Starting phenix.real_space_refine on Fri Dec 27 18:10:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tnz_26024/12_2024/7tnz_26024.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tnz_26024/12_2024/7tnz_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_26024/12_2024/7tnz_26024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tnz_26024/12_2024/7tnz_26024.map" model { file = "/net/cci-nas-00/data/ceres_data/7tnz_26024/12_2024/7tnz_26024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tnz_26024/12_2024/7tnz_26024.cif" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 4.22, per 1000 atoms: 0.70 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: 1.56 Conformation dependent library (CDL) restraints added in 896.8 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: 1.97 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: 2.00 Time building geometry restraints manager: 1.76 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 - 1.23: 5902 1.23 - 2.46: 2222 2.46 - 3.70: 269 3.70 - 4.93: 17 4.93 - 6.16: 4 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 - 17.67: 3442 17.67 - 35.35: 254 35.35 - 53.02: 58 53.02 - 70.70: 41 70.70 - 88.37: 14 Dihedral angle restraints: 3809 sinusoidal: 1814 harmonic: 1995 Sorted by residual: 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 dihedral pdb=" CB GLU A 591 " pdb=" CG GLU A 591 " pdb=" CD GLU A 591 " pdb=" OE1 GLU A 591 " ideal model delta sinusoidal sigma weight residual 0.00 -86.22 86.22 1 3.00e+01 1.11e-03 9.96e+00 ... (remaining 3806 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: 0.430 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.800 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 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 : 0.011 0.111 6154 Z= 0.707 Angle : 1.165 6.161 8414 Z= 0.855 Chirality : 0.068 0.204 954 Planarity : 0.004 0.032 991 Dihedral : 15.334 88.374 2513 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.003 TRP A 771 HIS 0.009 0.002 HIS A 444 PHE 0.024 0.003 PHE A 856 TYR 0.017 0.003 TYR A 566 ARG 0.004 0.001 ARG A 502 *********************** 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 : 0.655 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: 0.7457 (p0) cc_final: 0.6939 (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: 0.2247 time to fit residues: 39.9562 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 : 0.790 ------------------------------------------------------------------------------- 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 59 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN A 299 GLN A 341 ASN A 354 ASN A 500 GLN A 678 GLN ** A 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN A 867 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6154 Z= 0.218 Angle : 0.538 7.947 8414 Z= 0.271 Chirality : 0.039 0.163 954 Planarity : 0.004 0.040 991 Dihedral : 14.107 83.533 1118 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.92 % Favored : 93.93 % Rotamer: Outliers : 1.97 % Allowed : 11.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.32), residues: 676 helix: 1.12 (0.29), residues: 324 sheet: -3.97 (0.47), residues: 81 loop : -2.78 (0.32), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 873 HIS 0.011 0.001 HIS A 280 PHE 0.020 0.001 PHE A 616 TYR 0.010 0.001 TYR A 879 ARG 0.003 0.000 ARG A 575 *********************** 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 110 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.640 Fit side-chains REVERT: A 459 PHE cc_start: 0.8610 (m-80) cc_final: 0.8179 (m-10) REVERT: A 481 ASP cc_start: 0.8097 (m-30) cc_final: 0.7777 (m-30) REVERT: A 523 PHE cc_start: 0.8183 (t80) cc_final: 0.7457 (t80) REVERT: A 525 MET cc_start: 0.7428 (mtm) cc_final: 0.7117 (mtm) REVERT: A 547 LYS cc_start: 0.8588 (tppt) cc_final: 0.8184 (mmtm) REVERT: A 602 ARG cc_start: 0.8933 (mtm110) cc_final: 0.8629 (tpp80) REVERT: A 603 ASP cc_start: 0.8654 (t0) cc_final: 0.8040 (t0) REVERT: A 625 ASN cc_start: 0.8581 (t0) cc_final: 0.8179 (t0) REVERT: A 845 ARG cc_start: 