Starting phenix.real_space_refine on Thu Jul 2 03:27:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnz_26024/07_2026/7tnz_26024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnz_26024/07_2026/7tnz_26024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tnz_26024/07_2026/7tnz_26024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnz_26024/07_2026/7tnz_26024.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnz_26024/07_2026/7tnz_26024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnz_26024/07_2026/7tnz_26024.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tnz_26024/07_2026/7tnz_26024.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnz_26024/07_2026/7tnz_26024.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 24 5.49 5 S 33 5.16 5 C 3724 2.51 5 N 1026 2.21 5 O 1178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 5986 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5472 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 651} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 260 Classifications: {'RNA': 12} Modifications used: {'rna3p': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "C" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 253 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7} Link IDs: {'rna3p': 11} 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 4548 SG CYS A 810 61.041 58.191 17.936 1.00 89.32 S ATOM 4987 SG CYS A 864 59.505 57.429 14.128 1.00 94.72 S ATOM 5026 SG CYS A 869 62.267 55.718 15.502 1.00 96.38 S Time building chain proxies: 1.20, per 1000 atoms: 0.20 Number of scatterers: 5986 At special positions: 0 Unit cell: (96.12, 85.44, 82.236, 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 33 16.00 P 24 15.00 O 1178 8.00 N 1026 7.00 C 3724 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: 0.42 Conformation dependent library (CDL) restraints added in 350.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 49.4% alpha, 7.5% beta 11 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 244 through 250 removed outlier: 3.838A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 283 removed outlier: 3.799A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 271 " --> pdb=" O GLY A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 314 removed outlier: 3.861A pdb=" N GLN A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.988A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.961A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 377 Processing helix chain 'A' and resid 381 through 397 removed outlier: 4.450A pdb=" N GLY A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 435 removed outlier: 4.078A pdb=" N ASP A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 4.129A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 490 removed outlier: 3.863A pdb=" N ILE A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.765A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 603 removed outlier: 3.938A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'A' and resid 674 through 684 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 744 through 770 removed outlier: 4.144A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 759 " --> pdb=" O MET A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing helix chain 'A' and resid 836 through 840 removed outlier: 3.812A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 409 removed outlier: 7.910A pdb=" N THR A 409 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE A 262 " --> pdb=" O THR A 409 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.787A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU A 632 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 807 through 809 Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 845 Processing sheet with id=AA7, first strand: chain 'A' and resid 874 through 878 Processing sheet with id=AA8, first strand: chain 'A' and resid 893 through 895 258 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.58 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: 1657 1.33 - 1.45: 1010 1.45 - 