Starting phenix.real_space_refine on Thu Mar 6 09:40:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sd0_40348/03_2025/8sd0_40348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sd0_40348/03_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_40348/03_2025/8sd0_40348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sd0_40348/03_2025/8sd0_40348.map" model { file = "/net/cci-nas-00/data/ceres_data/8sd0_40348/03_2025/8sd0_40348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sd0_40348/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.97, 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: 1.37 Conformation dependent library (CDL) restraints added in 703.4 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: 1.71 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: 1.88 Time building geometry restraints manager: 1.64 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: 0.580 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: 0.050 Set scattering table: 0.060 Process input model: 19.110 Find NCS groups from input model: 0.050 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.660 ------------------------------------------------------------------------------- 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 : 0.624 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: 0.1897 time to fit residues: 26.9142 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 : 0.593 ------------------------------------------------------------------------------- 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 = 0.142152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115873 restraints weight = 8993.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119410 restraints weight = 5201.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121823 restraints weight = 3661.508| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 93.832 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 : 0.597 Fit side-chains revert: symmetry clash REVERT: A 777 ARG cc_start: 0.8530 (tpp80) cc_final: 0.8037 (tpp-160) outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 0.1633 time to fit residues: 24.1705 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 : 0.609 ------------------------------------------------------------------------------- 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: 0.9980 chunk 59 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 36 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.143392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117015 restraints weight = 8929.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120553 restraints weight = 5181.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122965 restraints weight = 3663.483| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1474 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= 0.140 Angle : 0.540 9.522 8264 Z= 0.269 Chirality : 0.038 0.134 946 Planarity : 0.004 0.048 936 Dihedral : 15.459 93.064 1176 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % 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: -0.49 (0.34), residues: 628 helix: 1.31 (0.30), residues: 297 sheet: -1.55 (0.60), residues: 70 loop : -1.96 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 646 HIS 0.002 0.000 HIS A 317 PHE 0.029 0.001 PHE A 616 TYR 0.023 0.001 TYR A 548 ARG 0.006 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 117 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.6697 (mmm160) cc_final: 0.6467 (mmm160) REVERT: A 777 ARG cc_start: 0.8551 (tpp80) cc_final: 0.8122 (tpp-160) outliers start: 21 outliers final: 12 residues processed: 115 average time/residue: 0.1583 time to fit residues: 24.5702 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 : 0.570 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 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 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 = 0.3787 r_free = 0.3787 target = 0.141738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115327 restraints weight = 9087.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118806 restraints weight = 5308.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121201 restraints weight = 3771.323| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6011 Z= 0.171 Angle : 0.550 9.236 8264 Z= 0.274 Chirality : 0.039 0.167 946 Planarity : 0.004 0.048 936 Dihedral : 15.409 92.042 1176 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.00 % Allowed : 24.35 % Favored : 71.65 % 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: 1.50 (0.31), residues: 297 sheet: -1.57 (0.59), residues: 70 loop : -1.87 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 646 HIS 0.002 0.000 HIS A 871 PHE 0.032 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 115 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.6733 (mmm160) cc_final: 0.6499 (mmm160) REVERT: A 623 HIS cc_start: 0.8416 (t-90) cc_final: 0.8195 (t-170) REVERT: A 777 ARG cc_start: 0.8575 (tpp80) cc_final: 0.8094 (tpp-160) outliers start: 23 outliers final: 15 residues processed: 111 average time/residue: 0.1695 time to fit residues: 25.5752 Evaluate side-chains 101 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 40 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 20 optimal weight: 0.0070 chunk 43 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.141678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115581 restraints weight = 8934.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118958 restraints weight = 5150.