Starting phenix.real_space_refine on Thu Jul 2 02:32:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dvr_27743/07_2026/8dvr_27743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dvr_27743/07_2026/8dvr_27743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2026/8dvr_27743.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2026/8dvr_27743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2026/8dvr_27743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2026/8dvr_27743.map" model { file = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2026/8dvr_27743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dvr_27743/07_2026/8dvr_27743.cif" } resolution = 3.3 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 24 5.49 5 S 31 5.16 5 C 3492 2.51 5 N 947 2.21 5 O 1106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s 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: 5601 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5123 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 445 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4191 SG CYS A 810 23.312 29.188 27.887 1.00 29.78 S ATOM 4630 SG CYS A 864 19.045 29.309 28.690 1.00 26.94 S ATOM 4669 SG CYS A 869 21.454 27.047 30.233 1.00 32.07 S Time building chain proxies: 1.10, per 1000 atoms: 0.20 Number of scatterers: 5601 At special positions: 0 Unit cell: (79.032, 99.324, 85.44, 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 24 15.00 O 1106 8.00 N 947 7.00 C 3492 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 152.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 5 sheets defined 51.3% alpha, 8.3% beta 10 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.515A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Proline residue: A 253 - end of helix removed outlier: 4.032A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 removed outlier: 3.835A pdb=" N LYS A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.912A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.827A 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 448 through 452 removed outlier: 3.994A pdb=" N GLN A 451 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 452 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 448 through 452' Processing helix chain 'A' and resid 469 through 487 Processing helix chain 'A' and resid 492 through 497 removed outlier: 4.511A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 Processing helix chain 'A' and resid 529 through 558 removed outlier: 3.858A pdb=" N ARG A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.724A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 602 removed outlier: 3.794A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 removed outlier: 4.162A 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 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing helix chain 'A' and resid 639 through 650 removed outlier: 3.529A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 771 removed outlier: 4.107A pdb=" N ILE A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 794 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.524A pdb=" N LYS A 839 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 840' Processing helix chain 'A' and resid 889 through 892 removed outlier: 3.556A pdb=" N PHE A 892 " --> pdb=" O ILE A 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 889 through 892' Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296 removed outlier: 7.183A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 461 through 462 removed outlier: 3.894A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819 removed outlier: 6.874A pdb=" N LEU A 808 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833 removed outlier: 4.500A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846 removed outlier: 5.749A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE A 862 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 714 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 0.82 Time building geometry restraints manager: 0.44 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: 1711 1.34 - 1.46: 902 1.46 - 1.57: 3057 1.57 - 1.69: 45 1.69 - 1.81: 43 Bond restraints: 5758 Sorted by residual: bond pdb=" C ILE