Starting phenix.real_space_refine on Tue Aug 4 17:56:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sd0_40348/08_2026/8sd0_40348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sd0_40348/08_2026/8sd0_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_40348/08_2026/8sd0_40348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sd0_40348/08_2026/8sd0_40348.map" model { file = "/net/cci-nas-00/data/ceres_data/8sd0_40348/08_2026/8sd0_40348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sd0_40348/08_2026/8sd0_40348.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 1.38, per 1000 atoms: 0.24 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: 0.52 Conformation dependent library (CDL) restraints added in 330.6 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: 0.42 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: 0.82 Time building geometry restraints manager: 0.68 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=" C1' G B 2 " pdb=" N9 G B 2 " ideal model delta sigma weight residual 1.483 1.459 0.024 1.50e-02 4.44e+03 2.52e+00 bond pdb=" N1 C B 19 " pdb=" C2 C B 19 " ideal model delta sigma weight residual 1.397 1.413 -0.016 1.00e-02 1.00e+04 2.46e+00 ... (remaining 6006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 8013 2.32 - 4.65: 203 4.65 - 6.97: 34 6.97 - 9.30: 11 9.30 - 11.62: 3 Bond angle restraints: 8264 Sorted by residual: angle pdb=" O5' U B 15 " pdb=" C5' U B 15 " pdb=" C4' U B 15 " ideal model delta sigma weight residual 109.40 113.41 -4.01 8.00e-01 1.56e+00 2.51e+01 angle pdb=" N1 C B 23 " pdb=" C2 C B 23 " pdb=" O2 C B 23 " ideal model delta sigma weight residual 118.90 121.69 -2.79 6.00e-01 2.78e+00 2.16e+01 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 ... (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: 698 0.050 - 0.100: 179 0.100 - 0.150: 57 0.150 - 0.200: 9 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 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 0.078 6015 Z= 0.233 Angle : 0.893 11.624 8264 Z= 0.539 Chirality : 0.052 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 : 9.60 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (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 ARG 0.023 0.001 ARG A 316 TYR 0.036 0.002 TYR A 548 PHE 0.026 0.002 PHE A 776 TRP 0.045 0.003 TRP A 646 HIS 0.002 0.001 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.21 ( 6011) covalent geometry : angle 0.89329 / 0.54 ( 8264) hydrogen bonds : bond 0.13540 / 9.87 ( 260) hydrogen bonds : angle 6.06561 / 4.15 ( 747) metal coordination : bond 0.00112 / 0.06 ( 3) Misc. bond : bond 0.07791 / 4.10 ( 1) *********************** 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 : 0.189 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: 0.0601 time to fit residues: 8.7519 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 : 0.209 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 623 HIS A 710 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.138456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112209 restraints weight = 9250.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115819 restraints weight = 5291.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118259 restraints weight = 3686.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119774 restraints weight = 2902.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120925 restraints weight = 2474.105| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6015 Z= 0.125 Angle : 0.560 7.647 8264 Z= 0.293 Chirality : 0.039 0.161 946 Planarity : 0.005 0.052 936 Dihedral : 15.508 92.028 1178 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.96 % Allowed : 25.57 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.33), residues: 628 helix: 0.91 (0.30), residues: 290 sheet: -1.90 (0.54), residues: 85 loop : -2.13 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 316 TYR 0.025 0.001 TYR A 548 PHE 0.023 0.001 PHE A 616 TRP 0.020 0.001 TRP A 646 HIS 0.010 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 6011) covalent geometry : angle 0.55994 / 0.29 ( 8264) hydrogen bonds : bond 0.05024 / 3.46 ( 260) hydrogen bonds : angle 4.50619 / 3.14 ( 747) metal coordination : bond 0.00152 / 0.08 ( 3) Misc. bond : bond 0.00571 / 0.30 ( 1) *********************** 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 106 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 777 ARG cc_start: 0.8475 (tpp80) cc_final: 0.7912 (tpp-160) outliers start: 17 outliers final: 7 residues processed: 103 average time/residue: 0.0598 time to fit residues: 8.5677 Evaluate side-chains 89 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 630 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU 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 21 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111353 restraints weight = 9152.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114855 restraints weight = 5269.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117235 restraints weight = 3693.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118782 restraints weight = 2914.