Starting phenix.real_space_refine on Fri Sep 11 01:00:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tnz_26024/09_2026/7tnz_26024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnz_26024/09_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_26024/09_2026/7tnz_26024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnz_26024/09_2026/7tnz_26024.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tnz_26024/09_2026/7tnz_26024.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tnz_26024/09_2026/7tnz_26024.cif" model { file = "/net/cci-nas-00/data/ceres_data/7tnz_26024/09_2026/7tnz_26024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnz_26024/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 1.60, per 1000 atoms: 0.27 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 317.7 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: 0.64 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: 1.13 Time building geometry restraints manager: 0.53 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 1.20e-02 6.94e+03 8.56e+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 - 1.95: 7498 1.95 - 3.89: 884 3.89 - 5.84: 25 5.84 - 7.78: 4 7.78 - 9.73: 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 119.70 114.04 5.66 1.20e+00 6.94e-01 2.23e+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 - 32.39: 3605 32.39 - 64.78: 87 64.78 - 97.17: 8 97.17 - 129.57: 1 129.57 - 161.96: 1 Dihedral angle restraints: 3702 sinusoidal: 1707 harmonic: 1995 Sorted by residual: dihedral pdb=" C1' 5GP B 1 " pdb=" C4' 5GP B 1 " pdb=" O4' 5GP B 1 " pdb=" C5' 5GP B 1 " ideal model delta sinusoidal sigma weight residual 60.00 -138.04 -161.96 1 2.00e+01 2.50e-03 4.68e+01 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=" O5' C B 11 " pdb=" C5' C B 11 " pdb=" C4' C B 11 " pdb=" C3' C B 11 " ideal model delta sinusoidal sigma weight residual 180.00 154.74 25.26 3 6.40e+00 2.44e-02 1.96e+01 ... (remaining 3699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 432 0.048 - 0.096: 324 0.096 - 0.144: 153 0.144 - 0.191: 21 0.191 - 0.239: 24 Chirality restraints: 954 Sorted by residual: chirality pdb=" P A B 3 " pdb=" OP1 A B 3 " pdb=" OP2 A B 3 " pdb=" O5' A B 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" P C C 13 " pdb=" OP1 C C 13 " pdb=" OP2 C C 13 " pdb=" O5' C C 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" P C C 23 " pdb=" OP1 C C 23 " pdb=" OP2 C C 23 " pdb=" O5' C C 23 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.23 2.00e-01 2.50e+01 1.38e+00 ... (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: 0.530 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.250 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.330 ------------------------------------------------------------------------------- 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= 0.835 Angle : 1.212 9.731 8414 Z= 0.852 Chirality : 0.077 0.239 954 Planarity : 0.004 0.032 991 Dihedral : 13.999 161.958 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 0.01100 / 0.82 ( 6154) covalent geometry : angle 1.21171 / 0.85 ( 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 : 0.165 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: 0.0926 time to fit residues: 16.6546 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 : 0.151 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.155540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.111340 restraints weight = 7485.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115397 restraints weight = 4721.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117929 restraints weight = 3688.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119284 restraints weight = 3204.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.120299 restraints weight = 2954.891| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6157 Z= 0.129 Angle : 0.601 8.766 8414 Z= 0.278 Chirality : 0.045 0.328 954 Planarity : 0.004 0.041 991 Dihedral : 10.196 165.269 1011 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.07 % Favored : 93.79 % Rotamer: Outliers : 1.81 % Allowed : 11.35 % Favored : 86.84 % 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: -1.53 (0.32), residues: 676 helix: 1.15 (0.29), residues: 324 sheet: -4.00 (0.44), residues: 86 loop : -2.76 (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 0.011 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6154) covalent geometry : angle 0.60120 / 0.28 ( 8414) hydrogen bonds : bond 0.03297 / 2.22 ( 286) hydrogen bonds : angle 3.63435 / 2.44 ( 806) metal coordination : bond 0.00594 / 0.31 ( 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 : 0.246 Fit side-chains REVERT: A 272 PHE cc_start: 0.8217 (t80) cc_final: 0.7936 (t80) REVERT: A 387 MET cc_start: 0.8760 (mmm) cc_final: 0.8522 (mmm) REVERT: A 523 PHE cc_start: 0.8023 (t80) cc_final: 0.7536 (t80) REVERT: A 547 LYS cc_start: 0.8365 (tppt) cc_final: 0.7975 (mmtm) REVERT: A 550 ASP cc_start: 0.8650 (m-30) cc_final: 0.8375 (m-30) REVERT: A 603 ASP cc_start: 0.8820 (t0) cc_final: 0.8246 (t0) REVERT: A 625 ASN cc_start: 0.8618 (t0) cc_final: 0.8328 (t0) REVERT: A 760 MET cc_start: 0.8673 (ttp) cc_final: 0.8431 (ttm) REVERT: A 845 ARG cc_start: 0.7390 (mtt-85) cc_final: 0.6852 (mtt90) REVERT: A 895 GLU cc_start: 0.7055 (tp30) cc_final: 0.6823 (tp30) outliers start: 11 outliers final: 6 residues processed: 105 average time/residue: 0.0863 time to fit residues: 11.7084 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 : 0.194 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN A 500 GLN A 557 HIS A 726 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113958 restraints weight = 7720.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.116792 restraints weight = 6112.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.118265 restraints weight = 4825.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118524 restraints weight = 4145.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118576 restraints weight = 4001.787| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 6157 Z= 0.211 Angle : 0.673 9.847 8414 Z= 0.314 Chirality : 0.048 0.347 954 Planarity : 0.004 0.043 991 Dihedral : 9.984 164.952 1011 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.69 % Favored : 92.16 % Rotamer: Outliers : 3.12 % Allowed : 12.83 % Favored : 84.05 % 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: -1.30 (0.32), residues: 676 helix: 1.25 (0.29), residues: 323 sheet: -4.09 (0.44), residues: 85 loop : -2.44 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 730 TYR 0.013 0.002 TYR A 717 PHE 0.019 0.002 PHE A 616 TRP 0.012 0.001 TRP A 873 HIS 0.007 0.002 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 ( 6154) covalent geometry : angle 0.67328 / 0.31 ( 8414) hydrogen bonds : bond 0.03865 / 2.59 ( 286) hydrogen bonds : angle 3.77515 / 2.55 ( 806) metal coordination : bond 0.00383 / 0.19 ( 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 114 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.230 Fit side-chains REVERT: A 523 PHE cc_start: 0.8000 (t80) cc_final: 0.7657 (t80) REVERT: A 603 ASP cc_start: 0.8796 (t0) cc_final: 0.8461 (t0) REVERT: A 625 ASN cc_start: 0.8397 (t0) cc_final: 0.8179 (t0) REVERT: A 695 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8686 (mt) REVERT: A 760 MET cc_start: 0.8797 (ttp) cc_final: 0.8389 (ttm) outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 0.0751 time to fit residues: 11.1136 Evaluate side-chains 93 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 341 ASN 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 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: 0.0570 chunk 18 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117738 restraints weight = 7774.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121830 restraints weight = 5134.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124431 restraints weight = 4097.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125708 restraints weight = 3604.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.126670 restraints weight = 3350.877| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6157 Z= 0.114 Angle : 0.592 8.781 8414 Z= 0.274 Chirality : 0.044 0.269 954 Planarity : 0.004 0.048 991 Dihedral : 10.054 165.983 1011 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.10 % Favored : 92.75 % Rotamer: Outliers : 3.62 % Allowed : 15.79 % 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: -1.00 (0.33), residues: 676 helix: 1.52 (0.29), residues: 323 sheet: -4.00 (0.49), residues: 79 loop : -2.37 (0.34), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 602 TYR 0.009 0.001 TYR A 246 PHE 0.029 0.001 PHE A 616 TRP 0.010 0.001 TRP A 873 HIS 0.009 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 6154) covalent geometry : angle 0.59222 / 0.27 ( 8414) hydrogen bonds : bond 0.03323 / 2.26 ( 286) hydrogen bonds : angle 3.65130 / 2.45 ( 806) metal coordination : bond 0.00086 / 0.04 ( 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 114 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.209 Fit side-chains REVERT: A 458 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7864 (mmmt) REVERT: A 523 PHE cc_start: 0.7952 (t80) cc_final: 0.7574 (t80) REVERT: A 603 ASP cc_start: 0.8851 (t0) cc_final: 0.8475 (t0) REVERT: A 695 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 706 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6296 (mt) REVERT: A 755 MET cc_start: 0.8421 (tpp) cc_final: 0.8195 (mmt) REVERT: A 760 MET cc_start: 0.8797 (ttp) cc_final: 0.8421 (ttm) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 0.0703 time to fit residues: 10.3656 Evaluate side-chains 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 443 LYS 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 579 PHE Chi-restraints excluded: chain A residue 629 ILE 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 827 GLU 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: 5.