Starting phenix.real_space_refine on Tue Feb 11 12:58:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sd0_40348/02_2025/8sd0_40348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sd0_40348/02_2025/8sd0_40348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sd0_40348/02_2025/8sd0_40348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sd0_40348/02_2025/8sd0_40348.map" model { file = "/net/cci-nas-00/data/ceres_data/8sd0_40348/02_2025/8sd0_40348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sd0_40348/02_2025/8sd0_40348.cif" } resolution = 3.8 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= 0.005 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 34 5.49 5 S 31 5.16 5 C 3598 2.51 5 N 985 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5829 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5140 Classifications: {'peptide': 636} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 608} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 688 Unusual residues: {'GTP': 1} Classifications: {'RNA': 31, 'undetermined': 1} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 14, 'rna3p_pyr': 14} Link IDs: {'rna2p': 3, 'rna3p': 27, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " 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 4208 SG CYS A 810 27.805 58.529 40.084 1.00 67.93 S ATOM 4647 SG CYS A 864 27.991 62.363 40.544 1.00 66.95 S ATOM 4686 SG CYS A 869 27.689 60.503 42.864 1.00 72.48 S Time building chain proxies: 3.96, per 1000 atoms: 0.68 Number of scatterers: 5829 At special positions: 0 Unit cell: (96.6, 81.9, 86.1, 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 31 16.00 P 34 15.00 O 1180 8.00 N 985 7.00 C 3598 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 770.8 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 " 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1222 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 51.4% alpha, 10.2% beta 5 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 244 through 256 Proline residue: A 253 - end of helix removed outlier: 3.741A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 333 through 340 Processing helix chain 'A' and resid 347 through 358 removed outlier: 3.690A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.951A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 366 " --> pdb=" O LEU A 363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 362 through 366' Processing helix chain 'A' and resid 374 through 377 Processing helix chain 'A' and resid 381 through 396 Processing helix chain 'A' and resid 419 through 435 Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.803A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.856A pdb=" N LEU A 496 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 520 Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 529 through 558 removed outlier: 3.725A pdb=" N ARG A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.704A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 4.113A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 3.555A pdb=" N GLU A 607 " --> pdb=" O PRO A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 removed outlier: 3.552A pdb=" N VAL A 640 " --> pdb=" O THR A 636 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 771 removed outlier: 4.087A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 771 " --> pdb=" O ARG A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 removed outlier: 4.130A pdb=" N PHE A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 840 removed outlier: 3.608A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 837 through 840' Processing helix chain 'A' and resid 889 through 892 Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 263 removed outlier: 6.565A pdb=" N ILE A 262 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 458 removed outlier: 6.615A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 458 removed outlier: 6.615A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR A 630 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA A 696 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU A 632 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 3.754A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 823 through 825 Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846 removed outlier: 5.865A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1673 1.34 - 1.46: 1226 1.46 - 1.58: 3002 1.58 - 1.70: 67 1.70 - 1.82: 43 Bond restraints: 6011 Sorted by residual: bond pdb=" C LEU A 252 " pdb=" N PRO A 253 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.20e-02 6.94e+03 6.61e+00 bond pdb=" CA PRO A 626 " pdb=" C PRO A 626 " ideal model delta sigma weight residual 1.522 1.545 -0.023 9.80e-03 1.04e+04 5.31e+00 bond pdb=" CB GLU A 751 " pdb=" CG GLU A 751 " ideal model delta sigma weight residual 1.520 1.587 -0.067 3.00e-02 1.11e+03 5.00e+00 bond pdb=" CB GLU A 620 " pdb=" CG GLU A 620 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.35e+00 bond pdb=" CB GLU A 581 " pdb=" CG GLU A 581 