Starting phenix.real_space_refine on Thu Jul 2 07:18:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lcz_62997/07_2026/9lcz_62997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lcz_62997/07_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_62997/07_2026/9lcz_62997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lcz_62997/07_2026/9lcz_62997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lcz_62997/07_2026/9lcz_62997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lcz_62997/07_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): 0.00s 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: 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: 1.35, 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: 0.52 Conformation dependent library (CDL) restraints added in 225.4 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: 0.79 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: 1.06 Time building geometry restraints manager: 0.68 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: 10130 1.60 - 3.20: 350 3.20 - 4.81: 37 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: 0.890 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.500 Find NCS groups from input model: 0.020 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:5.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- 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= 0.398 Angle : 0.749 8.011 10564 Z= 0.482 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 0.74877 / 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 : 0.157 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: 0.4431 time to fit residues: 39.8314 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 : 0.168 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.194677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.187618 restraints weight = 5906.707| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 0.50 r_work: 0.3713 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work: 0.3475 rms_B_bonded: 3.71 restraints_weight: 0.1250 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1090 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= 0.166 Angle : 0.625 6.433 10564 Z= 0.345 Chirality : 0.044 0.158 1275 Planarity : 0.005 0.048 1179 Dihedral : 20.953 84.963 1495 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: 0.86 (0.29), residues: 832 helix: 1.02 (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 0.007 0.001 TRP A 773 HIS 0.005 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 ( 7569) covalent geometry : angle 0.62471 / 0.35 (10564) hydrogen bonds : bond 0.04284 / 2.89 ( 456) hydrogen bonds : angle 4.34604 / 3.21 ( 1295) metal coordination : bond 0.02276 / 1.19 ( 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 70 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.174 Fit side-chains REVERT: A 702 ARG cc_start: 0.8525 (mtp85) cc_final: 0.8309 (mmm160) REVERT: A 721 THR cc_start: 0.8098 (m) cc_final: 0.7855 (p) outliers start: 9 outliers final: 6 residues processed: 67 average time/residue: 0.4020 time to fit residues: 28.7609 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 : 0.160 ------------------------------------------------------------------------------- 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: 0.9980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.193915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.186863 restraints weight = 5877.255| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 0.50 r_work: 0.3709 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1304 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= 0.150 Angle : 0.578 6.380 10564 Z= 0.319 Chirality : 0.041 0.129 1275 Planarity : 0.004 0.044 1179 Dihedral : 21.355 84.465 1495 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.82 % Allowed : 11.25 % Favored : 86.93 % 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: 1.14 (0.22), residues: 584 sheet: 0.62 (0.74), residues: 47 loop : -0.62 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.008 0.001 TYR A 697 PHE 0.002 0.001 PHE A 52 TRP 0.007 0.001 TRP A 773 HIS 0.004 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 7569) covalent geometry : angle 0.57762 / 0.32 (10564) hydrogen bonds : bond 0.03746 / 2.59 ( 456) hydrogen bonds : angle 4.19514 / 3.08 ( 1295) metal coordination : bond 0.00421 / 0.22 ( 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 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.184 Fit side-chains REVERT: A 721 THR cc_start: 0.8066 (m) cc_final: 0.7829 (p) outliers start: 12 outliers final: 6 residues processed: 61 average time/residue: 0.4084 time to fit residues: 26.5810 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 : 0.179 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.0570 chunk 70 optimal weight: 5.9990 chunk 74 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 225 GLN A 625 GLN A 659 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.194084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.185721 restraints weight = 6018.887| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.57 r_work: 0.3686 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7572 Z= 0.140 Angle : 0.565 6.391 10564 Z= 0.311 Chirality : 0.041 0.127 1275 Planarity : 0.004 0.047 1179 Dihedral : 21.433 83.636 1495 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.13 % Allowed : 12.92 % Favored : 84.95 % 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: 1.21 (0.22), residues: 584 sheet: 0.63 (0.74), residues: 47 loop : -0.65 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 176 TYR 0.008 0.001 TYR A 697 PHE 0.002 0.000 PHE A 52 TRP 0.009 0.001 TRP A 773 HIS 0.004 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 7569) covalent geometry : angle 0.56477 / 0.31 (10564) hydrogen bonds : bond 0.03358 / 2.33 ( 456) hydrogen bonds : angle 4.10145 / 3.02 ( 1295) metal coordination : bond 0.00261 / 0.13 ( 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 70 