1.57: 3395 1.57 - 1.69: 45 1.69 - 1.82: 47 Bond restraints: 6154 Sorted by residual: bond pdb=" O3' 5GP B 1 " pdb=" P G B 2 " ideal model delta sigma weight residual 1.607 1.718 -0.111 1.50e-02 4.44e+03 5.48e+01 bond pdb=" N VAL A 414 " pdb=" CA VAL A 414 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.06e-02 8.90e+03 1.04e+01 bond pdb=" N ILE A 704 " pdb=" CA ILE A 704 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" CA ALA A 700 " pdb=" CB ALA A 700 " ideal model delta sigma weight residual 1.530 1.481 0.049 1.56e-02 4.11e+03 9.69e+00 bond pdb=" CA SER A 437 " pdb=" CB SER A 437 " ideal model delta sigma weight residual 1.537 1.494 0.043 1.38e-02 5.25e+03 9.58e+00 ... (remaining 6149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 6810 1.58 - 3.16: 1526 3.16 - 4.74: 66 4.74 - 6.32: 9 6.32 - 7.90: 3 Bond angle restraints: 8414 Sorted by residual: angle pdb=" C3' 5GP B 1 " pdb=" O3' 5GP B 1 " pdb=" P G B 2 " ideal model delta sigma weight residual 120.20 114.04 6.16 1.50e+00 4.44e-01 1.69e+01 angle pdb=" N SER A 743 " pdb=" CA SER A 743 " pdb=" C SER A 743 " ideal model delta sigma weight residual 114.04 109.57 4.47 1.24e+00 6.50e-01 1.30e+01 angle pdb=" C THR A 347 " pdb=" N PRO A 348 " pdb=" CA PRO A 348 " ideal model delta sigma weight residual 119.24 122.81 -3.57 1.04e+00 9.25e-01 1.18e+01 angle pdb=" N ALA A 684 " pdb=" CA ALA A 684 " pdb=" C ALA A 684 " ideal model delta sigma weight residual 112.93 109.14 3.79 1.12e+00 7.97e-01 1.14e+01 angle pdb=" O ILE A 499 " pdb=" C ILE A 499 " pdb=" N GLN A 500 " ideal model delta sigma weight residual 121.85 124.37 -2.52 7.60e-01 1.73e+00 1.10e+01 ... (remaining 8409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 3500 21.82 - 43.63: 174 43.63 - 65.45: 18 65.45 - 87.26: 7 87.26 - 109.08: 3 Dihedral angle restraints: 3702 sinusoidal: 1707 harmonic: 1995 Sorted by residual: dihedral pdb=" C2' 5GP B 1 " pdb=" C1' 5GP B 1 " pdb=" N9 5GP B 1 " pdb=" C4 5GP B 1 " ideal model delta sinusoidal sigma weight residual 175.00 65.92 109.08 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" CA ARG A 859 " pdb=" C ARG A 859 " pdb=" N ALA A 860 " pdb=" CA ALA A 860 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CB GLU A 621 " pdb=" CG GLU A 621 " pdb=" CD GLU A 621 " pdb=" OE1 GLU A 621 " ideal model delta sinusoidal sigma weight residual 0.00 87.94 -87.94 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 3699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 400 0.041 - 0.082: 294 0.082 - 0.123: 207 0.123 - 0.164: 48 0.164 - 0.204: 5 Chirality restraints: 954 Sorted by residual: chirality pdb=" C3' 5GP B 1 " pdb=" C2' 5GP B 1 " pdb=" C4' 5GP B 1 " pdb=" O3' 5GP B 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.68 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA PHE A 856 " pdb=" N PHE A 856 " pdb=" C PHE A 856 " pdb=" CB PHE A 856 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA ILE A 360 " pdb=" N ILE A 360 " pdb=" C ILE A 360 " pdb=" CB ILE A 360 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 951 not shown) Planarity restraints: 991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C B 11 " -0.015 2.00e-02 2.50e+03 1.30e-02 3.81e+00 pdb=" N1 C B 11 " 0.029 2.00e-02 2.50e+03 pdb=" C2 C B 11 " -0.005 2.00e-02 2.50e+03 pdb=" O2 C B 11 " -0.009 2.00e-02 2.50e+03 pdb=" N3 C B 11 " 0.014 2.00e-02 2.50e+03 pdb=" C4 C B 11 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C B 11 " -0.008 2.00e-02 2.50e+03 pdb=" C5 C B 11 " -0.009 2.00e-02 2.50e+03 pdb=" C6 C B 11 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 9 " -0.015 2.00e-02 2.50e+03 9.11e-03 2.49e+00 pdb=" N9 G B 9 " 0.019 2.00e-02 2.50e+03 pdb=" C8 G B 9 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 9 " -0.009 2.00e-02 2.50e+03 pdb=" C5 G B 9 " 0.008 2.00e-02 2.50e+03 pdb=" C6 G B 9 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G B 9 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G B 9 " -0.011 2.00e-02 2.50e+03 pdb=" C2 G B 9 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G B 9 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G