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 ... (remaining 6006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 8054 2.32 - 4.65: 162 4.65 - 6.97: 34 6.97 - 9.30: 11 9.30 - 11.62: 3 Bond angle restraints: 8264 Sorted by residual: angle pdb=" CB GLU A 751 " pdb=" CG GLU A 751 " pdb=" CD GLU A 751 " ideal model delta sigma weight residual 112.60 120.19 -7.59 1.70e+00 3.46e-01 2.00e+01 angle pdb=" N ASP A 392 " pdb=" CA ASP A 392 " pdb=" C ASP A 392 " ideal model delta sigma weight residual 111.36 106.58 4.78 1.09e+00 8.42e-01 1.93e+01 angle pdb=" CB ARG A 316 " pdb=" CG ARG A 316 " pdb=" CD ARG A 316 " ideal model delta sigma weight residual 111.30 121.01 -9.71 2.30e+00 1.89e-01 1.78e+01 angle pdb=" CA GLU A 751 " pdb=" CB GLU A 751 " pdb=" CG GLU A 751 " ideal model delta sigma weight residual 114.10 122.16 -8.06 2.00e+00 2.50e-01 1.62e+01 angle pdb=" C ARG A 559 " pdb=" N MET A 560 " pdb=" CA MET A 560 " ideal model delta sigma weight residual 120.44 125.78 -5.34 1.36e+00 5.41e-01 1.54e+01 ... (remaining 8259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.47: 3164 18.47 - 36.94: 390 36.94 - 55.42: 96 55.42 - 73.89: 52 73.89 - 92.36: 10 Dihedral angle restraints: 3712 sinusoidal: 1837 harmonic: 1875 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 24.12 80.48 1 2.00e+01 2.50e-03 2.00e+01 dihedral pdb=" CA VAL A 877 " pdb=" C VAL A 877 " pdb=" N LYS A 878 " pdb=" CA LYS A 878 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA PHE A 853 " pdb=" C PHE A 853 " pdb=" N SER A 854 " pdb=" CA SER A 854 " ideal model delta harmonic sigma weight residual 180.00 161.29 18.71 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 732 0.050 - 0.100: 170 0.100 - 0.150: 31 0.150 - 0.200: 10 0.200 - 0.250: 3 Chirality restraints: 946 Sorted by residual: chirality pdb=" CB ILE A 261 " pdb=" CA ILE A 261 " pdb=" CG1 ILE A 261 " pdb=" CG2 ILE A 261 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE A 693 " pdb=" CA ILE A 693 " pdb=" CG1 ILE A 693 " pdb=" CG2 ILE A 693 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE A 695 " pdb=" CA ILE A 695 " pdb=" CG1 ILE A 695 " pdb=" CG2 ILE A 695 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 943 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 625 " 0.053 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 626 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 626 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 626 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 778 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" CD GLU A 778 " 0.053 2.00e-02 2.50e+03 pdb=" OE1 GLU A 778 " -0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 778 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 343 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C ILE A 343 " -0.049 2.00e-02 2.50e+03 pdb=" O ILE A 343 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 344 " 0.017 2.00e-02 2.50e+03 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1453 2.80 - 3.33: 5383 3.33 - 3.85: 9945 3.85 - 4.38: 10803 4.38 - 4.90: 18313 Nonbonded interactions: 45897 Sorted by model distance: nonbonded pdb=" C3' GTP B 1 " pdb=" OP2 G B 2 " model vdw 2.276 2.776 nonbonded pdb=" O GLU A 583 " pdb=" OG1 THR A 587 " model vdw 2.307 3.040 nonbonded pdb=" O SER A 891 " pdb=" OG SER A 891 " model vdw 2.329 3.040 nonbonded pdb=" CD1 LEU A 611 " pdb=" OH TYR A 715 " model vdw 2.333 3.460 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.352 3.040 ... (remaining 45892 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: 0.470 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.510 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.004 0.067 6011 Z= 0.251 Angle : 0.860 11.624 8264 Z= 0.451 Chirality : 0.047 0.250 946 Planarity : 0.007 0.094 936 Dihedral : 18.359 92.360 2490 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.52 % Allowed : 24.70 % Favored : 74.78 % 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: -1.62 (0.31), residues: 628 helix: 0.17 (0.29), residues: 283 sheet: -2.01 (0.53), residues: 86 loop : -2.12 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 646 HIS 0.002 0.001 HIS A 782 PHE 0.026 0.002 PHE A 776 TYR 0.036 0.002 TYR A 548 ARG 0.023 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.594 Fit side-chains REVERT: A 317 HIS cc_start: 0.6894 (m-70) cc_final: 0.5916 (m-70) REVERT: A 503 GLU cc_start: 0.7620 (pm20) cc_final: 0.6557 (pm20) REVERT: A 876 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.6992 (t70) REVERT: A 895 GLU cc_start: 0.7731 (pt0) cc_final: 0.7286 (pt0) outliers start: 3 outliers final: 1 residues processed: 109 average time/residue: 0.1886 time to fit residues: 26.7641 Evaluate side-chains 90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 500 GLN A 623 HIS A 710 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.142154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115875 restraints weight = 8993.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119415 restraints weight = 5202.