0.7631 (mtt-85) cc_final: 0.7063 (mtt90) REVERT: A 895 GLU cc_start: 0.7601 (tp30) cc_final: 0.7260 (tp30) outliers start: 12 outliers final: 7 residues processed: 106 average time/residue: 0.2100 time to fit residues: 29.0422 Evaluate side-chains 93 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 882 PHE 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 35 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN A 557 HIS A 726 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6154 Z= 0.290 Angle : 0.567 7.807 8414 Z= 0.286 Chirality : 0.041 0.194 954 Planarity : 0.004 0.044 991 Dihedral : 14.109 76.134 1118 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.25 % Favored : 92.60 % Rotamer: Outliers : 3.12 % Allowed : 12.99 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.32), residues: 676 helix: 1.26 (0.29), residues: 323 sheet: -4.16 (0.43), residues: 85 loop : -2.48 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 873 HIS 0.006 0.001 HIS A 623 PHE 0.018 0.002 PHE A 616 TYR 0.013 0.001 TYR A 717 ARG 0.002 0.000 ARG A 730 *********************** 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 111 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.655 Fit side-chains REVERT: A 459 PHE cc_start: 0.8743 (m-80) cc_final: 0.8315 (m-10) REVERT: A 481 ASP cc_start: 0.8116 (m-30) cc_final: 0.7790 (m-30) REVERT: A 523 PHE cc_start: 0.8212 (t80) cc_final: 0.7517 (t80) REVERT: A 525 MET cc_start: 0.7393 (mtm) cc_final: 0.7102 (mtm) REVERT: A 583 GLU cc_start: 0.8708 (mp0) cc_final: 0.8331 (mp0) REVERT: A 602 ARG cc_start: 0.8946 (mtm110) cc_final: 0.8675 (tpp80) REVERT: A 603 ASP cc_start: 0.8733 (t0) cc_final: 0.8121 (t0) REVERT: A 695 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8607 (mt) REVERT: A 845 ARG cc_start: 0.7715 (mtt-85) cc_final: 0.7131 (mtt90) REVERT: A 895 GLU cc_start: 0.7680 (tp30) cc_final: 0.7163 (tp30) outliers start: 19 outliers final: 11 residues processed: 108 average time/residue: 0.1719 time to fit residues: 24.5579 Evaluate side-chains 97 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 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 759 LYS 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 47 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6154 Z= 0.295 Angle : 0.562 9.232 8414 Z= 0.285 Chirality : 0.041 0.166 954 Planarity : 0.004 0.046 991 Dihedral : 14.144 75.026 1118 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.40 % Favored : 92.46 % Rotamer: Outliers : 4.28 % Allowed : 15.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.33), residues: 676 helix: 1.32 (0.29), residues: 324 sheet: -4.20 (0.43), residues: 85 loop : -2.43 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 873 HIS 0.008 0.001 HIS A 623 PHE 0.016 0.002 PHE A 856 TYR 0.011 0.001 TYR A 246 ARG 0.003 0.000 ARG A 730 *********************** 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 118 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.597 Fit side-chains REVERT: A 459 PHE cc_start: 0.8840 (m-80) cc_final: 0.8455 (m-10) REVERT: A 481 ASP cc_start: 0.8120 (m-30) cc_final: 0.7809 (m-30) REVERT: A 523 PHE cc_start: 0.8111 (t80) cc_final: 0.7453 (t80) REVERT: A 583 GLU cc_start: 0.8748 (mp0) cc_final: 0.8340 (mp0) REVERT: A 602 ARG cc_start: 0.8947 (mtm110) cc_final: 0.8682 (tpp80) REVERT: A 603 ASP cc_start: 0.8775 (t0) cc_final: 0.8229 (t0) REVERT: A 625 ASN cc_start: 0.8540 (t0) cc_final: 0.8273 (t0) REVERT: A 655 PHE cc_start: 0.8024 (p90) cc_final: 0.7494 (p90) REVERT: A 695 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8685 (mt) REVERT: A 845 ARG cc_start: 0.7689 (mtt-85) cc_final: 0.7077 (mtt90) outliers start: 26 outliers final: 15 residues processed: 110 average time/residue: 0.1899 time to fit residues: 27.5110 Evaluate side-chains 96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.790 ------------------------------------------------------------------------------- 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 489 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 