B 9 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G B 9 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 527 " -0.007 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C ASP A 527 " 0.026 2.00e-02 2.50e+03 pdb=" O ASP A 527 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 528 " -0.009 2.00e-02 2.50e+03 ... (remaining 988 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 879 2.79 - 3.32: 6134 3.32 - 3.84: 9707 3.84 - 4.37: 11552 4.37 - 4.90: 19112 Nonbonded interactions: 47384 Sorted by model distance: nonbonded pdb=" O ALA A 558 " pdb=" ND2 ASN A 608 " model vdw 2.258 3.120 nonbonded pdb=" O THR A 697 " pdb=" OG1 THR A 697 " model vdw 2.272 3.040 nonbonded pdb=" O LYS A 379 " pdb=" OP1 G B 5 " model vdw 2.286 3.040 nonbonded pdb=" N ASP A 701 " pdb=" OD1 ASP A 701 " model vdw 2.311 3.120 nonbonded pdb=" O CYS A 374 " pdb=" OG1 THR A 377 " model vdw 2.342 3.040 ... (remaining 47379 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 group one per residue 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.230 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.012 0.275 6157 Z= 0.833 Angle : 1.183 7.897 8414 Z= 0.858 Chirality : 0.068 0.204 954 Planarity : 0.004 0.032 991 Dihedral : 13.236 109.078 2406 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.80 % Favored : 92.75 % Rotamer: Outliers : 0.66 % Allowed : 3.45 % Favored : 95.89 % 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: -2.66 (0.29), residues: 676 helix: 0.17 (0.27), residues: 317 sheet: -4.32 (0.44), residues: 70 loop : -3.39 (0.28), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 502 TYR 0.017 0.003 TYR A 566 PHE 0.024 0.003 PHE A 856 TRP 0.011 0.003 TRP A 771 HIS 0.009 0.002 HIS A 444 Details of bonding type rmsd/Z covalent geometry : bond 0.01099 / 0.81 ( 6154) covalent geometry : angle 1.18329 / 0.86 ( 8414) hydrogen bonds : bond 0.09624 / 6.77 ( 286) hydrogen bonds : angle 4.62379 / 3.13 ( 806) metal coordination : bond 0.24247 / 12.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 248 LEU cc_start: 0.8598 (tp) cc_final: 0.8385 (tp) REVERT: A 369 MET cc_start: 0.7175 (mtt) cc_final: 0.6896 (mtp) REVERT: A 459 PHE cc_start: 0.8451 (m-80) cc_final: 0.8059 (m-10) REVERT: A 481 ASP cc_start: 0.7992 (m-30) cc_final: 0.7644 (m-30) REVERT: A 523 PHE cc_start: 0.8105 (t80) cc_final: 0.7344 (t80) REVERT: A 550 ASP cc_start: 0.8932 (m-30) cc_final: 0.8731 (m-30) REVERT: A 562 ASP cc_start: 0.7456 (p0) cc_final: 0.6938 (p0) REVERT: A 603 ASP cc_start: 0.8497 (t0) cc_final: 0.8012 (t0) REVERT: A 620 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8377 (mt-10) REVERT: A 625 ASN cc_start: 0.8627 (t0) cc_final: 0.8307 (t0) REVERT: A 759 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7737 (mttt) REVERT: A 845 ARG cc_start: 0.7639 (mtt-85) cc_final: 0.7155 (mtt90) outliers start: 4 outliers final: 1 residues processed: 141 average time/residue: 0.0916 time to fit residues: 16.5206 Evaluate side-chains 97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 706 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 299 GLN A 341 ASN A 354 ASN A 678 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.155696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.111582 restraints weight = 7475.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115694 restraints weight = 4725.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118174 restraints weight = 3676.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119723 restraints weight = 3192.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120543 restraints weight = 2937.810| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6157 Z= 0.123 Angle : 0.538 7.801 8414 Z= 0.266 Chirality : 0.039 0.164 954 Planarity : 0.004 0.040 991 Dihedral : 7.283 111.637 1011 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.21 % Favored : 93.64 % Rotamer: Outliers : 1.81 % Allowed : 11.02 % Favored : 87.17 % 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: -1.55 (0.32), residues: 676 helix: 1.13 (0.29), residues: 324 sheet: -4.00 (0.44), residues: 86 loop : -2.78 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.010 0.001 TYR A 879 PHE 0.021 0.001 PHE A 616 TRP 0.008 0.001 TRP A 873 HIS 0.010 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 6154) covalent geometry : angle 0.53790 / 0.27 ( 8414) hydrogen bonds : bond 0.03312 / 2.24 ( 286) hydrogen bonds : angle 3.64307 / 2.45 ( 806) metal coordination : bond 0.00443 / 0.