A 884 " pdb=" O ILE A 884 " ideal model delta sigma weight residual 1.232 1.241 -0.009 8.90e-03 1.26e+04 9.64e-01 bond pdb=" N PRO A 401 " pdb=" CA PRO A 401 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.60e-01 bond pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta sigma weight residual 1.449 1.461 -0.012 1.45e-02 4.76e+03 6.38e-01 bond pdb=" C VAL A 414 " pdb=" N GLY A 415 " ideal model delta sigma weight residual 1.331 1.319 0.011 1.46e-02 4.69e+03 5.79e-01 bond pdb=" CA ILE A 916 " pdb=" CB ILE A 916 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.55e-02 4.16e+03 4.96e-01 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 7739 1.42 - 2.84: 110 2.84 - 4.27: 19 4.27 - 5.69: 3 5.69 - 7.11: 1 Bond angle restraints: 7872 Sorted by residual: angle pdb=" N ILE A 897 " pdb=" CA ILE A 897 " pdb=" C ILE A 897 " ideal model delta sigma weight residual 111.90 109.07 2.83 8.10e-01 1.52e+00 1.22e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 111.90 109.36 2.54 8.10e-01 1.52e+00 9.82e+00 angle pdb=" N ALA A 410 " pdb=" CA ALA A 410 " pdb=" C ALA A 410 " ideal model delta sigma weight residual 114.04 110.54 3.50 1.24e+00 6.50e-01 7.98e+00 angle pdb=" C2' GTP B 201 " pdb=" C3' GTP B 201 " pdb=" C4' GTP B 201 " ideal model delta sigma weight residual 111.00 103.89 7.11 3.00e+00 1.11e-01 5.62e+00 angle pdb=" N ILE A 884 " pdb=" CA ILE A 884 " pdb=" C ILE A 884 " ideal model delta sigma weight residual 107.61 110.31 -2.70 1.19e+00 7.06e-01 5.14e+00 ... (remaining 7867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3130 17.86 - 35.71: 262 35.71 - 53.57: 53 53.57 - 71.43: 7 71.43 - 89.28: 9 Dihedral angle restraints: 3461 sinusoidal: 1589 harmonic: 1872 Sorted by residual: dihedral pdb=" C8 GTP B 201 " pdb=" C1' GTP B 201 " pdb=" N9 GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sinusoidal sigma weight residual 104.59 23.63 80.96 1 2.00e+01 2.50e-03 2.02e+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 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CB GLU A 895 " pdb=" CG GLU A 895 " pdb=" CD GLU A 895 " pdb=" OE1 GLU A 895 " ideal model delta sinusoidal sigma weight residual 0.00 -89.28 89.28 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 557 0.024 - 0.049: 201 0.049 - 0.073: 75 0.073 - 0.098: 43 0.098 - 0.122: 17 Chirality restraints: 893 Sorted by residual: chirality pdb=" CA ILE A 439 " pdb=" N ILE A 439 " pdb=" C ILE A 439 " pdb=" CB ILE A 439 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 875 " pdb=" N ILE A 875 " pdb=" C ILE A 875 " pdb=" CB ILE A 875 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA ILE A 629 " pdb=" N ILE A 629 " pdb=" C ILE A 629 " pdb=" CB ILE A 629 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 890 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 381 " -0.016 5.00e-02 4.00e+02 2.41e-02 9.31e-01 pdb=" N PRO A 382 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 382 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 382 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 300 " -0.013 5.00e-02 4.00e+02 1.98e-02 6.26e-01 pdb=" N PRO A 301 " 0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " -0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 884 " 0.013 5.00e-02 4.00e+02 1.96e-02 6.12e-01 pdb=" N PRO A 885 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO A 885 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 885 " 0.011 5.00e-02 4.00e+02 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1363 2.79 - 3.32: 5223 3.32 - 3.85: 9434 3.85 - 4.37: 10722 4.37 - 4.90: 18061 Nonbonded interactions: 44803 Sorted by model distance: nonbonded pdb=" ND2 ASN A 259 " pdb=" O ASP A 435 " model vdw 2.267 3.120 nonbonded pdb=" OG SER A 362 " pdb=" OG SER A 364 " model vdw 2.325 3.040 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.342 3.040 nonbonded pdb=" OH TYR A 622 " pdb=" OD1 ASN A 692 " model vdw 2.349 3.040 nonbonded pdb=" N ASP A 580 " pdb=" OD1 ASP A 580 " model vdw 2.355 3.120 ... (remaining 44798 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 individual isotropic 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.770 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 : 0.008 0.524 5762 Z= 0.288 Angle : 0.456 7.111 7872 Z= 