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN ** A 902 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.183226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.139924 restraints weight = 7740.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.141481 restraints weight = 5995.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.144470 restraints weight = 4929.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144793 restraints weight = 4112.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.145026 restraints weight = 3764.419| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2810 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= 0.116 Angle : 0.572 8.427 8414 Z= 0.265 Chirality : 0.044 0.242 954 Planarity : 0.004 0.051 991 Dihedral : 9.997 165.326 1011 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.62 % Allowed : 16.12 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.33), residues: 676 helix: 1.71 (0.29), residues: 323 sheet: -3.95 (0.49), residues: 79 loop : -2.21 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 664 TYR 0.008 0.001 TYR A 390 PHE 0.030 0.001 PHE A 616 TRP 0.010 0.001 TRP A 873 HIS 0.006 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6154) covalent geometry : angle 0.57230 / 0.27 ( 8414) hydrogen bonds : bond 0.03211 / 2.18 ( 286) hydrogen bonds : angle 3.57485 / 2.40 ( 806) metal coordination : bond 0.00122 / 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 115 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.133 Fit side-chains REVERT: A 523 PHE cc_start: 0.7761 (t80) cc_final: 0.7501 (t80) REVERT: A 550 ASP cc_start: 0.8607 (m-30) cc_final: 0.8308 (m-30) REVERT: A 603 ASP cc_start: 0.8839 (t0) cc_final: 0.8502 (t0) REVERT: A 625 ASN cc_start: 0.8500 (t0) cc_final: 0.8204 (t0) REVERT: A 695 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8705 (mt) REVERT: A 706 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6523 (mp) REVERT: A 755 MET cc_start: 0.8380 (tpp) cc_final: 0.8134 (mmt) REVERT: A 760 MET cc_start: 0.8746 (ttp) cc_final: 0.8430 (ttm) outliers start: 22 outliers final: 14 residues processed: 109 average time/residue: 0.0705 time to fit residues: 10.4222 Evaluate side-chains 99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 341 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE 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 695 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 827 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.0020 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.185396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142812 restraints weight = 7579.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.144772 restraints weight = 5726.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.146351 restraints weight = 4701.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.146805 restraints weight = 4029.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.148172 restraints weight = 3830.370| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6157 Z= 0.101 Angle : 0.573 8.419 8414 Z= 0.264 Chirality : 0.044 0.213 954 Planarity : 0.004 0.054 991 Dihedral : 10.016 165.347 1011 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.12 % Allowed : 17.43 % Favored : 79.44 % 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: -0.60 (0.34), residues: 676 helix: 1.75 (0.29), residues: 326 sheet: -3.77 (0.52), residues: 79 loop : -2.06 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 664 TYR 0.009 0.001 TYR A 390 PHE 0.034 0.001 PHE A 616 TRP 0.011 0.001 TRP A 873 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 6154) covalent geometry : angle 0.57335 / 0.26 ( 8414) hydrogen bonds : bond 0.03029 / 2.05 ( 286) hydrogen bonds : angle 3.52770 / 2.36 ( 806) metal coordination : bond 0.00056 / 0.03 ( 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 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.215 Fit side-chains REVERT: A 523 PHE cc_start: 0.7697 (t80) cc_final: 0.7448 (t80) REVERT: A 603 ASP cc_start: 0.8810 (t0) cc_final: 0.8495 (t0) REVERT: A 625 ASN cc_start: 0.8514 (t0) cc_final: 0.8264 (t0) REVERT: A 695 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8624 (mt) REVERT: A 755 MET cc_start: 0.8431 (tpp) cc_final: 0.8109 (mmt) REVERT: A 760 MET cc_start: 0.8707 (ttp) cc_final: 0.8415 (ttm) outliers start: 19 outliers final: 11 residues processed: 98 average time/residue: 0.0691 time to fit residues: 9.2573 Evaluate side-chains 90 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 759 LYS Chi-restraints excluded: chain A residue 827 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 25 optimal weight: 0.4980 chunk 53 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.161887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120302 restraints weight = 7739.