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.187 Fit side-chains REVERT: A 272 PHE cc_start: 0.8219 (t80) cc_final: 0.7942 (t80) REVERT: A 387 MET cc_start: 0.8733 (mmm) cc_final: 0.8494 (mmm) REVERT: A 523 PHE cc_start: 0.8016 (t80) cc_final: 0.7486 (t80) REVERT: A 547 LYS cc_start: 0.8412 (tppt) cc_final: 0.7974 (mmtm) REVERT: A 550 ASP cc_start: 0.8649 (m-30) cc_final: 0.8377 (m-30) REVERT: A 603 ASP cc_start: 0.8826 (t0) cc_final: 0.8260 (t0) REVERT: A 625 ASN cc_start: 0.8630 (t0) cc_final: 0.8347 (t0) REVERT: A 760 MET cc_start: 0.8676 (ttp) cc_final: 0.8438 (ttm) REVERT: A 845 ARG cc_start: 0.7399 (mtt-85) cc_final: 0.6856 (mtt90) outliers start: 11 outliers final: 6 residues processed: 105 average time/residue: 0.0810 time to fit residues: 11.0454 Evaluate side-chains 89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 0.0570 chunk 3 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 557 HIS A 726 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.106777 restraints weight = 7479.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.110688 restraints weight = 4729.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.113168 restraints weight = 3692.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114253 restraints weight = 3194.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115304 restraints weight = 2974.854| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6157 Z= 0.173 Angle : 0.573 7.771 8414 Z= 0.286 Chirality : 0.040 0.192 954 Planarity : 0.004 0.045 991 Dihedral : 7.067 110.164 1011 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.95 % Favored : 92.90 % Rotamer: Outliers : 2.80 % Allowed : 12.34 % Favored : 84.87 % 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: -1.24 (0.32), residues: 676 helix: 1.35 (0.29), residues: 323 sheet: -4.02 (0.45), residues: 85 loop : -2.49 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 730 TYR 0.011 0.001 TYR A 717 PHE 0.019 0.002 PHE A 616 TRP 0.011 0.001 TRP A 873 HIS 0.007 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 ( 6154) covalent geometry : angle 0.57326 / 0.29 ( 8414) hydrogen bonds : bond 0.03644 / 2.46 ( 286) hydrogen bonds : angle 3.67090 / 2.48 ( 806) metal coordination : bond 0.00287 / 0.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.173 Fit side-chains REVERT: A 523 PHE cc_start: 0.8111 (t80) cc_final: 0.7683 (t80) REVERT: A 583 GLU cc_start: 0.8484 (mp0) cc_final: 0.8235 (mp0) REVERT: A 603 ASP cc_start: 0.8923 (t0) cc_final: 0.8455 (t0) REVERT: A 625 ASN cc_start: 0.8540 (t0) cc_final: 0.8265 (t0) REVERT: A 695 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8548 (mt) REVERT: A 760 MET cc_start: 0.8763 (ttp) cc_final: 0.8435 (ttm) REVERT: A 845 ARG cc_start: 0.7500 (mtt-85) cc_final: 0.6908 (mtt90) outliers start: 17 outliers final: 10 residues processed: 107 average time/residue: 0.0719 time to fit residues: 10.4117 Evaluate side-chains 97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 42 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.155012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114643 restraints weight = 7733.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116579 restraints weight = 5999.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118213 restraints weight = 4908.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.118537 restraints weight = 4338.