0.269 Chirality : 0.035 0.122 893 Planarity : 0.002 0.024 924 Dihedral : 13.618 89.284 2241 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.40 % Allowed : 9.46 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.25 (0.31), residues: 627 helix: 0.37 (0.28), residues: 280 sheet: -3.31 (0.51), residues: 81 loop : -3.00 (0.32), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 575 TYR 0.003 0.000 TYR A 390 PHE 0.007 0.001 PHE A 856 TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00166 / 0.10 ( 5758) covalent geometry : angle 0.45573 / 0.27 ( 7872) hydrogen bonds : bond 0.12908 / 8.20 ( 269) hydrogen bonds : angle 5.04169 / 3.43 ( 764) metal coordination : bond 0.35537 / 17.80 ( 3) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.143 Fit side-chains revert: symmetry clash REVERT: A 492 ASP cc_start: 0.7105 (p0) cc_final: 0.6518 (t0) REVERT: A 759 LYS cc_start: 0.7895 (mtmt) cc_final: 0.7442 (ttpp) REVERT: A 763 ASP cc_start: 0.7733 (t70) cc_final: 0.7508 (t0) REVERT: A 789 PHE cc_start: 0.7957 (t80) cc_final: 0.7567 (t80) REVERT: A 889 ILE cc_start: 0.9123 (tp) cc_final: 0.8588 (tp) outliers start: 8 outliers final: 4 residues processed: 139 average time/residue: 0.0857 time to fit residues: 14.6914 Evaluate side-chains 93 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 499 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN A 341 ASN A 380 GLN A 495 ASN A 517 GLN A 573 ASN ** A 876 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.159655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133538 restraints weight = 6392.467| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.74 r_work: 0.3437 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5762 Z= 0.103 Angle : 0.478 7.740 7872 Z= 0.235 Chirality : 0.038 0.174 893 Planarity : 0.003 0.033 924 Dihedral : 5.995 87.015 941 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.50 % Allowed : 10.86 % Favored : 85.64 % 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: -1.13 (0.33), residues: 627 helix: 1.52 (0.30), residues: 288 sheet: -3.18 (0.50), residues: 84 loop : -2.63 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 811 TYR 0.007 0.001 TYR A 383 PHE 0.007 0.001 PHE A 371 TRP 0.005 0.001 TRP A 873 HIS 0.002 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 5758) covalent geometry : angle 0.47786 / 0.23 ( 7872) hydrogen bonds : bond 0.03284 / 2.23 ( 269) hydrogen bonds : angle 3.76369 / 2.57 ( 764) metal coordination : bond 0.00765 / 0.37 ( 3) Misc. bond : bond 0.00027 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.131 Fit side-chains REVERT: A 255 MET cc_start: 0.8655 (mtt) cc_final: 0.8196 (mtt) REVERT: A 289 GLN cc_start: 0.6843 (mp10) cc_final: 0.6560 (mp10) REVERT: A 632 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8174 (tt) REVERT: A 653 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7964 (pp) REVERT: A 759 LYS cc_start: 0.8082 (mtmt) cc_final: 0.7548 (ttpp) REVERT: A 763 ASP cc_start: 0.8260 (t70) cc_final: 0.7945 (t0) REVERT: A 771 TRP cc_start: 0.6532 (m-10) cc_final: 0.6273 (m-10) REVERT: A 789 PHE cc_start: 0.8326 (t80) cc_final: 0.7973 (t80) REVERT: A 872 ASP cc_start: 0.8192 (t0) cc_final: 0.7802 (t0) outliers start: 20 outliers final: 8 residues processed: 108 average time/residue: 0.0686 time to fit residues: 9.4958 Evaluate side-chains 87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 39 optimal weight: 0.0570 chunk 15 optimal weight: 0.0970 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN A 384 ASN A 573 ASN A 710 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133680 restraints weight = 6413.792| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.81 r_work: 0.3248 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5762 Z= 0.102 Angle : 0.490 8.124 7872 Z= 0.239 Chirality : 0.039 0.189 893 Planarity : 0.003 0.042 924 Dihedral : 6.112 90.344 937 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 4.03 % Allowed : 13.31 % Favored : 82.66 % 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: -0.62 (0.34), residues: 627 helix: 1.95 (0.30), residues: 289 sheet: -3.01 (0.52), residues: 84 loop : -2.38 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 811 TYR 0.007 0.001 TYR A 879 PHE 0.011 0.001 PHE