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124102 restraints weight = 5269.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.126526 restraints weight = 4242.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.127721 restraints weight = 3741.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128891 restraints weight = 3486.953| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6157 Z= 0.115 Angle : 0.575 8.228 8414 Z= 0.265 Chirality : 0.044 0.236 954 Planarity : 0.004 0.056 991 Dihedral : 9.931 164.875 1009 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.96 % Allowed : 17.76 % Favored : 79.28 % 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: -0.49 (0.34), residues: 676 helix: 1.80 (0.29), residues: 329 sheet: -3.79 (0.53), residues: 73 loop : -2.05 (0.36), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.009 0.001 TYR A 390 PHE 0.036 0.001 PHE A 616 TRP 0.010 0.001 TRP A 873 HIS 0.005 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6154) covalent geometry : angle 0.57488 / 0.27 ( 8414) hydrogen bonds : bond 0.03148 / 2.11 ( 286) hydrogen bonds : angle 3.46334 / 2.33 ( 806) metal coordination : bond 0.00127 / 0.06 ( 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: 18 poor density : 87 time to evaluate : 0.217 Fit side-chains REVERT: A 523 PHE cc_start: 0.7790 (t80) cc_final: 0.7529 (t80) REVERT: A 603 ASP cc_start: 0.8804 (t0) cc_final: 0.8517 (t0) REVERT: A 628 THR cc_start: 0.7141 (t) cc_final: 0.6845 (t) REVERT: A 760 MET cc_start: 0.8718 (ttp) cc_final: 0.8428 (ttm) outliers start: 18 outliers final: 14 residues processed: 98 average time/residue: 0.0653 time to fit residues: 9.0010 Evaluate side-chains 96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 827 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.160216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117998 restraints weight = 7817.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.121781 restraints weight = 5354.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124206 restraints weight = 4343.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125391 restraints weight = 3839.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125397 restraints weight = 3584.880| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3097 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= 0.137 Angle : 0.592 8.414 8414 Z= 0.274 Chirality : 0.045 0.240 954 Planarity : 0.004 0.056 991 Dihedral : 9.889 164.906 1009 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.47 % Allowed : 18.42 % 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: -0.49 (0.34), residues: 676 helix: 1.81 (0.29), residues: 328 sheet: -3.57 (0.57), residues: 66 loop : -2.17 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.010 0.001 TYR A 390 PHE 0.024 0.001 PHE A 471 TRP 0.010 0.001 TRP A 873 HIS 0.004 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6154) covalent geometry : angle 0.59243 / 0.27 ( 8414) hydrogen bonds : bond 0.03295 / 2.22 ( 286) hydrogen bonds : angle 3.50673 / 2.37 ( 806) metal coordination : bond 0.00183 / 0.09 ( 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 91 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.218 Fit side-chains REVERT: A 523 PHE cc_start: 0.7849 (t80) cc_final: 0.7603 (t80) REVERT: A 603 ASP cc_start: 0.8830 (t0) cc_final: 0.8548 (t0) REVERT: A 760 MET cc_start: 0.8749 (ttp) cc_final: 0.8454 (ttm) outliers start: 15 outliers final: 13 residues processed: 88 average time/residue: 0.0719 time to fit residues: 8.6331 Evaluate side-chains 89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 759 LYS Chi-restraints excluded: chain A residue 827 GLU 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: 0.6980 chunk 68 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.120321 restraints weight = 7780.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124181 restraints weight = 5271.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126240 restraints weight = 4259.