Starting phenix.real_space_refine on Tue Aug 4 23:34:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lcz_62997/08_2026/9lcz_62997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lcz_62997/08_2026/9lcz_62997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lcz_62997/08_2026/9lcz_62997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lcz_62997/08_2026/9lcz_62997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lcz_62997/08_2026/9lcz_62997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lcz_62997/08_2026/9lcz_62997.map" } resolution = 2.93 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= 0.001 sd= 0.156 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 58 5.49 5 S 21 5.16 5 C 4407 2.51 5 N 1330 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 7331 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6141 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 46, 'TRANS': 787} Chain: "B" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 589 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 600 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} 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 5824 SG CYS A 842 32.870 51.504 29.524 1.00 59.71 S ATOM 5846 SG CYS A 845 35.256 50.719 25.775 1.00 35.38 S Time building chain proxies: 1.29, per 1000 atoms: 0.18 Number of scatterers: 7331 At special positions: 0 Unit cell: (85.1067, 84.0294, 127.121, 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 58 15.00 O 1514 8.00 N 1330 7.00 C 4407 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: 0.47 Conformation dependent library (CDL) restraints added in 234.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 814 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 842 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 845 " 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 1 sheets defined 74.5% alpha, 3.5% beta 24 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 63 through 81 removed outlier: 3.587A pdb=" N LEU A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 97 through 113 removed outlier: 4.973A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 4.096A 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: 3.956A 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 removed outlier: 3.651A pdb=" N ALA A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) 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 Proline residue: A 213 - end of helix removed outlier: 3.536A pdb=" N HIS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 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 299 Processing helix chain 'A' and resid 302 through 320 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 324 through 332 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 388 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 504 removed outlier: 4.576A pdb=" N HIS A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 524 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 Proline residue: A 553 - end of helix Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 574 through 593 Proline residue: A 587 - end of helix removed outlier: 3.502A pdb=" N HIS A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) 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 removed outlier: 3.502A pdb=" N VAL A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 715 through 734 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.663A pdb=" N THR A 807 " --> pdb=" O PRO A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 843 through 849 removed outlier: 4.036A pdb=" N THR A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 768 removed outlier: 4.441A pdb=" N ALA A 708 " --> pdb=" O GLY A 796 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 831 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL A 862 " --> pdb=" O ALA A 831 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 833 " --> pdb=" O VAL A 862 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.60 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: 1730 1.33 - 1.45: 1578 1.45 - 1.57: 4122 1.57 - 1.69: 114 1.69 - 1.81: 25 Bond restraints: 7569 Sorted by residual: bond pdb=" C3' DG C 10 " pdb=" C2' DG C 10 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DG C 12 " pdb=" C2' DG C 12 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.99e+00 bond pdb=" C3' DA B -8 " pdb=" C2' DA B -8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 bond pdb=" C3' DA C 5 " pdb=" C2' DA C 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.42e+00 bond pdb=" C3' DA B -16 " pdb=" C2' DA B -16 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.99e+00 ... (remaining 7564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 10126 1.60 - 3.20: 352 3.20 - 