A 616 TRP 0.006 0.001 TRP A 873 HIS 0.003 0.000 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 5758) covalent geometry : angle 0.49023 / 0.24 ( 7872) hydrogen bonds : bond 0.03282 / 2.18 ( 269) hydrogen bonds : angle 3.63367 / 2.47 ( 764) metal coordination : bond 0.00139 / 0.07 ( 3) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.194 Fit side-chains REVERT: A 255 MET cc_start: 0.8821 (mtt) cc_final: 0.8502 (mtt) REVERT: A 492 ASP cc_start: 0.7229 (m-30) cc_final: 0.5975 (t0) REVERT: A 632 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8200 (tt) REVERT: A 647 ILE cc_start: 0.8476 (mt) cc_final: 0.8219 (mp) REVERT: A 653 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7951 (pp) REVERT: A 759 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7540 (ttpp) REVERT: A 763 ASP cc_start: 0.8174 (t70) cc_final: 0.7857 (t0) REVERT: A 816 LEU cc_start: 0.8831 (tp) cc_final: 0.8613 (tp) REVERT: A 872 ASP cc_start: 0.8326 (t0) cc_final: 0.8118 (t0) outliers start: 23 outliers final: 9 residues processed: 99 average time/residue: 0.0567 time to fit residues: 7.5364 Evaluate side-chains 84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 340 ASN A 495 ASN A 573 ASN A 710 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.153323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.124796 restraints weight = 6417.982| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.79 r_work: 0.3226 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5762 Z= 0.137 Angle : 0.530 8.591 7872 Z= 0.259 Chirality : 0.041 0.193 893 Planarity : 0.003 0.044 924 Dihedral : 6.412 94.575 937 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.63 % Allowed : 16.11 % Favored : 81.26 % 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: -0.48 (0.34), residues: 627 helix: 2.10 (0.31), residues: 285 sheet: -2.89 (0.49), residues: 92 loop : -2.25 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 811 TYR 0.010 0.001 TYR A 383 PHE 0.009 0.001 PHE A 371 TRP 0.004 0.001 TRP A 873 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 5758) covalent geometry : angle 0.52967 / 0.26 ( 7872) hydrogen bonds : bond 0.03520 / 2.36 ( 269) hydrogen bonds : angle 3.68193 / 2.47 ( 764) metal coordination : bond 0.00205 / 0.10 ( 3) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.130 Fit side-chains REVERT: A 492 ASP cc_start: 0.7272 (m-30) cc_final: 0.6015 (t0) REVERT: A 632 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8312 (tt) REVERT: A 647 ILE cc_start: 0.8707 (mt) cc_final: 0.8478 (mp) REVERT: A 653 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7809 (pp) REVERT: A 759 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7621 (ttpp) REVERT: A 763 ASP cc_start: 0.8214 (t70) cc_final: 0.7887 (t0) REVERT: A 816 LEU cc_start: 0.8970 (tp) cc_final: 0.8685 (tp) outliers start: 15 outliers final: 7 residues processed: 89 average time/residue: 0.0567 time to fit residues: 7.0261 Evaluate side-chains 76 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.156101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.126891 restraints weight = 6455.805| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.86 r_work: 0.3168 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5762 Z= 0.121 Angle : 0.512 8.402 7872 Z= 0.249 Chirality : 0.040 0.164 893 Planarity : 0.003 0.043 924 Dihedral : 6.470 94.807 937 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.28 % Allowed : 18.21 % Favored : 79.51 % 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: -0.27 (0.35), residues: 627 helix: 2.14 (0.30), residues: 294 sheet: -2.86 (0.52), residues: 85 loop : -2.13 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.008 0.001 TYR A 566 PHE 0.009 0.001 PHE A 371 TRP 0.003 0.001 TRP A 512 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 5758) covalent geometry : angle 0.51155 / 0.25 ( 7872) hydrogen bonds : bond 0.03420 / 2.29 ( 269) hydrogen bonds : angle 3.62654 / 2.44 ( 764) metal coordination : bond 0.00169 / 0.09 ( 3) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.160 Fit side-chains revert: symmetry clash REVERT: A 492 ASP cc_start: 0.7422 (m-30) cc_final: 0.5971 (t0) REVERT: A 616 PHE cc_start: 0.7427 (t80) cc_final: 0.7185 (t80) REVERT: A 632 