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121359 restraints weight = 3657.987| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1746 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= 0.176 Angle : 0.575 10.431 8264 Z= 0.284 Chirality : 0.039 0.186 946 Planarity : 0.003 0.047 936 Dihedral : 15.433 91.362 1176 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.52 % Allowed : 24.35 % 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: -0.29 (0.34), residues: 628 helix: 1.48 (0.31), residues: 297 sheet: -1.64 (0.60), residues: 72 loop : -1.80 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 646 HIS 0.004 0.001 HIS A 280 PHE 0.035 0.001 PHE A 616 TYR 0.028 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 125 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.6747 (mmm160) cc_final: 0.6519 (mmm160) REVERT: A 493 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 623 HIS cc_start: 0.8415 (t-90) cc_final: 0.8209 (t-170) REVERT: A 759 LYS cc_start: 0.8758 (tptp) cc_final: 0.8518 (tptp) REVERT: A 777 ARG cc_start: 0.8582 (tpp80) cc_final: 0.8132 (tpp-160) outliers start: 26 outliers final: 17 residues processed: 122 average time/residue: 0.1538 time to fit residues: 25.2780 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 : 0.570 ------------------------------------------------------------------------------- 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: 2.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 0.0050 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.140636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114372 restraints weight = 8978.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117834 restraints weight = 5249.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120187 restraints weight = 3711.782| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6011 Z= 0.196 Angle : 0.597 10.749 8264 Z= 0.295 Chirality : 0.040 0.185 946 Planarity : 0.004 0.047 936 Dihedral : 15.451 90.635 1176 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.52 % Allowed : 24.17 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.35), residues: 628 helix: 1.50 (0.31), residues: 297 sheet: -1.66 (0.60), residues: 72 loop : -1.81 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 646 HIS 0.002 0.000 HIS A 871 PHE 0.036 0.001 PHE A 616 TYR 0.031 0.001 TYR A 548 ARG 0.002 0.000 ARG A 466 *********************** 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 120 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.6794 (mmm160) cc_final: 0.6569 (mmm160) REVERT: A 470 LYS cc_start: 0.8156 (tppt) cc_final: 0.7927 (tppt) REVERT: A 493 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8463 (tt) REVERT: A 538 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 759 LYS cc_start: 0.8788 (tptp) cc_final: 0.8570 (tptp) REVERT: A 777 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8217 (tpp-160) outliers start: 26 outliers final: 18 residues processed: 116 average time/residue: 0.1735 time to fit residues: 27.2188 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 : 0.664 ------------------------------------------------------------------------------- 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 538 LEU 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 855 SER 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: 10.0000 chunk 51 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 41 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 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 = 0.3796 r_free = 0.3796 target = 0.142432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116300 restraints weight = 9015.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119859 restraints weight = 5169.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.122255 restraints weight = 3626.050| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1988 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= 0.153 Angle : 0.592 10.883 8264 Z= 0.292 Chirality : 0.039 0.204 946 Planarity : 0.003 0.046 936 Dihedral : 15.491 90.331 1176 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 4.52 % Allowed : 25.04 % Favored : 70.43 % 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: -1.74 (0.60), residues: 74 loop : -1.75 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 646 HIS 0.005 0.001 HIS A 623 PHE 0.033 0.001 PHE A 616 TYR 0.032 0.001 TYR A 548 ARG 0.002 0.000 ARG A 811 *********************** 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 125 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: A 493 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8449 (tt) REVERT: A 777 ARG cc_start: 0.8634 (tpp80) cc_final: 0.8217 (tpp-160) outliers start: 26 outliers final: 15 residues processed: 122 average time/residue: 0.1649 time to fit residues: 27.1434 Evaluate side-chains 105 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 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 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: 4.9990 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: 0.7980 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 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 = 0.3804 r_free = 0.3804 target = 0.143010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.116799 restraints weight = 8959.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120351 restraints weight = 5208.