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.253 Fit side-chains REVERT: A 824 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8361 (ttm170) outliers start: 14 outliers final: 5 residues processed: 63 average time/residue: 0.5070 time to fit residues: 33.9129 Evaluate side-chains 60 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.180 ------------------------------------------------------------------------------- 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 824 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.0370 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 175 GLN A 625 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 = 0.4050 r_free = 0.4050 target = 0.193770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.185531 restraints weight = 5955.311| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 0.57 r_work: 0.3686 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1520 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= 0.140 Angle : 0.556 6.383 10564 Z= 0.308 Chirality : 0.040 0.135 1275 Planarity : 0.004 0.047 1179 Dihedral : 21.457 82.789 1495 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.74 % Allowed : 12.77 % Favored : 84.50 % 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: 1.08 (0.29), residues: 832 helix: 1.25 (0.22), residues: 584 sheet: 0.59 (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 176 TYR 0.010 0.001 TYR A 697 PHE 0.002 0.000 PHE A 52 TRP 0.009 0.002 TRP A 773 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 ( 7569) covalent geometry : angle 0.55604 / 0.31 (10564) hydrogen bonds : bond 0.03319 / 2.30 ( 456) hydrogen bonds : angle 4.08938 / 3.00 ( 1295) metal coordination : bond 0.00285 / 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 75 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.164 Fit side-chains REVERT: A 702 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7787 (mmm160) REVERT: A 824 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8234 (ttm170) outliers start: 18 outliers final: 9 residues processed: 68 average time/residue: 0.4334 time to fit residues: 31.4386 Evaluate side-chains 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 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 762 SER Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 878 VAL 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: 0.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN A 625 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 = 0.4037 r_free = 0.4037 target = 0.192704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.184727 restraints weight = 5946.913| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 0.54 r_work: 0.3679 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work: 0.3379 rms_B_bonded: 4.93 restraints_weight: 0.1250 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1546 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= 0.157 Angle : 0.574 6.455 10564 Z= 0.315 Chirality : 0.041 0.129 1275 Planarity : 0.004 0.046 1179 Dihedral : 21.513 81.780 1495 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.13 % Allowed : 14.13 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 832 helix: 1.10 (0.21), residues: 586 sheet: 0.55 (0.74), residues: 47 loop : -0.86 (0.44), residues: 199 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 0.001 PHE A 52 TRP 0.014 0.002 TRP A 773 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 7569) covalent geometry : angle 0.57392 / 0.32 (10564) hydrogen bonds : bond 0.03513 / 2.44 ( 456) hydrogen bonds : angle 4.14109 / 3.04 ( 1295) metal coordination : bond 0.00392 / 0.20 ( 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 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.247 Fit side-chains REVERT: A 824 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8340 (ttm170) outliers start: 14 outliers final: 7 residues processed: 62 average time/residue: 0.4478 time to fit residues: 29.5788 Evaluate side-chains 59 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 23 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN A 659 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.193615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.185164 restraints weight = 6008.384| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 0.57 r_work: 0.3681 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1638 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= 0.138 Angle : 0.556 6.395 10564 Z= 0.308 Chirality : 0.040 0.131 1275 Planarity : 0.004 0.049 1179 Dihedral : 21.476 81.404 1495 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.28 % Allowed : 15.20 % 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: 0.91 (0.29), residues: 832 helix: 1.14 (0.22), residues: 587 sheet: 0.64 (0.74), residues: 47 loop : -0.85 (0.45), residues: 198 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 0.001 0.000 PHE A 852 TRP 0.009 0.002 TRP A 773 HIS 0.003 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 ( 7569) covalent geometry : angle 0.55649 / 0.31 (10564) hydrogen bonds : bond 0.03200 / 2.24 ( 456) hydrogen bonds : angle 4.07469 / 2.99 ( 1295) metal coordination : bond 0.00274 / 0.14 ( 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: 15 poor density : 55 time to evaluate : 0.252 Fit side-chains REVERT: A 824 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8313 (ttm170) outliers start: 15 outliers final: 6 residues processed: 64 average time/residue: 0.4592 time to fit residues: 31.2896 Evaluate side-chains 60 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 221 LEU Chi-restraints excluded: chain A residue 551 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.193591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.185471 restraints weight = 6024.090| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 0.55 r_work: 0.3688 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7572 Z= 0.139 Angle : 0.556 6.421 10564 Z= 0.308 Chirality : 0.040 0.135 1275 Planarity : 0.004 0.057 1179 Dihedral : 21.457 80.973 