629 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 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6154 Z= 0.183 Angle : 0.506 7.760 8414 Z= 0.256 Chirality : 0.039 0.161 954 Planarity : 0.004 0.051 991 Dihedral : 14.098 73.834 1118 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.95 % Favored : 92.90 % Rotamer: Outliers : 3.62 % Allowed : 16.61 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.33), residues: 676 helix: 1.59 (0.29), residues: 324 sheet: -4.10 (0.47), residues: 79 loop : -2.31 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 873 HIS 0.009 0.001 HIS A 623 PHE 0.036 0.001 PHE A 853 TYR 0.009 0.001 TYR A 390 ARG 0.002 0.000 ARG A 664 *********************** 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 113 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.673 Fit side-chains REVERT: A 459 PHE cc_start: 0.8813 (m-80) cc_final: 0.8513 (m-80) REVERT: A 481 ASP cc_start: 0.8140 (m-30) cc_final: 0.7808 (m-30) REVERT: A 523 PHE cc_start: 0.8117 (t80) cc_final: 0.7474 (t80) REVERT: A 525 MET cc_start: 0.7610 (mtm) cc_final: 0.7296 (ptp) REVERT: A 550 ASP cc_start: 0.8946 (m-30) cc_final: 0.8646 (m-30) REVERT: A 583 GLU cc_start: 0.8785 (mp0) cc_final: 0.8293 (mp0) REVERT: A 602 ARG cc_start: 0.8939 (mtm110) cc_final: 0.8676 (tpp80) REVERT: A 603 ASP cc_start: 0.8790 (t0) cc_final: 0.8253 (t0) REVERT: A 625 ASN cc_start: 0.8545 (t0) cc_final: 0.8217 (t0) REVERT: A 655 PHE cc_start: 0.8015 (p90) cc_final: 0.7500 (p90) REVERT: A 695 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8681 (mt) REVERT: A 823 VAL cc_start: 0.8479 (t) cc_final: 0.8252 (m) REVERT: A 845 ARG cc_start: 0.7751 (mtt-85) cc_final: 0.7164 (mtt90) REVERT: A 895 GLU cc_start: 0.7757 (tp30) cc_final: 0.7525 (tp30) outliers start: 22 outliers final: 10 residues processed: 107 average time/residue: 0.1849 time to fit residues: 26.1393 Evaluate side-chains 99 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.671 ------------------------------------------------------------------------------- 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 443 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 843 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 0.2980 chunk 38 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6154 Z= 0.269 Angle : 0.546 8.896 8414 Z= 0.275 Chirality : 0.040 0.142 954 Planarity : 0.004 0.052 991 Dihedral : 14.126 73.790 1118 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.45 % Allowed : 18.26 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.33), residues: 676 helix: 1.54 (0.29), residues: 325 sheet: -3.83 (0.49), residues: 86 loop : -2.22 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 873 HIS 0.010 0.001 HIS A 623 PHE 0.031 0.002 PHE A 853 TYR 0.010 0.001 TYR A 390 ARG 0.003 0.000 ARG A 730 *********************** 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 105 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 523 PHE cc_start: 0.7983 (t80) cc_final: 0.7452 (t80) REVERT: A 583 GLU cc_start: 0.8732 (mp0) cc_final: 0.8272 (mp0) REVERT: A 602 ARG cc_start: 0.8937 (mtm110) cc_final: 0.8666 (tpp80) REVERT: A 603 ASP cc_start: 0.8795 (t0) cc_final: 0.8254 (t0) REVERT: A 625 ASN cc_start: 0.8547 (t0) cc_final: 0.8226 (t0) REVERT: A 655 PHE cc_start: 0.8050 (p90) cc_final: 0.7548 (p90) REVERT: A 695 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8692 (mt) REVERT: A 845 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7166 (mtt90) REVERT: A 895 GLU cc_start: 0.7800 (tp30) cc_final: 0.7423 (tp30) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 0.1900 time to fit residues: 25.6610 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 : 0.693 ------------------------------------------------------------------------------- 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 412 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 629 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 695 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 806 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.0010 chunk 13 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6154 Z= 0.173 Angle : 0.502 7.717 8414 Z= 0.251 Chirality : 0.039 0.172 954 Planarity : 0.004 0.057 991 Dihedral : 14.099 73.843 1118 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.96 % Allowed : 19.