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118744 restraints weight = 4132.417| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6157 Z= 0.191 Angle : 0.573 9.388 8414 Z= 0.287 Chirality : 0.041 0.149 954 Planarity : 0.004 0.047 991 Dihedral : 7.068 110.337 1011 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.40 % Favored : 92.46 % Rotamer: Outliers : 3.45 % Allowed : 15.95 % Favored : 80.59 % 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: -1.23 (0.33), residues: 676 helix: 1.31 (0.28), residues: 326 sheet: -4.09 (0.45), residues: 85 loop : -2.44 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 730 TYR 0.010 0.001 TYR A 390 PHE 0.029 0.002 PHE A 616 TRP 0.012 0.002 TRP A 873 HIS 0.008 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 6154) covalent geometry : angle 0.57284 / 0.29 ( 8414) hydrogen bonds : bond 0.03765 / 2.54 ( 286) hydrogen bonds : angle 3.72881 / 2.51 ( 806) metal coordination : bond 0.00319 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.240 Fit side-chains REVERT: A 435 ASP cc_start: 0.8595 (t0) cc_final: 0.8245 (t0) REVERT: A 458 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7886 (mmmt) REVERT: A 523 PHE cc_start: 0.7862 (t80) cc_final: 0.7543 (t80) REVERT: A 550 ASP cc_start: 0.8699 (m-30) cc_final: 0.8401 (m-30) REVERT: A 583 GLU cc_start: 0.8344 (mp0) cc_final: 0.8083 (mp0) REVERT: A 603 ASP cc_start: 0.8804 (t0) cc_final: 0.8493 (t0) REVERT: A 755 MET cc_start: 0.8454 (tpp) cc_final: 0.8229 (mmt) REVERT: A 760 MET cc_start: 0.8814 (ttp) cc_final: 0.8408 (ttm) REVERT: A 845 ARG cc_start: 0.7590 (mtt-85) cc_final: 0.7112 (mtt90) outliers start: 21 outliers final: 14 residues processed: 110 average time/residue: 0.0666 time to fit residues: 9.9446 Evaluate side-chains 100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 32 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.159690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117252 restraints weight = 7861.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121393 restraints weight = 5055.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123981 restraints weight = 3960.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125519 restraints weight = 3455.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125956 restraints weight = 3185.567| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6157 Z= 0.120 Angle : 0.528 7.676 8414 Z= 0.262 Chirality : 0.039 0.170 954 Planarity : 0.004 0.050 991 Dihedral : 6.911 109.942 1011 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.80 % Favored : 93.05 % Rotamer: Outliers : 3.45 % Allowed : 16.45 % Favored : 80.10 % 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: -0.89 (0.33), residues: 676 helix: 1.63 (0.29), residues: 323 sheet: -4.05 (0.48), residues: 79 loop : -2.30 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 664 TYR 0.011 0.001 TYR A 390 PHE 0.037 0.002 PHE A 853 TRP 0.012 0.002 TRP A 873 HIS 0.009 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 6154) covalent geometry : angle 0.52789 / 0.26 ( 8414) hydrogen bonds : bond 0.03261 / 2.22 ( 286) hydrogen bonds : angle 3.59779 / 2.42 ( 806) metal coordination : bond 0.00127 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.220 Fit side-chains REVERT: A 435 ASP cc_start: 0.8577 (t0) cc_final: 0.8183 (t0) REVERT: A 458 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7956 (mmmt) REVERT: A 523 PHE cc_start: 0.7894 (t80) cc_final: 0.7511 (t80) REVERT: A 550 ASP cc_start: 0.8724 (m-30) cc_final: 0.8401 (m-30) REVERT: A 583 GLU cc_start: 0.8370 (mp0) cc_final: 0.8087 (mp0) REVERT: A 603 ASP cc_start: 0.8899 (t0) cc_final: 0.8534 (t0) REVERT: A 695 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8721 (mt) REVERT: A 755 MET cc_start: 0.8395 (tpp) cc_final: 0.8167 (mmt) REVERT: A 760 MET cc_start: 0.8802 (ttp) cc_final: 0.8425 (ttm) REVERT: A 845 ARG cc_start: 0.7613 (mtt-85) cc_final: 0.7055 (mtt90) REVERT: A 895 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7420 (mm-30) outliers start: 21 outliers final: 11 residues processed: 102 average time/residue: 0.0738 time to fit residues: 10.2618 Evaluate side-chains 98 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.160041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.118525 restraints weight = 7629.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122367 restraints weight = 5158.