4.81: 39 4.81 - 6.41: 36 6.41 - 8.01: 11 Bond angle restraints: 10564 Sorted by residual: angle pdb=" O4' DG C -2 " pdb=" C4' DG C -2 " pdb=" C3' DG C -2 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT C 18 " pdb=" C4 DT C 18 " pdb=" O4 DT C 18 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT B -7 " pdb=" C4 DT B -7 " pdb=" O4 DT B -7 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT C 4 " pdb=" C4 DT C 4 " pdb=" O4 DT C 4 " 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 -23 " pdb=" C4 DT B -23 " pdb=" O4 DT B -23 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 10559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 3653 16.66 - 33.33: 476 33.33 - 49.99: 193 49.99 - 66.66: 85 66.66 - 83.32: 8 Dihedral angle restraints: 4415 sinusoidal: 2060 harmonic: 2355 Sorted by residual: dihedral pdb=" CA THR A 107 " pdb=" C THR A 107 " pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta harmonic sigma weight residual -180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.78e+00 dihedral pdb=" CG ARG A 210 " pdb=" CD ARG A 210 " pdb=" NE ARG A 210 " pdb=" CZ ARG A 210 " ideal model delta sinusoidal sigma weight residual 90.00 130.79 -40.79 2 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CA GLU A 292 " pdb=" CB GLU A 292 " pdb=" CG GLU A 292 " pdb=" CD GLU A 292 " ideal model delta sinusoidal sigma weight residual 60.00 109.32 -49.32 3 1.50e+01 4.44e-03 8.76e+00 ... (remaining 4412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1259 0.123 - 0.246: 6 0.246 - 0.369: 1 0.369 - 0.492: 0 0.492 - 0.615: 9 Chirality restraints: 1275 Sorted by residual: chirality pdb=" P DC C -3 " pdb=" OP1 DC C -3 " pdb=" OP2 DC C -3 " pdb=" O5' DC C -3 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" P DC B 1 " pdb=" OP1 DC B 1 " pdb=" OP2 DC B 1 " pdb=" O5' DC B 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" P DC B -13 " pdb=" OP1 DC B -13 " pdb=" OP2 DC B -13 " pdb=" O5' DC B -13 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 8.02e+00 ... (remaining 1272 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 660 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C ALA A 660 " -0.068 2.00e-02 2.50e+03 pdb=" O ALA A 660 " 0.026 2.00e-02 2.50e+03 pdb=" N HIS A 661 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 810 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C ARG A 810 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG A 810 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 811 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 427 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.026 5.00e-02 4.00e+02 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1050 2.76 - 3.29: 6780 3.29 - 3.83: 12732 3.83 - 4.36: 15353 4.36 - 4.90: 25475 Nonbonded interactions: 61390 Sorted by model distance: nonbonded pdb=" O VAL A 329 " pdb=" OG SER A 333 " model vdw 2.223 3.040 nonbonded pdb=" O VAL A 295 " pdb=" OG SER A 299 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG A 702 " pdb=" OG1 THR A 782 " model vdw 2.298 3.120 nonbonded pdb=" O GLY A 800 " pdb=" NZ LYS A 818 " model vdw 2.298 3.120 nonbonded pdb=" O CYS A 845 " pdb=" OG1 THR A 849 " model vdw 2.319 3.040 ... (remaining 61385 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: 1.360 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.970 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.006 0.289 7572 Z= 0.399 Angle : 0.752 8.011 10564 Z= 0.485 Chirality : 0.065 0.615 1275 Planarity : 0.005 0.047 1179 Dihedral : 18.655 83.322 2903 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 832 helix: 0.97 (0.22), residues: 577 sheet: 0.85 (0.71), residues: 47 loop : -0.56 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 678 TYR 0.007 0.001 TYR A 697 PHE 0.003 0.001 PHE A 52 TRP 0.005 0.001 TRP A 773 HIS 0.003 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.38 ( 7569) covalent geometry : angle 0.75204 / 0.48 (10564) hydrogen bonds : bond 0.14568 / 9.94 ( 456) hydrogen bonds : angle 5.99223 / 4.48 ( 1295) metal coordination : bond 0.17246 / 9.