Starting phenix.real_space_refine on Thu Jul 2 02:09:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sd0_40348/07_2026/8sd0_40348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sd0_40348/07_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_40348/07_2026/8sd0_40348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sd0_40348/07_2026/8sd0_40348.map" model { file = "/net/cci-nas-00/data/ceres_data/8sd0_40348/07_2026/8sd0_40348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sd0_40348/07_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-dev-6108/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: 1.01, per 1000 atoms: 0.17 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: 0.34 Conformation dependent library (CDL) restraints added in 256.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1222 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 6 sheets defined 51.4% alpha, 10.2% beta 5 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 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: 0.81 Time building geometry restraints manager: 0.47 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=" 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 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 ... (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=" 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 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 ... (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: 0.450 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.930 Find NCS groups from input model: 0.020 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.420 ------------------------------------------------------------------------------- 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= 0.229 Angle : 0.860 11.624 8264 Z= 0.504 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 : 9.60 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 0.00402 / 0.21 ( 6011) covalent geometry : angle 0.86030 / 0.50 ( 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 : 0.141 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: 0.0654 time to fit residues: 9.2936 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 : 0.127 ------------------------------------------------------------------------------- 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: 10.0000 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 = 0.3745 r_free = 0.3745 target = 0.138332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112078 restraints weight = 9258.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115638 restraints weight = 5319.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118059 restraints weight = 3721.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.119680 restraints weight = 2927.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120713 restraints weight = 2478.693| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6015 Z= 0.125 Angle : 0.556 7.746 8264 Z= 0.291 Chirality : 0.039 0.159 946 Planarity : 0.005 0.050 936 Dihedral : 15.581 93.778 1178 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.13 % Allowed : 25.22 % 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 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: -0.97 (0.33), residues: 628 helix: 0.98 (0.30), residues: 290 sheet: -1.90 (0.53), residues: 85 loop : -2.13 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 316 TYR 0.025 0.001 TYR A 548 PHE 0.021 0.001 PHE A 616 TRP 0.018 0.001 TRP A 646 HIS 0.009 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 6011) covalent geometry : angle 0.55576 / 0.29 ( 8264) hydrogen bonds : bond 0.04771 / 3.26 ( 260) hydrogen bonds : angle 4.45102 / 3.10 ( 747) metal coordination : bond 0.00155 / 0.08 ( 3) Misc. bond : bond 0.00528 / 0.28 ( 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 110 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 777 ARG cc_start: 0.8463 (tpp80) cc_final: 0.7935 (tpp-160) outliers start: 18 outliers final: 7 residues processed: 106 average time/residue: 0.0600 time to fit residues: 8.6972 Evaluate side-chains 92 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114202 restraints weight = 8975.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117689 restraints weight = 5208.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120064 restraints weight = 3688.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.121559 restraints weight = 2928.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122625 restraints weight = 2516.760| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6015 Z= 0.148 Angle : 0.554 7.956 8264 Z= 0.289 Chirality : 0.039 0.154 946 Planarity : 0.004 0.052 936 Dihedral : 15.462 93.291 1176 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.00 % Allowed : 23.83 % 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 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: -0.64 (0.34), residues: 628 helix: 1.26 (0.31), residues: 290 sheet: -1.74 (0.60), residues: 75 loop : -2.00 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 316 TYR 0.020 0.001 TYR A 548 PHE 0.029 0.001 PHE A 616 TRP 0.019 0.001 TRP A 646 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6011) covalent geometry : angle 0.55398 / 0.29 ( 8264) hydrogen bonds : bond 0.04536 / 3.13 ( 260) hydrogen bonds : angle 4.26573 / 2.99 ( 747) metal coordination : bond 0.00280 / 0.14 ( 3) Misc. bond : bond 0.00143 / 0.08 ( 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 115 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 316 ARG cc_start: 0.6737 (mmm160) cc_final: 0.6491 (mmm160) REVERT: A 778 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6821 (mp0) outliers start: 23 outliers final: 14 residues processed: 110 average time/residue: 0.0526 time to fit residues: 8.1056 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 : 0.242 ------------------------------------------------------------------------------- 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 500 GLN Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 778 GLU 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: 3.