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124782 restraints weight = 4137.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126070 restraints weight = 3638.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.126070 restraints weight = 3371.486| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6157 Z= 0.108 Angle : 0.507 7.722 8414 Z= 0.250 Chirality : 0.039 0.166 954 Planarity : 0.004 0.054 991 Dihedral : 6.824 108.287 1011 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.95 % Allowed : 16.94 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.33), residues: 676 helix: 1.77 (0.29), residues: 326 sheet: -3.94 (0.49), residues: 79 loop : -2.33 (0.35), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 664 TYR 0.011 0.001 TYR A 390 PHE 0.034 0.001 PHE A 616 TRP 0.013 0.002 TRP A 646 HIS 0.009 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 6154) covalent geometry : angle 0.50738 / 0.25 ( 8414) hydrogen bonds : bond 0.03110 / 2.11 ( 286) hydrogen bonds : angle 3.53308 / 2.38 ( 806) metal coordination : bond 0.00117 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.205 Fit side-chains REVERT: A 435 ASP cc_start: 0.8528 (t0) cc_final: 0.8309 (t0) REVERT: A 458 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7882 (mmmt) REVERT: A 523 PHE cc_start: 0.7793 (t80) cc_final: 0.7529 (t80) REVERT: A 550 ASP cc_start: 0.8618 (m-30) cc_final: 0.8297 (m-30) REVERT: A 603 ASP cc_start: 0.8804 (t0) cc_final: 0.8537 (t0) REVERT: A 695 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8597 (mt) REVERT: A 706 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6602 (mp) REVERT: A 755 MET cc_start: 0.8432 (tpp) cc_final: 0.8164 (mmt) REVERT: A 760 MET cc_start: 0.8768 (ttp) cc_final: 0.8411 (ttm) REVERT: A 845 ARG cc_start: 0.7602 (mtt-85) cc_final: 0.7065 (mtt90) outliers start: 24 outliers final: 15 residues processed: 101 average time/residue: 0.0693 time to fit residues: 9.5603 Evaluate side-chains 96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.158047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116263 restraints weight = 7678.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120076 restraints weight = 5186.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122454 restraints weight = 4167.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123696 restraints weight = 3666.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124151 restraints weight = 3411.853| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6157 Z= 0.140 Angle : 0.524 8.992 8414 Z= 0.260 Chirality : 0.039 0.155 954 Planarity : 0.004 0.055 991 Dihedral : 6.857 107.927 1011 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.11 % Allowed : 18.59 % Favored : 77.30 % 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: -0.70 (0.34), residues: 676 helix: 1.78 (0.29), residues: 326 sheet: -3.59 (0.52), residues: 86 loop : -2.31 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 730 TYR 0.011 0.001 TYR A 390 PHE 0.037 0.002 PHE A 616 TRP 0.016 0.002 TRP A 646 HIS 0.007 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 6154) covalent geometry : angle 0.52394 / 0.26 ( 8414) hydrogen bonds : bond 0.03340 / 2.25 ( 286) hydrogen bonds : angle 3.55426 / 2.40 ( 806) metal coordination : bond 0.00201 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.238 Fit side-chains REVERT: A 435 ASP cc_start: 0.8583 (t0) cc_final: 0.8332 (t0) REVERT: A 458 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7864 (mmmt) REVERT: A 523 PHE cc_start: 0.7883 (t80) cc_final: 0.7612 (t80) REVERT: A 550 ASP cc_start: 0.8639 (m-30) cc_final: 0.8319 (m-30) REVERT: A 603 ASP cc_start: 0.8823 (t0) cc_final: 0.8548 (t0) REVERT: A 625 ASN cc_start: 0.8284 (t0) cc_final: 0.7985 (t0) REVERT: A 706 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6654 (mp) REVERT: A 755 MET cc_start: 0.8408 (tpp) cc_final: 0.8152 (mmt) REVERT: A 760 MET cc_start: 0.8767 (ttp) cc_final: 0.8398 (ttm) REVERT: A 845 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.7094 (mtt90) outliers start: 25 outliers final: 16 residues processed: 100 average time/residue: 0.0690 time to fit residues: 9.4083 Evaluate side-chains 94 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 641 ASP Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 664 ARG Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117154 restraints weight = 7673.