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.165 Fit side-chains REVERT: A 702 ARG cc_start: 0.8340 (mtp85) cc_final: 0.8121 (mtp180) REVERT: A 721 THR cc_start: 0.8392 (m) cc_final: 0.8065 (p) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.5692 time to fit residues: 51.1539 Evaluate side-chains 58 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN A 175 GLN A 625 GLN A 766 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.194662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.188261 restraints weight = 5908.857| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 0.46 r_work: 0.3729 rms_B_bonded: 1.00 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work: 0.3466 rms_B_bonded: 3.94 restraints_weight: 0.1250 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7572 Z= 0.169 Angle : 0.622 6.430 10564 Z= 0.345 Chirality : 0.043 0.151 1275 Planarity : 0.005 0.047 1179 Dihedral : 20.835 85.397 1495 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.37 % Allowed : 8.51 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.29), residues: 832 helix: 1.04 (0.22), residues: 582 sheet: 0.70 (0.74), residues: 47 loop : -0.57 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 702 TYR 0.007 0.001 TYR A 697 PHE 0.003 0.001 PHE A 52 TRP 0.006 0.001 TRP A 773 HIS 0.007 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 ( 7569) covalent geometry : angle 0.62171 / 0.35 (10564) hydrogen bonds : bond 0.04407 / 2.97 ( 456) hydrogen bonds : angle 4.35182 / 3.21 ( 1295) metal coordination : bond 0.01969 / 1.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.245 Fit side-chains REVERT: A 721 THR cc_start: 0.8121 (m) cc_final: 0.7870 (p) outliers start: 9 outliers final: 6 residues processed: 65 average time/residue: 0.5296 time to fit residues: 36.6123 Evaluate side-chains 58 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 762 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 80 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 175 GLN A 625 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.195518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.188501 restraints weight = 5867.309| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 0.50 r_work: 0.3731 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7572 Z= 0.133 Angle : 0.562 6.330 10564 Z= 0.311 Chirality : 0.041 0.120 1275 Planarity : 0.004 0.046 1179 Dihedral : 21.244 85.015 1495 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.82 % Allowed : 10.64 % Favored : 87.54 % 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: 832 helix: 1.26 (0.22), residues: 583 sheet: 0.76 (0.75), residues: 47 loop : -0.49 (0.44), residues: 202 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 0.002 0.000 PHE A 52 TRP 0.007 0.001 TRP A 773 HIS 0.003 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 7569) covalent geometry : angle 0.56170 / 0.31 (10564) hydrogen bonds : bond 0.03416 / 2.36 ( 456) hydrogen bonds : angle 4.12417 / 3.03 ( 1295) metal coordination : bond 0.00441 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.188 Fit side-chains REVERT: A 721 THR cc_start: 0.8083 (m) cc_final: 0.7832 (p) outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 0.4701 time to fit residues: 31.5618 Evaluate side-chains 59 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 871 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 1 optimal weight: 0.0370 chunk 70 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 625 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.192210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.183756 restraints weight = 6003.708| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 0.58 r_work: 0.3662 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7572 Z= 0.178 Angle : 0.615 6.490 10564 Z= 0.333 Chirality : 0.043 0.154 1275 Planarity : 0.004 0.045 1179 Dihedral : 21.477 83.265 1495 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.13 % Allowed : 13.53 % Favored : 84.35 % 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: 832 helix: 1.09 (0.21), residues: 585 sheet: 0.52 (0.74), residues: 47 loop : -0.80 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.010 0.001 TYR A 697 PHE 0.003 0.001 PHE A 52 TRP 0.007 0.001 TRP A 773 HIS 0.005 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 ( 7569) covalent geometry : angle 0.61491 / 0.33 (10564) hydrogen bonds : bond 0.04012 / 2.77 ( 456) hydrogen bonds : angle 4.22421 / 3.11 ( 1295) metal coordination : bond 0.00465 / 0.24 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.264 Fit side-chains REVERT: A 702 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7791 (mmm160) REVERT: A 824 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8337 (ttm170) outliers start: 14 outliers final: 7 residues processed: 65 average time/residue: 0.5443 time to fit residues: 37.5695 Evaluate side-chains 64 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 175 GLN A 225 GLN A 659 GLN A 812 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.193541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.184954 restraints weight = 5964.290| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 0.59 r_work: 0.3676 rms_B_bonded: 1.36 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7572 Z= 0.141 Angle : 0.568 6.384 10564 Z= 0.312 Chirality : 0.041 0.128 1275 Planarity : 0.004 0.047 1179 Dihedral : 21.481 82.930 1495 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 13.53 