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.119750 restraints weight = 2481.727| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6015 Z= 0.115 Angle : 0.537 7.640 8264 Z= 0.280 Chirality : 0.039 0.138 946 Planarity : 0.004 0.050 936 Dihedral : 15.423 92.165 1176 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.48 % Allowed : 23.48 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.33), residues: 628 helix: 1.28 (0.31), residues: 290 sheet: -1.73 (0.59), residues: 75 loop : -2.01 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 316 TYR 0.024 0.001 TYR A 548 PHE 0.028 0.001 PHE A 616 TRP 0.019 0.001 TRP A 646 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 6011) covalent geometry : angle 0.53681 / 0.28 ( 8264) hydrogen bonds : bond 0.04426 / 3.06 ( 260) hydrogen bonds : angle 4.21664 / 2.96 ( 747) metal coordination : bond 0.00167 / 0.08 ( 3) Misc. bond : bond 0.00106 / 0.06 ( 1) *********************** 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 114 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 777 ARG cc_start: 0.8500 (tpp80) cc_final: 0.8004 (tpp-160) outliers start: 20 outliers final: 13 residues processed: 110 average time/residue: 0.0645 time to fit residues: 9.8189 Evaluate side-chains 101 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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 506 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 0.0000 chunk 10 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN 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 = 0.3788 r_free = 0.3788 target = 0.142305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116227 restraints weight = 9058.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.119769 restraints weight = 5209.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122012 restraints weight = 3658.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.123715 restraints weight = 2921.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124719 restraints weight = 2476.389| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6015 Z= 0.108 Angle : 0.537 7.571 8264 Z= 0.279 Chirality : 0.038 0.130 946 Planarity : 0.004 0.048 936 Dihedral : 15.405 92.093 1176 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.17 % Allowed : 23.13 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.34), residues: 628 helix: 1.33 (0.30), residues: 296 sheet: -1.49 (0.61), residues: 70 loop : -1.97 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 316 TYR 0.016 0.001 TYR A 548 PHE 0.028 0.001 PHE A 616 TRP 0.018 0.001 TRP A 646 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 6011) covalent geometry : angle 0.53727 / 0.28 ( 8264) hydrogen bonds : bond 0.04117 / 2.82 ( 260) hydrogen bonds : angle 4.16263 / 2.92 ( 747) metal coordination : bond 0.00122 / 0.06 ( 3) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** 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: 24 poor density : 91 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 PHE cc_start: 0.7625 (m-10) cc_final: 0.7422 (m-10) REVERT: A 623 HIS cc_start: 0.8310 (t-90) cc_final: 0.8057 (t-170) REVERT: A 777 ARG cc_start: 0.8534 (tpp80) cc_final: 0.8040 (tpp-160) outliers start: 24 outliers final: 14 residues processed: 111 average time/residue: 0.0667 time to fit residues: 10.3407 Evaluate side-chains 101 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 496 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 775 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 13 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 42 optimal weight: 8.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3790 r_free = 0.3790 target = 0.142062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115801 restraints weight = 9093.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119356 restraints weight = 5230.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121800 restraints weight = 3681.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123415 restraints weight = 2900.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.124288 restraints weight = 2466.425| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6015 Z= 0.122 Angle : 0.553 8.260 8264 Z= 0.286 Chirality : 0.038 0.137 946 Planarity : 0.004 0.048 936 Dihedral : 15.361 91.751 1176 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.52 % Allowed : 23.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.34), residues: 628 helix: 1.32 (0.31), residues: 297 sheet: -1.55 (0.60), residues: 70 loop : -1.91 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 316 TYR 0.022 0.001 TYR A 548 PHE 0.037 0.001 PHE A 616 TRP 0.013 0.001 TRP A 646 HIS 0.002 0.000 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 6011) covalent geometry : angle 0.55336 / 0.29 ( 8264) hydrogen bonds : bond 0.04040 / 2.75 ( 260) hydrogen bonds : angle 4.11954 / 2.90 ( 747) metal coordination : bond 0.00180 / 0.09 ( 3) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** 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 115 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7556 (tt0) cc_final: 0.7186 (tt0) REVERT: A 623 HIS cc_start: 0.8368 (t-90) cc_final: 0.8145 (t-170) REVERT: A 777 ARG cc_start: 0.8561 (tpp80) cc_final: 0.8079 (tpp-160) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.0601 time to fit residues: 9.3368 Evaluate side-chains 105 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.204 ------------------------------------------------------------------------------- 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 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 496 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 718 VAL Chi-restraints excluded: chain A residue 775 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 34 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 710 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.138951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112637 restraints weight = 9062.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116071 restraints weight = 5275.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118395 restraints weight = 3737.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.119873 restraints weight = 2985.