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127950 restraints weight = 3790.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.128698 restraints weight = 3514.583| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6157 Z= 0.109 Angle : 0.573 8.573 8414 Z= 0.265 Chirality : 0.044 0.215 954 Planarity : 0.004 0.060 991 Dihedral : 9.944 165.273 1009 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.47 % Allowed : 18.59 % Favored : 78.95 % 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: -0.43 (0.34), residues: 676 helix: 1.81 (0.29), residues: 330 sheet: -3.43 (0.57), residues: 66 loop : -2.14 (0.35), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 602 TYR 0.009 0.001 TYR A 390 PHE 0.041 0.001 PHE A 616 TRP 0.011 0.001 TRP A 873 HIS 0.006 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6154) covalent geometry : angle 0.57313 / 0.27 ( 8414) hydrogen bonds : bond 0.03148 / 2.12 ( 286) hydrogen bonds : angle 3.48009 / 2.35 ( 806) metal coordination : bond 0.00106 / 0.05 ( 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 94 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.218 Fit side-chains REVERT: A 523 PHE cc_start: 0.7841 (t80) cc_final: 0.7624 (t80) REVERT: A 760 MET cc_start: 0.8728 (ttp) cc_final: 0.8411 (ttm) outliers start: 15 outliers final: 14 residues processed: 89 average time/residue: 0.0699 time to fit residues: 8.5360 Evaluate side-chains 90 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.159162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117859 restraints weight = 7820.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119650 restraints weight = 6313.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120873 restraints weight = 5207.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121504 restraints weight = 4611.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121711 restraints weight = 4354.401| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6157 Z= 0.156 Angle : 0.610 8.844 8414 Z= 0.284 Chirality : 0.045 0.238 954 Planarity : 0.004 0.060 991 Dihedral : 9.883 165.054 1009 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.80 % Allowed : 18.59 % Favored : 78.62 % 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: -0.51 (0.34), residues: 676 helix: 1.81 (0.29), residues: 328 sheet: -3.37 (0.52), residues: 86 loop : -2.09 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 602 TYR 0.010 0.001 TYR A 390 PHE 0.023 0.001 PHE A 471 TRP 0.012 0.001 TRP A 873 HIS 0.007 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 6154) covalent geometry : angle 0.60991 / 0.28 ( 8414) hydrogen bonds : bond 0.03388 / 2.28 ( 286) hydrogen bonds : angle 3.55199 / 2.41 ( 806) metal coordination : bond 0.00223 / 0.11 ( 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 92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 523 PHE cc_start: 0.7766 (t80) cc_final: 0.7391 (t80) REVERT: A 760 MET cc_start: 0.8777 (ttp) cc_final: 0.8417 (ttm) outliers start: 17 outliers final: 15 residues processed: 89 average time/residue: 0.0712 time to fit residues: 8.6240 Evaluate side-chains 89 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 341 ASN Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 706 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.183074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.139007 restraints weight = 7599.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.143773 restraints weight = 4883.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.146618 restraints weight = 3831.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.148161 restraints weight = 3338.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.149593 restraints weight = 3078.252| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6157 Z= 0.113 Angle : 0.585 8.359 8414 Z= 0.271 Chirality : 0.044 0.207 954 Planarity : 0.004 0.062 991 Dihedral : 9.943 165.396 1009 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.47 % Allowed : 18.59 % Favored : 78.95 % 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: -0.43 (0.34), residues: 676 helix: 1.81 (0.29), residues: 330 sheet: -3.45 (0.52), residues: 77 loop : -2.03 (0.36), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 602 TYR 0.010 0.001 TYR A 390 PHE 0.047 0.002 PHE A 616 TRP 0.011 0.001 TRP A 873 HIS 0.013 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 6154) covalent geometry : angle 0.58541 / 0.27 ( 8414) hydrogen bonds : bond 0.03162 / 2.13 ( 286) hydrogen bonds : angle 3.51059 / 2.38 ( 806) metal coordination : bond 0.00115 / 0.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1131.49 seconds wall clock time: 20 minutes 18.65 seconds (1218.65 seconds total)