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.97 (0.29), residues: 832 helix: 1.17 (0.22), residues: 585 sheet: 0.53 (0.74), residues: 47 loop : -0.72 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 176 TYR 0.010 0.001 TYR A 697 PHE 0.002 0.000 PHE A 52 TRP 0.008 0.002 TRP A 773 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 7569) covalent geometry : angle 0.56844 / 0.31 (10564) hydrogen bonds : bond 0.03339 / 2.32 ( 456) hydrogen bonds : angle 4.12099 / 3.03 ( 1295) metal coordination : bond 0.00298 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.244 Fit side-chains REVERT: A 60 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7851 (mp) REVERT: A 824 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8251 (ttm170) outliers start: 17 outliers final: 7 residues processed: 67 average time/residue: 0.4971 time to fit residues: 35.5978 Evaluate side-chains 64 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 824 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 175 GLN A 661 HIS A 812 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.193558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.186156 restraints weight = 5938.264| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 0.51 r_work: 0.3700 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7572 Z= 0.141 Angle : 0.561 6.424 10564 Z= 0.309 Chirality : 0.040 0.120 1275 Planarity : 0.004 0.046 1179 Dihedral : 21.459 82.181 1495 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.43 % Allowed : 13.68 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 832 helix: 1.22 (0.22), residues: 584 sheet: 0.55 (0.74), residues: 47 loop : -0.65 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.010 0.001 TYR A 697 PHE 0.002 0.000 PHE A 52 TRP 0.010 0.002 TRP A 773 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 7569) covalent geometry : angle 0.56067 / 0.31 (10564) hydrogen bonds : bond 0.03303 / 2.30 ( 456) hydrogen bonds : angle 4.09798 / 3.01 ( 1295) metal coordination : bond 0.00253 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.269 Fit side-chains REVERT: A 60 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7834 (mp) REVERT: A 824 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8298 (ttm170) outliers start: 16 outliers final: 7 residues processed: 65 average time/residue: 0.5506 time to fit residues: 38.1226 Evaluate side-chains 63 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 175 GLN A 659 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.193825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.186485 restraints weight = 6004.461| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 0.51 r_work: 0.3706 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work: 0.3413 rms_B_bonded: 4.76 restraints_weight: 0.1250 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7572 Z= 0.137 Angle : 0.565 9.211 10564 Z= 0.309 Chirality : 0.040 0.201 1275 Planarity : 0.004 0.048 1179 Dihedral : 21.428 81.608 1495 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.43 % Allowed : 14.89 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.19 (0.29), residues: 832 helix: 1.31 (0.22), residues: 583 sheet: 0.64 (0.74), residues: 47 loop : -0.56 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 143 TYR 0.011 0.001 TYR A 697 PHE 0.002 0.000 PHE A 852 TRP 0.012 0.002 TRP A 773 HIS 0.002 0.000 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 7569) covalent geometry : angle 0.56543 / 0.31 (10564) hydrogen bonds : bond 0.03182 / 2.22 ( 456) hydrogen bonds : angle 4.06545 / 2.99 ( 1295) metal coordination : bond 0.00251 / 0.13 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.254 Fit side-chains REVERT: A 60 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 258 GLU cc_start: 0.7591 (tp30) cc_final: 0.7358 (mp0) REVERT: A 824 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8326 (ttm170) outliers start: 16 outliers final: 7 residues processed: 64 average time/residue: 0.5681 time to fit residues: 38.7048 Evaluate side-chains 61 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.194204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.186084 restraints weight = 6024.135| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 0.55 r_work: 0.3692 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7572 Z= 0.129 Angle : 0.553 6.398 10564 Z= 0.305 Chirality : 0.040 0.133 1275 Planarity : 0.004 0.050 1179 Dihedral : 21.374 81.237 1495 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.98 % Allowed : 15.35 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 832 helix: 1.28 (0.22), residues: 585 sheet: 0.77 (0.75), residues: 47 loop : -0.71 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 143 TYR 0.011 0.001 TYR A 697 PHE 0.001 0.000 PHE A 