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121814 restraints weight = 3666.305| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6011 Z= 0.176 Angle : 0.553 7.839 8264 Z= 0.281 Chirality : 0.038 0.152 946 Planarity : 0.004 0.051 936 Dihedral : 15.506 93.830 1178 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.48 % Allowed : 24.35 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.83 (0.33), residues: 628 helix: 1.10 (0.31), residues: 291 sheet: -1.92 (0.53), residues: 85 loop : -2.04 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 646 HIS 0.010 0.001 HIS A 623 PHE 0.022 0.001 PHE A 616 TYR 0.027 0.001 TYR A 548 ARG 0.008 0.001 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 777 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8039 (tpp-160) outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 0.1602 time to fit residues: 23.6795 Evaluate side-chains 99 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 29 optimal weight: 0.4980 chunk 59 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.142762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116276 restraints weight = 8957.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119795 restraints weight = 5226.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122247 restraints weight = 3700.452| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6011 Z= 0.146 Angle : 0.544 9.584 8264 Z= 0.271 Chirality : 0.038 0.134 946 Planarity : 0.004 0.048 936 Dihedral : 15.453 92.769 1176 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.65 % Allowed : 24.00 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.34), residues: 628 helix: 1.32 (0.30), residues: 297 sheet: -1.55 (0.60), residues: 70 loop : -1.95 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 646 HIS 0.002 0.000 HIS A 317 PHE 0.028 0.001 PHE A 616 TYR 0.025 0.001 TYR A 548 ARG 0.005 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.6829 (mmm160) cc_final: 0.6614 (mmm160) REVERT: A 387 MET cc_start: 0.9065 (mmm) cc_final: 0.8813 (mmm) REVERT: A 506 THR cc_start: 0.9115 (p) cc_final: 0.8722 (p) REVERT: A 777 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8136 (tpp-160) outliers start: 21 outliers final: 12 residues processed: 117 average time/residue: 0.1641 time to fit residues: 25.9740 Evaluate side-chains 100 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 1 optimal weight: 0.0470 chunk 22 optimal weight: 8.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN ** A 868 ASN ** 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 = 0.3795 r_free = 0.3795 target = 0.142645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.116532 restraints weight = 9006.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120089 restraints weight = 5178.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122491 restraints weight = 3657.413| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6011 Z= 0.142 Angle : 0.534 9.604 8264 Z= 0.265 Chirality : 0.038 0.176 946 Planarity : 0.003 0.046 936 Dihedral : 15.435 92.237 1176 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.35 % Allowed : 23.83 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.34), residues: 628 helix: 1.51 (0.31), residues: 297 sheet: -1.68 (0.59), residues: 72 loop : -1.88 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 646 HIS 0.001 0.000 HIS A 847 PHE 0.027 0.001 PHE A 616 TYR 0.024 0.001 TYR A 548 ARG 0.003 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.6765 (mmm160) cc_final: 0.6529 (mmm160) REVERT: A 387 MET cc_start: 0.9088 (mmm) cc_final: 0.8554 (mmm) REVERT: A 460 PHE cc_start: 0.7648 (m-10) cc_final: 0.7429 (m-10) REVERT: A 623 HIS cc_start: 0.8413 (t-90) cc_final: 0.8183 (t-170) REVERT: A 755 MET cc_start: 0.8099 (mmm) cc_final: 0.7747 (mmm) REVERT: A 777 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8130 (tpp-160) outliers start: 25 outliers final: 13 residues processed: 117 average time/residue: 0.1639 time to fit residues: 25.8148 Evaluate side-chains 100 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 9 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 784 GLN ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.115082 restraints weight = 8974.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118558 restraints weight = 5250.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120931 restraints weight = 3721.918| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6011 Z= 0.203 Angle : 0.589 10.516 8264 Z= 0.293 Chirality : 0.040 0.187 946 Planarity : 0.004 0.047 936 Dihedral : 15.420 91.006 1176 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.35 % Allowed : 23.65 % Favored : 72.00 % 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: -0.31 (0.34), residues: 628 helix: 1.50 (0.31), residues: 297 sheet: -1.68 (0.59), residues: 72 loop : -1.84 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 646 HIS 0.003 0.000 HIS A 871 PHE 0.035 0.002 PHE A 616 TYR 0.023 0.001 TYR A 548 ARG 0.004 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.9159 (mmm) cc_final: 0.8579 (mmm) REVERT: A 470 LYS cc_start: 0.8115 (tppt) cc_final: 0.7914 (tppt) REVERT: A 493 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8459 (tt) REVERT: A 623 HIS cc_start: 0.8455 (t-90) cc_final: 0.8254 (t-170) REVERT: A 777 ARG cc_start: 0.8608 (tpp80) cc_final: 0.8200 (tpp-160) outliers start: 25 outliers final: 17 residues processed: 116 average time/residue: 0.1912 time to fit residues: 29.6815 Evaluate side-chains 108 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 40 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 500 GLN ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116377 restraints weight = 8927.