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN A 557 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 = 0.3734 r_free = 0.3734 target = 0.137393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110746 restraints weight = 9157.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.114147 restraints weight = 5385.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116481 restraints weight = 3826.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118011 restraints weight = 3046.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118995 restraints weight = 2620.890| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6015 Z= 0.196 Angle : 0.593 8.483 8264 Z= 0.307 Chirality : 0.041 0.166 946 Planarity : 0.004 0.053 936 Dihedral : 15.450 92.591 1176 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 5.04 % Allowed : 23.83 % 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: -0.56 (0.34), residues: 628 helix: 1.37 (0.31), residues: 291 sheet: -1.85 (0.58), residues: 75 loop : -1.96 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.019 0.001 TYR A 548 PHE 0.028 0.002 PHE A 616 TRP 0.013 0.001 TRP A 646 HIS 0.005 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 ( 6011) covalent geometry : angle 0.59300 / 0.31 ( 8264) hydrogen bonds : bond 0.04412 / 3.02 ( 260) hydrogen bonds : angle 4.23728 / 2.99 ( 747) metal coordination : bond 0.00380 / 0.19 ( 3) Misc. bond : bond 0.00252 / 0.13 ( 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 118 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7708 (tt0) cc_final: 0.7364 (tt0) REVERT: A 316 ARG cc_start: 0.6820 (mmm160) cc_final: 0.6571 (mmm160) REVERT: A 387 MET cc_start: 0.9227 (mmm) cc_final: 0.8740 (mmm) REVERT: A 623 HIS cc_start: 0.8349 (t-90) cc_final: 0.8127 (t-170) REVERT: A 778 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6768 (mp0) outliers start: 29 outliers final: 21 residues processed: 112 average time/residue: 0.0540 time to fit residues: 8.4068 Evaluate side-chains 106 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 434 LEU 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 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 770 THR Chi-restraints excluded: chain A residue 778 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.138644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112313 restraints weight = 9114.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115766 restraints weight = 5296.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118081 restraints weight = 3758.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119591 restraints weight = 2995.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120511 restraints weight = 2565.925| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1619 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= 0.141 Angle : 0.568 8.279 8264 Z= 0.291 Chirality : 0.039 0.155 946 Planarity : 0.004 0.052 936 Dihedral : 15.503 92.993 1176 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.87 % Allowed : 24.00 % 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: -0.46 (0.34), residues: 628 helix: 1.50 (0.31), residues: 289 sheet: -1.82 (0.58), residues: 75 loop : -1.95 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.018 0.001 TYR A 548 PHE 0.036 0.001 PHE A 616 TRP 0.010 0.001 TRP A 646 HIS 0.006 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 6011) covalent geometry : angle 0.56795 / 0.29 ( 8264) hydrogen bonds : bond 0.04259 / 2.94 ( 260) hydrogen bonds : angle 4.14427 / 2.93 ( 747) metal coordination : bond 0.00232 / 0.12 ( 3) Misc. bond : bond 0.00046 / 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 118 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7712 (tt0) cc_final: 0.7386 (tt0) REVERT: A 316 ARG cc_start: 0.6805 (mmm160) cc_final: 0.6562 (mmm160) REVERT: A 387 MET cc_start: 0.9214 (mmm) cc_final: 0.8812 (mmm) REVERT: A 493 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 778 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6757 (mp0) outliers start: 28 outliers final: 19 residues processed: 112 average time/residue: 0.0509 time to fit residues: 7.7862 Evaluate side-chains 106 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 506 THR 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 770 THR Chi-restraints excluded: chain A residue 778 GLU 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: 1.9990 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 0.0270 chunk 64 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.140610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.113957 restraints weight = 9049.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117473 restraints weight = 5234.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.119834 restraints weight = 3706.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.121378 restraints weight = 2954.