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.34), residues: 676 helix: 1.78 (0.29), residues: 324 sheet: -4.04 (0.49), residues: 73 loop : -2.16 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 512 HIS 0.008 0.001 HIS A 623 PHE 0.026 0.001 PHE A 853 TYR 0.010 0.001 TYR A 390 ARG 0.002 0.000 ARG A 730 *********************** 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 103 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.8809 (m-80) cc_final: 0.8557 (m-80) REVERT: A 523 PHE cc_start: 0.7999 (t80) cc_final: 0.7495 (t80) REVERT: A 550 ASP cc_start: 0.8876 (m-30) cc_final: 0.8565 (m-30) REVERT: A 583 GLU cc_start: 0.8710 (mp0) cc_final: 0.8240 (mp0) REVERT: A 603 ASP cc_start: 0.8816 (t0) cc_final: 0.8265 (t0) REVERT: A 655 PHE cc_start: 0.7961 (p90) cc_final: 0.7501 (p90) REVERT: A 759 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7596 (ptmm) REVERT: A 845 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.7199 (mtt90) REVERT: A 895 GLU cc_start: 0.7792 (tp30) cc_final: 0.7269 (tp30) outliers start: 18 outliers final: 11 residues processed: 98 average time/residue: 0.1865 time to fit residues: 24.4656 Evaluate side-chains 92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 489 ILE Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 709 CYS Chi-restraints excluded: chain A residue 759 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6154 Z= 0.198 Angle : 0.519 8.709 8414 Z= 0.258 Chirality : 0.039 0.170 954 Planarity : 0.004 0.057 991 Dihedral : 14.081 73.783 1116 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.47 % Allowed : 20.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.34), residues: 676 helix: 1.82 (0.29), residues: 323 sheet: -3.96 (0.50), residues: 73 loop : -2.19 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 873 HIS 0.006 0.001 HIS A 623 PHE 0.023 0.001 PHE A 853 TYR 0.011 0.001 TYR A 390 ARG 0.003 0.000 ARG A 602 *********************** 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 96 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.744 Fit side-chains revert: symmetry clash REVERT: A 523 PHE cc_start: 0.7983 (t80) cc_final: 0.7390 (t80) REVERT: A 550 ASP cc_start: 0.8899 (m-30) cc_final: 0.8583 (m-30) REVERT: A 583 GLU cc_start: 0.8683 (mp0) cc_final: 0.8234 (mp0) REVERT: A 603 ASP cc_start: 0.8827 (t0) cc_final: 0.8273 (t0) REVERT: A 625 ASN cc_start: 0.8583 (t0) cc_final: 0.8315 (t0) REVERT: A 628 THR cc_start: 0.6997 (t) cc_final: 0.6671 (t) REVERT: A 655 PHE cc_start: 0.7901 (p90) cc_final: 0.7544 (p90) REVERT: A 706 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6511 (mp) REVERT: A 759 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7590 (ptmm) REVERT: A 845 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.7188 (mtt90) REVERT: A 895 GLU cc_start: 0.7813 (tp30) cc_final: 0.7215 (tp30) outliers start: 15 outliers final: 12 residues processed: 92 average time/residue: 0.1850 time to fit residues: 22.9334 Evaluate side-chains 92 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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 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 709 CYS Chi-restraints excluded: chain A residue 759 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.0170 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6154 Z= 0.170 Angle : 0.502 8.168 8414 Z= 0.250 Chirality : 0.039 0.161 954 Planarity : 0.004 0.061 991 Dihedral : 14.071 73.832 1116 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.63 % Allowed : 20.23 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.34), residues: 676 helix: 1.93 (0.29), residues: 323 sheet: -3.84 (0.51), residues: 73 loop : -2.12 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 873 HIS 0.006 0.001 HIS A 623 