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119773 restraints weight = 5172.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122174 restraints weight = 3681.453| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6011 Z= 0.161 Angle : 0.590 11.060 8264 Z= 0.291 Chirality : 0.040 0.195 946 Planarity : 0.004 0.046 936 Dihedral : 15.471 90.721 1176 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.35 % Allowed : 24.52 % Favored : 71.13 % 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: -0.30 (0.34), residues: 628 helix: 1.54 (0.31), residues: 297 sheet: -1.78 (0.59), residues: 74 loop : -1.83 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 646 HIS 0.004 0.000 HIS A 280 PHE 0.033 0.001 PHE A 616 TYR 0.029 0.001 TYR A 548 ARG 0.010 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.9120 (mmm) cc_final: 0.8592 (mmm) REVERT: A 460 PHE cc_start: 0.7727 (m-10) cc_final: 0.7468 (m-10) REVERT: A 470 LYS cc_start: 0.8115 (tppt) cc_final: 0.7914 (tppt) REVERT: A 493 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8439 (tt) REVERT: A 777 ARG cc_start: 0.8676 (tpp80) cc_final: 0.8260 (tpp-160) outliers start: 25 outliers final: 17 residues processed: 115 average time/residue: 0.1664 time to fit residues: 25.7658 Evaluate side-chains 108 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 42 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 623 HIS ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113808 restraints weight = 9064.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117332 restraints weight = 5258.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119516 restraints weight = 3716.551| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6011 Z= 0.225 Angle : 0.632 10.753 8264 Z= 0.314 Chirality : 0.041 0.197 946 Planarity : 0.004 0.047 936 Dihedral : 15.448 89.720 1176 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 4.35 % Allowed : 25.04 % Favored : 70.61 % 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: -0.27 (0.35), residues: 628 helix: 1.56 (0.31), residues: 297 sheet: -1.66 (0.60), residues: 72 loop : -1.86 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 646 HIS 0.005 0.001 HIS A 280 PHE 0.039 0.002 PHE A 616 TYR 0.032 0.001 TYR A 548 ARG 0.010 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.9197 (mmm) cc_final: 0.8619 (mmm) REVERT: A 493 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8442 (tt) REVERT: A 538 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8603 (mp) REVERT: A 546 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.8248 (ttp80) REVERT: A 777 ARG cc_start: 0.8678 (tpp80) cc_final: 0.8275 (tpp-160) REVERT: A 878 LYS cc_start: 0.7296 (pttt) cc_final: 0.7078 (pttt) outliers start: 25 outliers final: 18 residues processed: 113 average time/residue: 0.1605 time to fit residues: 24.5504 Evaluate side-chains 109 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 623 HIS ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.140860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114721 restraints weight = 8996.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118232 restraints weight = 5180.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120643 restraints weight = 3633.990| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6011 Z= 0.173 Angle : 0.626 11.070 8264 Z= 0.309 Chirality : 0.040 0.192 946 Planarity : 0.004 0.046 936 Dihedral : 15.496 89.555 1176 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.35 % Allowed : 25.39 % Favored : 70.26 % 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: -0.26 (0.35), residues: 628 helix: 1.52 (0.31), residues: 297 sheet: -1.60 (0.61), residues: 72 loop : -1.81 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 646 HIS 0.013 0.001 HIS A 623 PHE 0.038 0.001 PHE A 616 TYR 0.034 0.001 TYR A 548 ARG 0.008 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.499 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.9152 (mmm) cc_final: 0.8590 (mmm) REVERT: A 460 PHE cc_start: 0.7757 (m-10) cc_final: 0.7485 (m-10) REVERT: A 493 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8442 (tt) REVERT: A 538 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8593 (mp) REVERT: A 546 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8263 (ttp80) REVERT: A 777 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8276 (tpp-160) outliers start: 25 outliers final: 17 residues processed: 115 average time/residue: 0.1506 time to fit residues: 23.6785 Evaluate side-chains 110 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 538 LEU Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN A 500 GLN ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.142275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116915 restraints weight = 8942.