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121053 restraints weight = 5183.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.123131 restraints weight = 4138.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124794 restraints weight = 3665.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.125813 restraints weight = 3381.083| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6157 Z= 0.122 Angle : 0.525 8.915 8414 Z= 0.259 Chirality : 0.039 0.198 954 Planarity : 0.004 0.057 991 Dihedral : 6.835 108.837 1011 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.29 % Allowed : 19.24 % Favored : 77.47 % 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: -0.59 (0.34), residues: 676 helix: 1.84 (0.29), residues: 326 sheet: -3.89 (0.51), residues: 73 loop : -2.19 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 730 TYR 0.011 0.001 TYR A 390 PHE 0.023 0.001 PHE A 853 TRP 0.012 0.002 TRP A 873 HIS 0.007 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 6154) covalent geometry : angle 0.52514 / 0.26 ( 8414) hydrogen bonds : bond 0.03259 / 2.18 ( 286) hydrogen bonds : angle 3.53559 / 2.38 ( 806) metal coordination : bond 0.00140 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.298 Fit side-chains REVERT: A 435 ASP cc_start: 0.8581 (t0) cc_final: 0.8357 (t0) REVERT: A 458 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7891 (mmmt) REVERT: A 523 PHE cc_start: 0.7872 (t80) cc_final: 0.7645 (t80) REVERT: A 550 ASP cc_start: 0.8630 (m-30) cc_final: 0.8306 (m-30) REVERT: A 706 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6629 (mp) REVERT: A 755 MET cc_start: 0.8443 (tpp) cc_final: 0.8169 (mmt) REVERT: A 760 MET cc_start: 0.8753 (ttp) cc_final: 0.8371 (ttm) REVERT: A 845 ARG cc_start: 0.7624 (mtt-85) cc_final: 0.7107 (mtt90) outliers start: 20 outliers final: 16 residues processed: 93 average time/residue: 0.0649 time to fit residues: 8.2148 Evaluate side-chains 92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 759 LYS Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 0.0770 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.156686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112518 restraints weight = 7873.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116436 restraints weight = 5251.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118643 restraints weight = 4218.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120320 restraints weight = 3714.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.120335 restraints weight = 3436.464| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6157 Z= 0.209 Angle : 0.587 9.177 8414 Z= 0.293 Chirality : 0.042 0.260 954 Planarity : 0.004 0.059 991 Dihedral : 7.022 107.963 1011 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.78 % Allowed : 18.75 % Favored : 77.47 % 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 (0.33), residues: 676 helix: 1.63 (0.29), residues: 327 sheet: -3.65 (0.50), residues: 86 loop : -2.25 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 730 TYR 0.011 0.001 TYR A 390 PHE 0.047 0.002 PHE A 616 TRP 0.015 0.002 TRP A 873 HIS 0.006 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 ( 6154) covalent geometry : angle 0.58674 / 0.29 ( 8414) hydrogen bonds : bond 0.03793 / 2.54 ( 286) hydrogen bonds : angle 3.68854 / 2.49 ( 806) metal coordination : bond 0.00332 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.289 Fit side-chains REVERT: A 435 ASP cc_start: 0.8598 (t0) cc_final: 0.8322 (t0) REVERT: A 458 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7917 (mmmt) REVERT: A 523 PHE cc_start: 0.7939 (t80) cc_final: 0.7488 (t80) REVERT: A 550 ASP cc_start: 0.8733 (m-30) cc_final: 0.8383 (m-30) REVERT: A 625 ASN cc_start: 0.8397 (t0) cc_final: 0.8087 (t0) REVERT: A 760 MET cc_start: 0.8821 (ttp) cc_final: 0.8397 (ttm) REVERT: A 845 ARG cc_start: 0.7656 (mtt-85) cc_final: 0.7084 (mtt90) outliers start: 23 outliers final: 19 residues processed: 92 average time/residue: 0.0664 time to fit residues: 8.3162 Evaluate side-chains 95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 28 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.160085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116528 restraints weight = 7813.