PHE 0.021 0.001 PHE A 853 TYR 0.010 0.001 TYR A 390 ARG 0.002 0.000 ARG A 730 *********************** 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 101 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.788 Fit side-chains REVERT: A 523 PHE cc_start: 0.7967 (t80) cc_final: 0.7416 (t80) REVERT: A 550 ASP cc_start: 0.8878 (m-30) cc_final: 0.8565 (m-30) REVERT: A 583 GLU cc_start: 0.8651 (mp0) cc_final: 0.8228 (mp0) REVERT: A 603 ASP cc_start: 0.8887 (t0) cc_final: 0.8380 (t0) REVERT: A 655 PHE cc_start: 0.7857 (p90) cc_final: 0.7572 (p90) REVERT: A 706 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6377 (mp) REVERT: A 845 ARG cc_start: 0.7783 (mtt-85) cc_final: 0.7206 (mtt90) REVERT: A 895 GLU cc_start: 0.7742 (tp30) cc_final: 0.7164 (tp30) outliers start: 16 outliers final: 14 residues processed: 93 average time/residue: 0.1660 time to fit residues: 20.9230 Evaluate side-chains 95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 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 709 CYS Chi-restraints excluded: chain A residue 718 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 5 optimal weight: 0.0670 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6154 Z= 0.213 Angle : 0.528 8.658 8414 Z= 0.263 Chirality : 0.040 0.210 954 Planarity : 0.004 0.059 991 Dihedral : 14.071 73.763 1116 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.47 % Allowed : 20.39 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.34), residues: 676 helix: 1.90 (0.29), residues: 323 sheet: -3.87 (0.51), residues: 73 loop : -2.08 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 873 HIS 0.015 0.001 HIS A 623 PHE 0.050 0.002 PHE A 616 TYR 0.011 0.001 TYR A 390 ARG 0.004 0.000 ARG A 602 ********************** 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 95 residues out of total 609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.703 Fit side-chains REVERT: A 523 PHE cc_start: 0.7900 (t80) cc_final: 0.7428 (t80) REVERT: A 550 ASP cc_start: 0.8937 (m-30) cc_final: 0.8616 (m-30) REVERT: A 583 GLU cc_start: 0.8636 (mp0) cc_final: 0.8205 (mp0) REVERT: A 603 ASP cc_start: 0.8886 (t0) cc_final: 0.8377 (t0) REVERT: A 625 ASN cc_start: 0.8579 (t0) cc_final: 0.8248 (t0) REVERT: A 655 PHE cc_start: 0.7857 (p90) cc_final: 0.7620 (p90) REVERT: A 706 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6495 (mp) REVERT: A 845 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.7166 (mtt90) REVERT: A 895 GLU cc_start: 0.7781 (tp30) cc_final: 0.7158 (tp30) REVERT: A 915 LYS cc_start: 0.7834 (mttt) cc_final: 0.7599 (mtpp) outliers start: 15 outliers final: 14 residues processed: 89 average time/residue: 0.1778 time to fit residues: 21.4738 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 : 0.616 ------------------------------------------------------------------------------- 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 362 SER 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 709 CYS Chi-restraints excluded: chain A residue 718 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.180893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.137507 restraints weight = 7487.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142224 restraints weight = 4817.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145260 restraints weight = 3776.578| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6154 Z= 0.197 Angle : 0.523 8.145 8414 Z= 0.262 Chirality : 0.040 0.189 954 Planarity : 0.004 0.060 991 Dihedral : 14.066 73.794 1116 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.63 % Allowed : 20.23 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.34), residues: 676 helix: 1.93 (0.29), residues: 323 sheet: -3.78 (0.52), residues: 73 loop : -2.06 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 873 HIS 0.014 0.001 HIS A 623 PHE 0.039 0.002 PHE A 685 TYR 0.011 0.001 TYR A 390 ARG 0.002 0.000 ARG A 730 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1422.08 seconds wall clock time: 27 minutes 55.29 seconds (1675.29 seconds total)