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122706 restraints weight = 3667.772| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2122 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= 0.167 Angle : 0.635 11.409 8264 Z= 0.313 Chirality : 0.040 0.208 946 Planarity : 0.004 0.052 936 Dihedral : 15.483 89.604 1176 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.17 % Allowed : 25.91 % 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: -0.25 (0.35), residues: 628 helix: 1.53 (0.31), residues: 297 sheet: -1.75 (0.60), residues: 74 loop : -1.76 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 646 HIS 0.005 0.001 HIS A 280 PHE 0.041 0.002 PHE A 616 TYR 0.031 0.001 TYR A 548 ARG 0.011 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: 24 poor density : 96 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 493 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 777 ARG cc_start: 0.8633 (tpp80) cc_final: 0.8234 (tpp-160) outliers start: 24 outliers final: 16 residues processed: 116 average time/residue: 0.1833 time to fit residues: 29.1629 Evaluate side-chains 107 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 21 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 0.0870 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3795 r_free = 0.3795 target = 0.142381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117007 restraints weight = 8928.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120471 restraints weight = 5112.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.122815 restraints weight = 3560.445| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2182 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= 0.168 Angle : 0.635 11.480 8264 Z= 0.312 Chirality : 0.040 0.200 946 Planarity : 0.004 0.049 936 Dihedral : 15.480 88.840 1176 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.65 % Allowed : 26.09 % 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: -0.24 (0.35), residues: 628 helix: 1.52 (0.31), residues: 297 sheet: -1.69 (0.60), residues: 74 loop : -1.73 (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 0.041 0.001 PHE A 616 TYR 0.033 0.001 TYR A 548 ARG 0.011 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 114 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.627 Fit side-chains revert: symmetry clash REVERT: A 493 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8462 (tt) REVERT: A 559 ARG cc_start: 0.8062 (ttp-110) cc_final: 0.7681 (ttp-110) REVERT: A 573 ASN cc_start: 0.8352 (m110) cc_final: 0.8115 (m110) REVERT: A 777 ARG cc_start: 0.8633 (tpp80) cc_final: 0.8252 (tpp-160) outliers start: 21 outliers final: 17 residues processed: 111 average time/residue: 0.1558 time to fit residues: 23.5528 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 : 0.624 ------------------------------------------------------------------------------- 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 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 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 37 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 0.0470 chunk 22 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.143348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117123 restraints weight = 9041.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120686 restraints weight = 5192.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.123017 restraints weight = 3636.150| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6011 Z= 0.167 Angle : 0.636 11.589 8264 Z= 0.313 Chirality : 0.040 0.204 946 Planarity : 0.004 0.046 936 Dihedral : 15.468 88.066 1176 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.48 % Allowed : 26.26 % 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: -1.85 (0.57), residues: 80 loop : -1.69 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 646 HIS 0.001 0.000 HIS A 281 PHE 0.041 0.002 PHE A 616 TYR 0.034 0.001 TYR A 548 ARG 0.011 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 112 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 255 MET cc_start: 0.8383 (mmt) cc_final: 0.7984 (tpt) REVERT: A 493 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8478 (tt) REVERT: A 559 ARG cc_start: 0.8086 (ttp-110) cc_final: 0.7731 (ttp-110) REVERT: A 573 ASN cc_start: 0.8342 (m110) cc_final: 0.8120 (m110) REVERT: A 777 ARG cc_start: 0.8631 (tpp80) cc_final: 0.8237 (tpp-160) outliers start: 20 outliers final: 15 residues processed: 107 average time/residue: 0.1445 time to fit residues: 21.3477 Evaluate side-chains 106 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 PHE 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 493 LEU 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 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: 1.9990 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** A 876 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115751 restraints weight = 9067.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119257 restraints weight = 5248.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121653 restraints weight = 3683.212| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2276 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= 0.187 Angle : 0.639 11.633 8264 Z= 0.314 Chirality : 0.040 0.190 946 Planarity : 0.004 0.047 936 Dihedral : 15.438 86.382 1176 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 3.48 % Allowed : 26.26 % 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: -0.23 (0.35), residues: 628 helix: 1.55 (0.32), residues: 297 sheet: -1.77 (0.62), residues: 68 loop : -1.75 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 646 HIS 0.002 0.000 HIS A 871 PHE 0.039 0.002 PHE A 616 TYR 0.033 0.001 TYR A 548 ARG 0.010 0.000 ARG A 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.37 seconds wall clock time: 35 minutes 23.98 seconds (2123.98 seconds total)