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120380 restraints weight = 5109.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122741 restraints weight = 3560.309| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6011 Z= 0.165 Angle : 0.644 11.237 8264 Z= 0.319 Chirality : 0.040 0.203 946 Planarity : 0.004 0.046 936 Dihedral : 15.514 89.052 1176 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.83 % Allowed : 26.09 % Favored : 70.09 % 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: -0.31 (0.35), residues: 628 helix: 1.47 (0.31), residues: 297 sheet: -1.74 (0.60), residues: 74 loop : -1.78 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 646 HIS 0.005 0.001 HIS A 280 PHE 0.041 0.001 PHE A 616 TYR 0.031 0.001 TYR A 548 ARG 0.007 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.9089 (mmm) cc_final: 0.8624 (mmm) REVERT: A 493 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8445 (tt) REVERT: A 546 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8190 (ttp80) REVERT: A 559 ARG cc_start: 0.8069 (ttp-110) cc_final: 0.7694 (ttp-110) REVERT: A 573 ASN cc_start: 0.8376 (m110) cc_final: 0.8154 (m110) REVERT: A 777 ARG cc_start: 0.8624 (tpp80) cc_final: 0.8243 (tpp-160) outliers start: 22 outliers final: 16 residues processed: 114 average time/residue: 0.1633 time to fit residues: 25.2075 Evaluate side-chains 109 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 500 GLN Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 0.0570 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN ** A 868 ASN ** 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 = 0.3785 r_free = 0.3785 target = 0.141422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.115236 restraints weight = 9122.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118738 restraints weight = 5270.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121082 restraints weight = 3698.421| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6011 Z= 0.193 Angle : 0.647 11.011 8264 Z= 0.320 Chirality : 0.041 0.193 946 Planarity : 0.004 0.046 936 Dihedral : 15.471 88.126 1176 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.00 % Allowed : 25.22 % Favored : 70.78 % 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: -0.32 (0.35), residues: 628 helix: 1.47 (0.31), residues: 297 sheet: -1.77 (0.57), residues: 78 loop : -1.77 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 646 HIS 0.003 0.001 HIS A 280 PHE 0.042 0.002 PHE A 616 TYR 0.034 0.001 TYR A 548 ARG 0.007 0.000 ARG A 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 387 MET cc_start: 0.9131 (mmm) cc_final: 0.8607 (mmm) REVERT: A 460 PHE cc_start: 0.7649 (m-10) cc_final: 0.7395 (m-10) REVERT: A 493 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8458 (tt) REVERT: A 546 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8235 (ttp80) REVERT: A 559 ARG cc_start: 0.8098 (ttp-110) cc_final: 0.7747 (ttp-110) REVERT: A 573 ASN cc_start: 0.8388 (m110) cc_final: 0.8162 (m110) REVERT: A 646 TRP cc_start: 0.9059 (t60) cc_final: 0.8766 (t60) REVERT: A 777 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8233 (tpp-160) outliers start: 23 outliers final: 16 residues processed: 108 average time/residue: 0.1577 time to fit residues: 22.7649 Evaluate side-chains 106 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 855 SER Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 894 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 10 optimal weight: 0.2980 chunk 38 optimal weight: 0.0670 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.0020 chunk 52 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 46 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.2926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.145927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119987 restraints weight = 9084.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123597 restraints weight = 5163.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126040 restraints weight = 3601.638| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6011 Z= 0.158 Angle : 0.631 11.140 8264 Z= 0.313 Chirality : 0.040 0.188 946 Planarity : 0.003 0.047 936 Dihedral : 15.502 87.176 1176 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.48 % Allowed : 26.61 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.31 (0.35), residues: 628 helix: 1.44 (0.31), residues: 297 sheet: -1.80 (0.58), residues: 80 loop : -1.71 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 646 HIS 0.002 0.000 HIS A 280 PHE 0.039 0.001 PHE A 616 TYR 0.032 0.001 TYR A 548 ARG 0.006 0.000 ARG A 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.12 seconds wall clock time: 35 minutes 20.60 seconds (2120.60 seconds total)