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120893 restraints weight = 2559.753| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6015 Z= 0.181 Angle : 0.608 8.459 8264 Z= 0.311 Chirality : 0.040 0.164 946 Planarity : 0.004 0.049 936 Dihedral : 15.318 91.182 1176 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 5.57 % Allowed : 24.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.34), residues: 628 helix: 1.38 (0.31), residues: 297 sheet: -1.70 (0.59), residues: 72 loop : -1.90 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.028 0.001 TYR A 548 PHE 0.036 0.002 PHE A 616 TRP 0.012 0.001 TRP A 646 HIS 0.007 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 6011) covalent geometry : angle 0.60804 / 0.31 ( 8264) hydrogen bonds : bond 0.04173 / 2.82 ( 260) hydrogen bonds : angle 4.17480 / 2.95 ( 747) metal coordination : bond 0.00349 / 0.17 ( 3) Misc. bond : bond 0.00058 / 0.03 ( 1) *********************** 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: 32 poor density : 87 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7657 (tt0) cc_final: 0.7322 (tt0) REVERT: A 623 HIS cc_start: 0.8421 (t-90) cc_final: 0.8219 (t-170) REVERT: A 777 ARG cc_start: 0.8579 (tpp80) cc_final: 0.8104 (tpp-160) outliers start: 32 outliers final: 21 residues processed: 113 average time/residue: 0.0671 time to fit residues: 10.4357 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 : 0.212 ------------------------------------------------------------------------------- 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 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 531 GLU 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 694 LEU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 775 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 25 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3771 r_free = 0.3771 target = 0.140619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114435 restraints weight = 9011.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117857 restraints weight = 5216.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120295 restraints weight = 3679.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121691 restraints weight = 2914.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.122819 restraints weight = 2509.804| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6015 Z= 0.121 Angle : 0.594 9.217 8264 Z= 0.300 Chirality : 0.040 0.181 946 Planarity : 0.004 0.048 936 Dihedral : 15.396 91.335 1176 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.34), residues: 628 helix: 1.37 (0.31), residues: 297 sheet: -1.50 (0.60), residues: 70 loop : -1.86 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 316 TYR 0.030 0.001 TYR A 548 PHE 0.033 0.001 PHE A 616 TRP 0.020 0.001 TRP A 646 HIS 0.002 0.000 HIS A 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6011) covalent geometry : angle 0.59418 / 0.30 ( 8264) hydrogen bonds : bond 0.04052 / 2.78 ( 260) hydrogen bonds : angle 4.12713 / 2.92 ( 747) metal coordination : bond 0.00139 / 0.07 ( 3) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** 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 117 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 91 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7681 (tt0) cc_final: 0.7421 (tt0) REVERT: A 479 MET cc_start: 0.8153 (mmt) cc_final: 0.7919 (mmt) REVERT: A 777 ARG cc_start: 0.8539 (tpp80) cc_final: 0.8077 (tpp-160) outliers start: 26 outliers final: 20 residues processed: 113 average time/residue: 0.0680 time to fit residues: 10.6051 Evaluate side-chains 105 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 694 LEU 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 11 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.0570 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 HIS ** 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 = 0.3783 r_free = 0.3783 target = 0.141439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115276 restraints weight = 8956.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.118783 restraints weight = 5165.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.121139 restraints weight = 3641.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122656 restraints weight = 2896.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.123747 restraints weight = 2468.514| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6015 Z= 0.117 Angle : 0.607 11.140 8264 Z= 0.305 Chirality : 0.040 0.199 946 Planarity : 0.004 0.047 936 Dihedral : 15.397 91.158 1176 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.35 % Allowed : 25.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.35), residues: 628 helix: 1.38 (0.31), residues: 297 sheet: -1.43 (0.61), residues: 70 loop : -1.83 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.032 0.001 TYR A 548 PHE 0.042 0.002 PHE A 616 TRP 0.019 0.001 TRP A 646 HIS 0.008 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 6011) covalent geometry : angle 0.60688 / 0.31 ( 8264) hydrogen bonds : bond 0.04011 / 2.75 ( 260) hydrogen bonds : angle 4.09034 / 2.90 ( 747) metal coordination : bond 0.00138 / 0.07 ( 3) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** 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 113 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7646 (tt0) cc_final: 0.7383 (tt0) REVERT: A 479 MET cc_start: 0.8093 (mmt) cc_final: 0.7876 (mmt) REVERT: A 777 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8136 (tpp-160) outliers start: 25 outliers final: 20 residues processed: 109 average time/residue: 0.0674 time to fit residues: 10.1178 Evaluate side-chains 104 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 623 HIS Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 694 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 63 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 280 HIS 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 = 0.3765 r_free = 0.3765 target = 0.139677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113516 restraints weight = 9181.