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.122302 restraints weight = 2534.619| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1681 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= 0.113 Angle : 0.562 10.377 8264 Z= 0.287 Chirality : 0.039 0.143 946 Planarity : 0.004 0.050 936 Dihedral : 15.529 93.285 1176 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 5.39 % Allowed : 24.17 % 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: -0.40 (0.34), residues: 628 helix: 1.41 (0.31), residues: 295 sheet: -1.53 (0.60), residues: 70 loop : -1.92 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.023 0.001 TYR A 548 PHE 0.015 0.001 PHE A 616 TRP 0.009 0.001 TRP A 646 HIS 0.006 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6011) covalent geometry : angle 0.56159 / 0.29 ( 8264) hydrogen bonds : bond 0.04129 / 2.84 ( 260) hydrogen bonds : angle 4.08380 / 2.88 ( 747) metal coordination : bond 0.00130 / 0.06 ( 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: 31 poor density : 88 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7667 (tt0) cc_final: 0.7343 (tt0) REVERT: A 316 ARG cc_start: 0.6676 (mmm160) cc_final: 0.6469 (mmm160) REVERT: A 387 MET cc_start: 0.9179 (mmm) cc_final: 0.8550 (mmm) REVERT: A 493 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8385 (tt) REVERT: A 778 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6643 (mp0) outliers start: 31 outliers final: 19 residues processed: 113 average time/residue: 0.0639 time to fit residues: 9.7528 Evaluate side-chains 106 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 506 THR 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 694 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL 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: 0.0030 chunk 24 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.114486 restraints weight = 9010.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.118026 restraints weight = 5193.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120440 restraints weight = 3655.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.122046 restraints weight = 2890.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.122963 restraints weight = 2460.897| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1744 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= 0.113 Angle : 0.576 10.369 8264 Z= 0.291 Chirality : 0.039 0.175 946 Planarity : 0.004 0.050 936 Dihedral : 15.519 93.030 1176 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 5.04 % Allowed : 25.39 % Favored : 69.57 % 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: 1.45 (0.31), residues: 295 sheet: -1.46 (0.60), residues: 70 loop : -1.89 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.030 0.001 TYR A 548 PHE 0.015 0.001 PHE A 616 TRP 0.009 0.001 TRP A 646 HIS 0.002 0.000 HIS A 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6011) covalent geometry : angle 0.57567 / 0.29 ( 8264) hydrogen bonds : bond 0.04059 / 2.78 ( 260) hydrogen bonds : angle 4.04031 / 2.86 ( 747) metal coordination : bond 0.00120 / 0.06 ( 3) Misc. bond : bond 0.00052 / 0.03 ( 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 121 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7659 (tt0) cc_final: 0.7340 (tt0) REVERT: A 316 ARG cc_start: 0.6692 (mmm160) cc_final: 0.6485 (mmm160) REVERT: A 387 MET cc_start: 0.9142 (mmm) cc_final: 0.8529 (mmm) REVERT: A 493 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8345 (tt) REVERT: A 778 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6629 (mp0) outliers start: 29 outliers final: 20 residues processed: 115 average time/residue: 0.0576 time to fit residues: 9.0151 Evaluate side-chains 109 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 506 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL 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: 1.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 0.2980 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.115029 restraints weight = 8959.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.118523 restraints weight = 5186.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120898 restraints weight = 3656.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122458 restraints weight = 2895.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123471 restraints weight = 2476.099| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6015 Z= 0.116 Angle : 0.591 10.885 8264 Z= 0.298 Chirality : 0.039 0.197 946 Planarity : 0.004 0.049 936 Dihedral : 15.521 92.670 1176 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.52 % Allowed : 25.91 % Favored : 69.57 % 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: -0.36 (0.35), residues: 628 helix: 1.48 (0.31), residues: 295 sheet: -1.78 (0.56), residues: 78 loop : -1.81 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 811 TYR 0.031 0.001 TYR A 548 PHE 0.016 0.001 PHE A 616 TRP 0.025 0.001 TRP A 646 HIS 0.005 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 6011) covalent geometry : angle 0.59108 / 0.30 ( 8264) hydrogen bonds : bond 0.04020 / 2.76 ( 260) hydrogen bonds : angle 4.01353 / 2.84 ( 747) metal coordination : bond 0.00122 / 0.06 ( 3) Misc. bond : bond 0.00052 / 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 118 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7650 (tt0) cc_final: 0.7320 (tt0) REVERT: A 316 ARG cc_start: 0.6660 (mmm160) cc_final: 0.6449 (mmm160) REVERT: A 387 MET cc_start: 0.9117 (mmm) cc_final: 0.8533 (mmm) REVERT: A 493 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 778 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6617 (mp0) outliers start: 26 outliers final: 20 residues processed: 113 average time/residue: 0.0596 time to fit residues: 9.1146 Evaluate side-chains 109 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 778 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL 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: 1.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3764 r_free = 0.3764 target = 0.139872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113793 restraints weight = 9041.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117324 restraints weight = 5151.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119657 restraints weight = 3600.