A 709 " pdb=" CA ILE A 709 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.15e+00 bond pdb=" N ILE A 711 " pdb=" CA ILE A 711 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 9.03e+00 bond pdb=" C3' DG B -20 " pdb=" C2' DG B -20 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.00e+00 ... (remaining 7455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10101 1.67 - 3.33: 259 3.33 - 5.00: 29 5.00 - 6.67: 9 6.67 - 8.33: 1 Bond angle restraints: 10399 Sorted by residual: angle pdb=" N3 DT C 21 " pdb=" C4 DT C 21 " pdb=" O4 DT C 21 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B -11 " pdb=" C4 DT B -11 " pdb=" O4 DT B -11 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B -17 " pdb=" C4 DT B -17 " pdb=" O4 DT B -17 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT C 9 " pdb=" C4 DT C 9 " pdb=" O4 DT C 9 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 10394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 4021 33.59 - 67.19: 325 67.19 - 100.78: 12 100.78 - 134.37: 0 134.37 - 167.97: 2 Dihedral angle restraints: 4360 sinusoidal: 2011 harmonic: 2349 Sorted by residual: dihedral pdb=" CA ARG A 448 " pdb=" C ARG A 448 " pdb=" N LEU A 449 " pdb=" CA LEU A 449 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DC B -13 " pdb=" C3' DC B -13 " pdb=" O3' DC B -13 " pdb=" P DC B -12 " ideal model delta sinusoidal sigma weight residual 220.00 52.03 167.97 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC B -10 " pdb=" C3' DC B -10 " pdb=" O3' DC B -10 " pdb=" P DA B -9 " ideal model delta sinusoidal sigma weight residual 220.00 65.04 154.96 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 4357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 865 0.038 - 0.077: 272 0.077 - 0.115: 108 0.115 - 0.153: 8 0.153 - 0.191: 3 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CA ILE A 711 " pdb=" N ILE A 711 " pdb=" C ILE A 711 " pdb=" CB ILE A 711 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" C3' DC B -13 " pdb=" C4' DC B -13 " pdb=" O3' DC B -13 " pdb=" C2' DC B -13 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ILE A 709 " pdb=" N ILE A 709 " pdb=" C ILE A 709 " pdb=" CB ILE A 709 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 1253 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 392 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 393 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 562 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 563 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 427 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.023 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 81 2.66 - 3.22: 6433 3.22 - 3.78: 11857 3.78 - 4.34: 15214 4.34 - 4.90: 24856 Nonbonded interactions: 58441 Sorted by model distance: nonbonded pdb=" CG HIS A 814 " pdb="ZN ZN A 901 " model vdw 2.097 1.960 nonbonded pdb=" OG1 THR A 596 " pdb=" OE1 GLN A 599 " model vdw 2.200 3.040 nonbonded pdb=" O VAL A 363 " pdb=" OG SER A 367 " model vdw 2.257 3.040 nonbonded pdb=" O GLN A 441 " pdb=" OG1 THR A 445 " model vdw 2.281 3.040 nonbonded pdb=" O VAL A 397 " pdb=" OG SER A 401 " model vdw 2.285 3.040 ... (remaining 58436 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 0.322 7462 Z= 0.343 Angle : 0.615 8.332 10399 Z= 0.441 Chirality : 0.043 0.191 1256 Planarity : 0.004 0.045 1172 Dihedral : 20.414 167.967 2852 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 830 helix: 1.49 (0.23), residues: 558 sheet: -0.95 (0.96), residues: 30 loop : -0.59 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 702 TYR 0.015 0.001 TYR A 697 PHE 0.004 0.001 PHE A 852 TRP 0.007 0.001 TRP A 773 HIS 0.002 0.000 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.32 ( 7460) covalent geometry : angle 0.61454 / 0.44 (10399) hydrogen bonds : bond 0.14645 / 16.01 ( 454) hydrogen bonds : angle 5.16805 / 6.68 ( 1284) metal coordination : bond 0.22783 / 11.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.253 Fit side-chains REVERT: A 319 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7336 (mm110) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0712 time to fit residues: 10.4653 Evaluate side-chains 63 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 583 GLN A 817 GLN A 827 ASN A 835 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.204150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3896 r_free = 0.3896 target = 0.164025 restraints weight = 7035.222| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 0.94 r_work: 0.3549 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7462 Z= 0.136 Angle : 0.582 8.984 10399 Z= 0.313 Chirality : 0.044 0.307 1256 Planarity : 0.005 0.045 1172 Dihedral : 21.963 173.130 1449 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.98 % Allowed : 7.33 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.29), residues: 830 helix: 1.40 (0.22), residues: 582 sheet: -1.15 (0.79), residues: 42 loop : -0.58 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 584 TYR 0.017 0.002 TYR A 806 PHE 0.010 0.001 PHE A 852 TRP 0.003 0.001 TRP A 96 HIS 0.009 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 7460) covalent geometry : angle 0.58175 / 0.31 (10399) hydrogen bonds : bond 0.03462 / 3.89 ( 454) hydrogen bonds : angle 4.28905 / 5.41 ( 1284) metal coordination : bond 0.00273 / 0.14 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.238 Fit side-chains REVERT: A 319 GLN cc_start: 0.7930 (tm-30) cc_final: 0.7306 (mm110) REVERT: A 725 LEU cc_start: 0.9095 (mt) cc_final: 0.8634 (mt) REVERT: A 803 ASP cc_start: 0.4268 (t70) cc_final: 0.3878 (t70) REVERT: A 822 TYR cc_start: 0.8354 (t80) cc_final: 0.7483 (t80) outliers start: 13 outliers final: 4 residues processed: 69 average time/residue: 0.0604 time to fit residues: 6.3890 Evaluate side-chains 56 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 165 ASP Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 791 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 25 optimal weight: 0.0980 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 217 GLN A 645 GLN A 835 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.191596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.174595 restraints weight = 6926.302| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 0.60 r_work: 0.3612 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 7462 Z= 0.276 Angle : 0.744 9.407 10399 Z= 0.385 Chirality : 0.050 0.405 1256 Planarity : 0.005 0.054 1172 Dihedral : 22.648 173.935 1449 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 9.77 % Favored : 87.63 % 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: 0.47 (0.28), residues: 830 helix: 0.94 (0.21), residues: 586 sheet: -0.88 (0.75), residues: 45 loop : -1.07 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 414 TYR 0.010 0.001 TYR A 697 PHE 0.007 0.001 PHE A 52 TRP 0.005 0.001 TRP A 142 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.28 ( 7460) covalent geometry : angle 0.74446 / 0.38 (10399) hydrogen bonds : bond 0.04778 / 5.21 ( 454) hydrogen bonds : angle 4.34280 / 5.51 ( 1284) metal coordination : bond 0.00641 / 0.32 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 0.196 Fit side-chains REVERT: A 56 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.7213 (m-70) REVERT: A 319 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7496 (mm110) REVERT: A 700 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8469 (tt) outliers start: 17 outliers final: 10 residues processed: 76 average time/residue: 0.0641 time to fit residues: 7.3965 Evaluate side-chains 69 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 44 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 645 GLN ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 HIS 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 = 0.193593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.174641 restraints weight = 7025.090| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 0.59 r_work: 0.3541 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7462 Z= 0.141 Angle : 0.593 7.555 10399 Z= 0.311 Chirality : 0.044 0.303 1256 Planarity : 0.005 0.054 1172 Dihedral : 22.690 174.657 1449 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.29 % Allowed : 11.45 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.66 (0.29), residues: 830 helix: 1.09 (0.21), residues: 585 sheet: -0.37 (0.81), residues: 45 loop : -1.19 (0.38), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 584 TYR 0.008 0.001 TYR A 697 PHE 0.006 0.001 PHE A 852 TRP 0.002 0.001 TRP A 96 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 7460) covalent geometry : angle 0.59262 / 0.31 (10399) hydrogen bonds : bond 0.03211 / 3.55 ( 454) hydrogen bonds : angle 4.14628 / 5.20 ( 1284) metal coordination : bond 0.00156 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.245 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 71 average time/residue: 0.0628 time to fit residues: 6.8194 Evaluate side-chains 63 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 28 optimal weight: 0.0370 chunk 59 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN A 645 GLN A 835 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.192715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.172502 restraints weight = 7030.921| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 0.60 r_work: 0.3554 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7462 Z= 0.141 Angle : 0.582 7.132 10399 Z= 0.306 Chirality : 0.043 0.311 1256 Planarity : 