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120629 restraints weight = 5142.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.123184 restraints weight = 4092.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124520 restraints weight = 3585.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125018 restraints weight = 3324.567| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6157 Z= 0.130 Angle : 0.535 8.537 8414 Z= 0.267 Chirality : 0.040 0.161 954 Planarity : 0.004 0.061 991 Dihedral : 6.905 109.994 1011 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.96 % Allowed : 19.74 % Favored : 77.30 % 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: -0.65 (0.34), residues: 676 helix: 1.78 (0.29), residues: 327 sheet: -3.43 (0.50), residues: 90 loop : -2.25 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 730 TYR 0.011 0.001 TYR A 390 PHE 0.022 0.001 PHE A 853 TRP 0.014 0.002 TRP A 873 HIS 0.006 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6154) covalent geometry : angle 0.53517 / 0.27 ( 8414) hydrogen bonds : bond 0.03319 / 2.22 ( 286) hydrogen bonds : angle 3.59263 / 2.43 ( 806) metal coordination : bond 0.00161 / 0.08 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1352 Ramachandran restraints generated. 676 Oldfield, 0 Emsley, 676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.131 Fit side-chains revert: symmetry clash REVERT: A 435 ASP cc_start: 0.8579 (t0) cc_final: 0.8369 (t0) REVERT: A 458 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7888 (mmmt) REVERT: A 523 PHE cc_start: 0.7862 (t80) cc_final: 0.7473 (t80) REVERT: A 550 ASP cc_start: 0.8653 (m-30) cc_final: 0.8322 (m-30) REVERT: A 625 ASN cc_start: 0.8321 (t0) cc_final: 0.8013 (t0) REVERT: A 706 ILE cc_start: 0.6868 (pt) cc_final: 0.6579 (mp) REVERT: A 760 MET cc_start: 0.8811 (ttp) cc_final: 0.8401 (ttm) outliers start: 18 outliers final: 15 residues processed: 96 average time/residue: 0.0539 time to fit residues: 7.0715 Evaluate side-chains 92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 827 GLU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.0000 chunk 63 optimal weight: 0.9980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.182598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144581 restraints weight = 7517.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146310 restraints weight = 6984.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.149847 restraints weight = 6001.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.150202 restraints weight = 4085.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151643 restraints weight = 3641.975| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6157 Z= 0.109 Angle : 0.524 8.404 8414 Z= 0.263 Chirality : 0.039 0.197 954 Planarity : 0.004 0.060 991 Dihedral : 6.789 108.733 1009 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.80 % Allowed : 19.90 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.34), residues: 676 helix: 1.85 (0.29), residues: 328 sheet: -3.39 (0.53), residues: 86 loop : -2.08 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 602 TYR 0.011 0.001 TYR A 390 PHE 0.052 0.002 PHE A 616 TRP 0.011 0.002 TRP A 873 HIS 0.014 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6154) covalent geometry : angle 0.52397 / 0.26 ( 8414) hydrogen bonds : bond 0.03127 / 2.11 ( 286) hydrogen bonds : angle 3.54737 / 2.40 ( 806) metal coordination : bond 0.00102 / 0.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1031.02 seconds wall clock time: 18 minutes 30.52 seconds (1110.52 seconds total)