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121128 restraints weight = 2843.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.122278 restraints weight = 2438.997| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6015 Z= 0.137 Angle : 0.621 10.728 8264 Z= 0.314 Chirality : 0.040 0.195 946 Planarity : 0.004 0.050 936 Dihedral : 15.504 92.212 1176 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 4.52 % Allowed : 25.74 % Favored : 69.74 % 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: -0.36 (0.35), residues: 628 helix: 1.44 (0.31), residues: 297 sheet: -1.76 (0.57), residues: 78 loop : -1.81 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 811 TYR 0.033 0.001 TYR A 548 PHE 0.031 0.002 PHE A 471 TRP 0.022 0.001 TRP A 646 HIS 0.002 0.000 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 6011) covalent geometry : angle 0.62093 / 0.31 ( 8264) hydrogen bonds : bond 0.04055 / 2.78 ( 260) hydrogen bonds : angle 4.03762 / 2.86 ( 747) metal coordination : bond 0.00200 / 0.10 ( 3) Misc. bond : bond 0.00055 / 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 115 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.125 Fit side-chains revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7653 (tt0) cc_final: 0.7321 (tt0) REVERT: A 387 MET cc_start: 0.9142 (mmm) cc_final: 0.8550 (mmm) REVERT: A 493 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8358 (tt) REVERT: A 777 ARG cc_start: 0.8457 (tpp80) cc_final: 0.8052 (tpp-160) REVERT: A 778 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6676 (mp0) outliers start: 26 outliers final: 18 residues processed: 110 average time/residue: 0.0609 time to fit residues: 8.8836 Evaluate side-chains 106 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 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 778 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL 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: 6.9990 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3779 r_free = 0.3779 target = 0.140982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114623 restraints weight = 9111.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118157 restraints weight = 5232.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.120529 restraints weight = 3689.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.122125 restraints weight = 2915.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.123147 restraints weight = 2491.031| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6015 Z= 0.127 Angle : 0.638 10.847 8264 Z= 0.323 Chirality : 0.040 0.197 946 Planarity : 0.004 0.049 936 Dihedral : 15.534 92.080 1176 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % 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 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: -0.36 (0.35), residues: 628 helix: 1.44 (0.31), residues: 297 sheet: -1.75 (0.57), residues: 78 loop : -1.81 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 316 TYR 0.035 0.001 TYR A 548 PHE 0.030 0.001 PHE A 471 TRP 0.022 0.001 TRP A 646 HIS 0.002 0.000 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 6011) covalent geometry : angle 0.63763 / 0.32 ( 8264) hydrogen bonds : bond 0.04028 / 2.77 ( 260) hydrogen bonds : angle 4.04077 / 2.86 ( 747) metal coordination : bond 0.00139 / 0.07 ( 3) Misc. bond : bond 0.00054 / 0.03 ( 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: 24 poor density : 88 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 249 GLU cc_start: 0.7643 (tt0) cc_final: 0.7304 (tt0) REVERT: A 387 MET cc_start: 0.9130 (mmm) cc_final: 0.8537 (mmm) REVERT: A 493 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8354 (tt) REVERT: A 777 ARG cc_start: 0.8472 (tpp80) cc_final: 0.8076 (tpp-160) REVERT: A 778 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6671 (mp0) outliers start: 24 outliers final: 19 residues processed: 109 average time/residue: 0.0561 time to fit residues: 8.2276 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 : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN 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 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 778 GLU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 843 VAL 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 65 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3757 r_free = 0.3757 target = 0.138973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112616 restraints weight = 9026.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116067 restraints weight = 5261.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118378 restraints weight = 3735.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.119901 restraints weight = 2981.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.120776 restraints weight = 2556.014| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6015 Z= 0.190 Angle : 0.667 11.140 8264 Z= 0.339 Chirality : 0.041 0.184 946 Planarity : 0.004 0.050 936 Dihedral : 15.481 91.508 1176 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.35 % Allowed : 25.57 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.40 (0.35), residues: 628 helix: 1.40 (0.31), residues: 297 sheet: -1.75 (0.57), residues: 78 loop : -1.84 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 316 TYR 0.033 0.002 TYR A 548 PHE 0.027 0.002 PHE A 471 TRP 0.022 0.001 TRP A 646 HIS 0.004 0.001 HIS A 871 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 ( 6011) covalent geometry : angle 0.66715 / 0.34 ( 8264) hydrogen bonds : bond 0.04146 / 2.83 ( 260) hydrogen bonds : angle 4.10131 / 2.91 ( 747) metal coordination : bond 0.00352 / 0.18 ( 3) Misc. bond : bond 0.00049 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 881.36 seconds wall clock time: 15 minutes 58.63 seconds (958.63 seconds total)