52 TRP 0.010 0.002 TRP A 773 HIS 0.002 0.000 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 ( 7569) covalent geometry : angle 0.55288 / 0.31 (10564) hydrogen bonds : bond 0.03029 / 2.12 ( 456) hydrogen bonds : angle 4.02750 / 2.96 ( 1295) metal coordination : bond 0.00196 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.227 Fit side-chains REVERT: A 60 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7804 (mp) REVERT: A 786 VAL cc_start: 0.8843 (t) cc_final: 0.8637 (t) REVERT: A 824 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8308 (ttm170) outliers start: 13 outliers final: 7 residues processed: 62 average time/residue: 0.5392 time to fit residues: 35.6150 Evaluate side-chains 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.193283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.184919 restraints weight = 5942.503| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 0.57 r_work: 0.3676 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7572 Z= 0.144 Angle : 0.566 7.137 10564 Z= 0.310 Chirality : 0.040 0.134 1275 Planarity : 0.004 0.051 1179 Dihedral : 21.392 80.741 1495 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.13 % Allowed : 15.35 % Favored : 82.52 % 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: 1.07 (0.29), residues: 832 helix: 1.26 (0.22), residues: 584 sheet: 0.73 (0.75), residues: 47 loop : -0.78 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 143 TYR 0.011 0.001 TYR A 697 PHE 0.002 0.001 PHE A 852 TRP 0.010 0.002 TRP A 142 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 7569) covalent geometry : angle 0.56608 / 0.31 (10564) hydrogen bonds : bond 0.03247 / 2.27 ( 456) hydrogen bonds : angle 4.06673 / 2.99 ( 1295) metal coordination : bond 0.00307 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.256 Fit side-chains REVERT: A 60 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7884 (mp) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.5726 time to fit residues: 34.7877 Evaluate side-chains 58 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 0.0970 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.193638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.185486 restraints weight = 5948.683| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.56 r_work: 0.3691 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7572 Z= 0.136 Angle : 0.570 7.740 10564 Z= 0.312 Chirality : 0.040 0.134 1275 Planarity : 0.004 0.056 1179 Dihedral : 21.376 80.612 1495 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.67 % Allowed : 16.11 % Favored : 82.22 % 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: 1.03 (0.29), residues: 832 helix: 1.23 (0.22), residues: 585 sheet: 0.81 (0.76), residues: 47 loop : -0.83 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 143 TYR 0.011 0.001 TYR A 697 PHE 0.002 0.000 PHE A 852 TRP 0.010 0.002 TRP A 142 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 7569) covalent geometry : angle 0.56952 / 0.31 (10564) hydrogen bonds : bond 0.03108 / 2.18 ( 456) hydrogen bonds : angle 4.04396 / 2.97 ( 1295) metal coordination : bond 0.00232 / 0.12 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.270 Fit side-chains REVERT: A 60 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7770 (mp) REVERT: A 102 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 258 GLU cc_start: 0.7456 (tp30) cc_final: 0.7228 (mp0) outliers start: 11 outliers final: 7 residues processed: 58 average time/residue: 0.5584 time to fit residues: 34.5842 Evaluate side-chains 58 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 659 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.193816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.186659 restraints weight = 5908.935| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 0.50 r_work: 0.3710 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7572 Z= 0.135 Angle : 0.563 7.877 10564 Z= 0.309 Chirality : 0.040 0.133 1275 Planarity : 0.004 0.056 1179 Dihedral : 21.364 80.438 1495 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.98 % Allowed : 16.11 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.30), residues: 832 helix: 1.26 (0.22), residues: 585 sheet: 0.85 (0.76), residues: 47 loop : -0.84 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 143 TYR 0.011 0.001 TYR A 697 PHE 0.003 0.001 PHE A 852 TRP 0.011 0.002 TRP A 142 HIS 0.003 0.000 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 7569) covalent geometry : angle 0.56336 / 0.31 (10564) hydrogen bonds : bond 0.03094 / 2.17 ( 456) hydrogen bonds : angle 4.03870 / 2.97 ( 1295) metal coordination : bond 0.00241 / 0.12 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2225.60 seconds wall clock time: 38 minutes 42.62 seconds (2322.62 seconds total)