1495 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.13 % Allowed : 15.05 % Favored : 82.83 % 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: 1.18 (0.22), residues: 586 sheet: 0.72 (0.75), residues: 47 loop : -0.81 (0.45), residues: 199 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 0.001 0.000 PHE A 52 TRP 0.008 0.002 TRP A 142 HIS 0.002 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 ( 7569) covalent geometry : angle 0.55621 / 0.31 (10564) hydrogen bonds : bond 0.03203 / 2.23 ( 456) hydrogen bonds : angle 4.06869 / 2.99 ( 1295) metal coordination : bond 0.00263 / 0.13 ( 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 68 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.232 Fit side-chains REVERT: A 824 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8299 (ttm170) outliers start: 14 outliers final: 8 residues processed: 62 average time/residue: 0.4692 time to fit residues: 30.9936 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 : 0.176 ------------------------------------------------------------------------------- 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 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 762 SER 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: 2.9990 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4036 r_free = 0.4036 target = 0.192376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.183938 restraints weight = 5936.463| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 0.57 r_work: 0.3660 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7572 Z= 0.162 Angle : 0.587 7.281 10564 Z= 0.321 Chirality : 0.041 0.133 1275 Planarity : 0.005 0.060 1179 Dihedral : 21.495 80.483 1495 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.98 % Allowed : 15.65 % Favored : 82.37 % 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: 0.79 (0.29), residues: 832 helix: 1.08 (0.21), residues: 585 sheet: 0.63 (0.75), residues: 47 loop : -1.01 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 143 TYR 0.011 0.001 TYR A 697 PHE 0.002 0.001 PHE A 852 TRP 0.011 0.002 TRP A 142 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 7569) covalent geometry : angle 0.58749 / 0.32 (10564) hydrogen bonds : bond 0.03526 / 2.46 ( 456) hydrogen bonds : angle 4.14916 / 3.05 ( 1295) metal coordination : bond 0.00388 / 0.20 ( 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 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.221 Fit side-chains REVERT: A 60 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7827 (mp) REVERT: A 824 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8268 (ttm170) outliers start: 13 outliers final: 9 residues processed: 61 average time/residue: 0.4372 time to fit residues: 28.4092 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 : 0.170 ------------------------------------------------------------------------------- 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 591 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 23 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 chunk 29 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.193656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.186321 restraints weight = 5950.008| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 0.51 r_work: 0.3709 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1735 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= 0.132 Angle : 0.558 7.820 10564 Z= 0.309 Chirality : 0.040 0.135 1275 Planarity : 0.004 0.056 1179 Dihedral : 21.444 80.587 1495 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.98 % Allowed : 15.65 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 832 helix: 1.11 (0.21), residues: 587 sheet: 0.75 (0.76), residues: 47 loop : -0.99 (0.45), residues: 198 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 0.001 0.000 PHE A 52 TRP 0.012 0.002 TRP A 142 HIS 0.003 0.001 HIS A 470 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 7569) covalent geometry : angle 0.55805 / 0.31 (10564) hydrogen bonds : bond 0.03064 / 2.15 ( 456) hydrogen bonds : angle 4.05424 / 2.98 ( 1295) metal coordination : bond 0.00185 / 0.09 ( 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 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.238 Fit side-chains REVERT: A 60 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7717 (mt) REVERT: A 102 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7562 (mt) outliers start: 13 outliers final: 7 residues processed: 60 average time/residue: 0.5084 time to fit residues: 32.5508 Evaluate side-chains 59 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 591 GLN Chi-restraints excluded: chain A residue 745 VAL 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: 0.9980 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 GLN A 659 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.192714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.184299 restraints weight = 5919.228| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 0.57 r_work: 0.3671 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1761 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= 0.154 Angle : 0.579 7.893 10564 Z= 0.318 Chirality : 0.041 0.132 1275 Planarity : 0.005 0.052 1179 Dihedral : 21.469 80.288 1495 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.98 % Allowed : 15.96 % Favored : 82.07 % 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: 1.15 (0.22), residues: 585 sheet: 0.71 (0.75), residues: 47 loop : -1.00 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 143 TYR 0.011 0.001 TYR A 697 PHE 0.004 0.001 PHE A 852 TRP 0.013 0.002 TRP A 142 HIS 0.003 0.001 HIS A 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 7569) covalent geometry : angle 0.57851 / 0.32 (10564) hydrogen bonds : bond 0.03389 / 2.37 ( 456) hydrogen bonds : angle 4.11839 / 3.03 ( 1295) metal coordination : bond 0.00338 / 0.17 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1869.01 seconds wall clock time: 32 minutes 33.64 seconds (1953.64 seconds total)