0.005 0.055 1172 Dihedral : 22.660 173.376 1449 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.75 % Allowed : 12.21 % Favored : 85.04 % 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: 0.78 (0.29), residues: 830 helix: 1.18 (0.21), residues: 585 sheet: -0.20 (0.83), residues: 45 loop : -1.18 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 414 TYR 0.008 0.001 TYR A 697 PHE 0.005 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7460) covalent geometry : angle 0.58231 / 0.31 (10399) hydrogen bonds : bond 0.03066 / 3.37 ( 454) hydrogen bonds : angle 4.07505 / 5.12 ( 1284) metal coordination : bond 0.00176 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.225 Fit side-chains REVERT: A 822 TYR cc_start: 0.7812 (t80) cc_final: 0.7547 (t80) outliers start: 18 outliers final: 12 residues processed: 70 average time/residue: 0.0665 time to fit residues: 6.9177 Evaluate side-chains 62 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 HIS A 423 HIS A 645 GLN A 835 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.193242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.175761 restraints weight = 7064.269| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 0.55 r_work: 0.3667 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7462 Z= 0.130 Angle : 0.564 6.871 10399 Z= 0.298 Chirality : 0.043 0.306 1256 Planarity : 0.005 0.054 1172 Dihedral : 22.659 174.018 1449 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.29 % Allowed : 13.44 % Favored : 84.27 % 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: 0.86 (0.29), residues: 830 helix: 1.25 (0.21), residues: 586 sheet: 0.06 (0.84), residues: 45 loop : -1.24 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 702 TYR 0.007 0.001 TYR A 697 PHE 0.005 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 ( 7460) covalent geometry : angle 0.56427 / 0.30 (10399) hydrogen bonds : bond 0.02891 / 3.18 ( 454) hydrogen bonds : angle 4.03963 / 5.08 ( 1284) metal coordination : bond 0.00184 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.242 Fit side-chains REVERT: A 56 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.7049 (m-70) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.0667 time to fit residues: 6.7582 Evaluate side-chains 59 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS A 217 GLN ** A 423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 835 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.193584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.176392 restraints weight = 7034.565| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 0.55 r_work: 0.3668 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7462 Z= 0.125 Angle : 0.562 7.652 10399 Z= 0.295 Chirality : 0.043 0.303 1256 Planarity : 0.005 0.053 1172 Dihedral : 22.636 173.672 1449 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.44 % Allowed : 13.59 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.29), residues: 830 helix: 1.29 (0.21), residues: 586 sheet: 0.04 (0.83), residues: 45 loop : -1.21 (0.38), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 584 TYR 0.007 0.001 TYR A 697 PHE 0.005 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.012 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 7460) covalent geometry : angle 0.56199 / 0.30 (10399) hydrogen bonds : bond 0.02833 / 3.09 ( 454) hydrogen bonds : angle 4.02034 / 5.06 ( 1284) metal coordination : bond 0.00181 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.254 Fit side-chains REVERT: A 76 ASP cc_start: 0.7603 (m-30) cc_final: 0.7361 (t0) REVERT: A 701 MET cc_start: 0.8271 (ttm) cc_final: 0.7937 (ttt) REVERT: A 822 TYR cc_start: 0.8083 (t80) cc_final: 0.7692 (t80) outliers start: 16 outliers final: 11 residues processed: 61 average time/residue: 0.0616 time to fit residues: 5.7609 Evaluate side-chains 60 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 49 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 80 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 23 optimal weight: 0.0040 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN A 645 GLN A 835 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.194476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.176857 restraints weight = 7043.221| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 0.56 r_work: 0.3683 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7462 Z= 0.115 Angle : 0.542 7.981 10399 Z= 0.286 Chirality : 0.042 0.298 1256 Planarity : 0.005 0.053 1172 Dihedral : 22.579 173.570 1449 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.29 % Allowed : 13.89 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.29), residues: 830 helix: 1.38 (0.22), residues: 587 sheet: 0.04 (0.82), residues: 45 loop : -1.14 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 584 TYR 0.005 0.001 TYR A 881 PHE 0.005 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 7460) covalent geometry : angle 0.54178 / 0.29 (10399) hydrogen bonds : bond 0.02600 / 2.88 ( 454) hydrogen bonds : angle 3.96092 / 4.98 ( 1284) metal coordination : bond 0.00156 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.235 Fit side-chains REVERT: A 76 ASP cc_start: 0.7457 (m-30) cc_final: 0.7230 (t0) outliers start: 15 outliers final: 9 residues processed: 62 average time/residue: 0.0626 time to fit residues: 5.8764 Evaluate side-chains 60 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 36 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS A 645 GLN A 835 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.193217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.175758 restraints weight = 6926.874| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 0.54 r_work: 0.3662 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7462 Z= 0.129 Angle : 0.558 7.845 10399 Z= 0.293 Chirality : 0.042 0.307 1256 Planarity : 0.005 0.052 1172 Dihedral : 22.584 173.127 1449 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.83 % Allowed : 13.89 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.29), residues: 830 helix: 1.36 (0.22), residues: 587 sheet: 0.06 (0.81), residues: 45 loop : -1.05 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 702 TYR 0.008 0.001 TYR A 697 PHE 0.004 0.001 PHE A 852 TRP 0.002 0.001 TRP A 773 HIS 0.006 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 7460) covalent geometry : angle 0.55805 / 0.29 (10399) hydrogen bonds : bond 0.02832 / 3.11 ( 454) hydrogen bonds : angle 3.97047 / 5.00 ( 1284) metal coordination : bond 0.00188 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.273 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 59 average time/residue: 0.0637 time to fit residues: 5.7850 Evaluate side-chains 59 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 0.0000 chunk 86 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN A 645 GLN A 835 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.193954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 155)---------------| | r_work = 0.3727 r_free = 0.3727 target = 0.150322 restraints weight = 7056.152| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.12 r_work: 0.3399 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7462 Z= 0.118 Angle : 0.546 8.105 10399 Z= 0.287 Chirality : 0.042 0.300 1256 Planarity : 0.005 0.052 1172 Dihedral : 22.575 174.018 1449 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.68 % Allowed : 14.50 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.29), residues: 830 helix: 1.39 (0.22), residues: 585 sheet: 0.14 (0.82), residues: 45 loop : -1.04 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 702 TYR 0.007 0.001 TYR A 697 PHE 0.005 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 7460) covalent geometry : angle 0.54561 / 0.29 (10399) hydrogen bonds : bond 0.02616 / 2.89 ( 454) hydrogen bonds : angle 3.95734 / 4.98 ( 1284) metal coordination : bond 0.00140 / 0.07 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.249 Fit side-chains REVERT: A 822 TYR cc_start: 0.8486 (t80) cc_final: 0.8225 (t80) outliers start: 11 outliers final: 9 residues processed: 55 average time/residue: 0.0625 time to fit residues: 5.2945 Evaluate side-chains 56 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 65 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN A 253 HIS A 645 GLN A 835 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.191602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.172259 restraints weight = 6964.147| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 0.56 r_work: 0.3528 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7462 Z= 0.156 Angle : 0.583 8.251 10399 Z= 0.305 Chirality : 0.044 0.326 1256 Planarity : 0.005 0.052 1172 Dihedral : 22.633 173.680 1449 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.83 % Allowed : 14.96 % Favored : 83.21 % 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: 0.99 (0.29), residues: 830 helix: 1.31 (0.22), residues: 585 sheet: 0.03 (0.80), residues: 45 loop : -1.04 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 702 TYR 0.009 0.001 TYR A 697 PHE 0.004 0.001 PHE A 852 TRP 0.002 0.001 TRP A 96 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 7460) covalent geometry : angle 0.58258 / 0.31 (10399) hydrogen bonds : bond 0.03143 / 3.43 ( 454) hydrogen bonds : angle 4.01423 / 5.07 ( 1284) metal coordination : bond 0.00230 / 0.12 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1731.23 seconds wall clock time: 30 minutes 26.63 seconds (1826.63 seconds total)