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.116976 restraints weight = 5281.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119313 restraints weight = 3713.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120716 restraints weight = 2950.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121771 restraints weight = 2541.395| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6015 Z= 0.159 Angle : 0.641 10.423 8264 Z= 0.322 Chirality : 0.041 0.199 946 Planarity : 0.004 0.048 936 Dihedral : 15.363 90.783 1176 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.17 % Allowed : 25.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.35), residues: 628 helix: 1.40 (0.31), residues: 297 sheet: -1.76 (0.57), residues: 78 loop : -1.80 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 466 TYR 0.031 0.001 TYR A 548 PHE 0.045 0.002 PHE A 616 TRP 0.018 0.001 TRP A 646 HIS 0.015 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 ( 6011) covalent geometry : angle 0.64121 / 0.32 ( 8264) hydrogen bonds : bond 0.04106 / 2.81 ( 260) hydrogen bonds : angle 4.13849 / 2.93 ( 747) metal coordination : bond 0.00282 / 0.14 ( 3) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** 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 111 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7720 (tt0) cc_final: 0.7389 (tt0) REVERT: A 546 ARG cc_start: 0.8479 (ttt-90) cc_final: 0.8172 (ttt180) REVERT: A 777 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8187 (tpp-160) outliers start: 24 outliers final: 20 residues processed: 106 average time/residue: 0.0645 time to fit residues: 9.4410 Evaluate side-chains 108 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 694 LEU 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 7 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 2 optimal weight: 0.1980 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 280 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 = 0.3794 r_free = 0.3794 target = 0.142010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115814 restraints weight = 9148.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119346 restraints weight = 5237.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.121711 restraints weight = 3664.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.123354 restraints weight = 2892.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.124222 restraints weight = 2460.769| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6015 Z= 0.116 Angle : 0.618 10.892 8264 Z= 0.310 Chirality : 0.040 0.202 946 Planarity : 0.004 0.048 936 Dihedral : 15.452 90.676 1176 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.48 % Allowed : 25.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.35), residues: 628 helix: 1.40 (0.31), residues: 297 sheet: -1.74 (0.57), residues: 78 loop : -1.75 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 466 TYR 0.031 0.001 TYR A 548 PHE 0.042 0.002 PHE A 616 TRP 0.018 0.001 TRP A 646 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 6011) covalent geometry : angle 0.61846 / 0.31 ( 8264) hydrogen bonds : bond 0.04003 / 2.75 ( 260) hydrogen bonds : angle 4.09774 / 2.90 ( 747) metal coordination : bond 0.00107 / 0.05 ( 3) Misc. bond : bond 0.00044 / 0.02 ( 1) ********************** 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 : 0.206 Fit side-chains revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7689 (tt0) cc_final: 0.7366 (tt0) REVERT: A 546 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8213 (ttp80) REVERT: A 777 ARG cc_start: 0.8534 (tpp80) cc_final: 0.8139 (tpp-160) outliers start: 20 outliers final: 17 residues processed: 109 average time/residue: 0.0712 time to fit residues: 10.5805 Evaluate side-chains 105 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 496 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 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 65 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 784 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 = 0.3752 r_free = 0.3752 target = 0.138750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112516 restraints weight = 9025.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.115911 restraints weight = 5297.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118182 restraints weight = 3756.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119673 restraints weight = 3003.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.120522 restraints weight = 2584.184| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6015 Z= 0.191 Angle : 0.689 10.381 8264 Z= 0.347 Chirality : 0.042 0.187 946 Planarity : 0.004 0.048 936 Dihedral : 15.380 90.046 1176 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.17 % Allowed : 25.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.35), residues: 628 helix: 1.33 (0.32), residues: 297 sheet: -1.83 (0.61), residues: 68 loop : -1.89 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 466 TYR 0.033 0.002 TYR A 548 PHE 0.045 0.002 PHE A 616 TRP 0.018 0.001 TRP A 646 HIS 0.004 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 6011) covalent geometry : angle 0.68869 / 0.35 ( 8264) hydrogen bonds : bond 0.04234 / 2.90 ( 260) hydrogen bonds : angle 4.22101 / 2.99 ( 747) metal coordination : bond 0.00375 / 0.19 ( 3) Misc. bond : bond 0.00057 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1054.52 seconds wall clock time: 18 minutes 57.92 seconds (1137.92 seconds total)