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8374 (tt) REVERT: A 653 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7968 (pp) REVERT: A 759 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7593 (ttpp) REVERT: A 763 ASP cc_start: 0.8390 (t70) cc_final: 0.8084 (t0) REVERT: A 816 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8708 (tp) outliers start: 13 outliers final: 8 residues processed: 77 average time/residue: 0.0498 time to fit residues: 5.3290 Evaluate side-chains 77 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122056 restraints weight = 6443.588| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.82 r_work: 0.3158 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5762 Z= 0.132 Angle : 0.526 8.787 7872 Z= 0.255 Chirality : 0.040 0.169 893 Planarity : 0.003 0.040 924 Dihedral : 6.598 95.702 936 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.50 % Allowed : 18.74 % Favored : 77.76 % 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: -0.17 (0.35), residues: 627 helix: 2.17 (0.30), residues: 294 sheet: -2.70 (0.52), residues: 85 loop : -2.04 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.008 0.001 TYR A 566 PHE 0.008 0.001 PHE A 371 TRP 0.004 0.001 TRP A 512 HIS 0.002 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 5758) covalent geometry : angle 0.52593 / 0.25 ( 7872) hydrogen bonds : bond 0.03532 / 2.36 ( 269) hydrogen bonds : angle 3.65574 / 2.46 ( 764) metal coordination : bond 0.00159 / 0.08 ( 3) Misc. bond : bond 0.00070 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.197 Fit side-chains REVERT: A 492 ASP cc_start: 0.7271 (m-30) cc_final: 0.6030 (t0) REVERT: A 616 PHE cc_start: 0.7433 (t80) cc_final: 0.7225 (t80) REVERT: A 632 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8315 (tt) REVERT: A 647 ILE cc_start: 0.8803 (mt) cc_final: 0.8583 (mp) REVERT: A 653 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7950 (pp) REVERT: A 759 LYS cc_start: 0.8033 (mtmt) cc_final: 0.7530 (ttpp) REVERT: A 763 ASP cc_start: 0.8250 (t70) cc_final: 0.7930 (t0) REVERT: A 794 GLN cc_start: 0.7299 (OUTLIER) cc_final: 0.6961 (pp30) REVERT: A 816 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8698 (tp) outliers start: 20 outliers final: 12 residues processed: 84 average time/residue: 0.0586 time to fit residues: 6.7412 Evaluate side-chains 79 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 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 489 ILE Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.155256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125785 restraints weight = 6527.934| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.86 r_work: 0.3128 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5762 Z= 0.124 Angle : 0.545 8.772 7872 Z= 0.261 Chirality : 0.041 0.209 893 Planarity : 0.003 0.037 924 Dihedral : 6.604 95.997 936 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.50 % Allowed : 19.09 % Favored : 77.41 % 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: -0.04 (0.35), residues: 627 helix: 2.24 (0.30), residues: 294 sheet: -2.57 (0.53), residues: 85 loop : -1.97 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 811 TYR 0.008 0.001 TYR A 390 PHE 0.009 0.001 PHE A 371 TRP 0.004 0.001 TRP A 512 HIS 0.002 0.000 HIS A 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 5758) covalent geometry : angle 0.54473 / 0.26 ( 7872) hydrogen bonds : bond 0.03474 / 2.32 ( 269) hydrogen bonds : angle 3.64461 / 2.45 ( 764) metal coordination : bond 0.00155 / 0.08 ( 3) Misc. bond : bond 0.00060 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.193 Fit side-chains REVERT: A 460 PHE cc_start: 0.8523 (m-80) cc_final: 0.8294 (m-80) REVERT: A 487 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7892 (mttp) REVERT: A 492 ASP cc_start: 0.7346 (m-30) cc_final: 0.6081 (t0) REVERT: A 521 MET cc_start: 0.7832 (OUTLIER) cc_final: 0.7602 (mtp) REVERT: A 632 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8334 (tt) REVERT: A 647 ILE cc_start: 0.8832 (mt) cc_final: 0.8619 (mp) REVERT: A 653 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7959 (pp) REVERT: A 759 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7523 (ttpp) REVERT: A 763 ASP cc_start: 0.8294 (t70) cc_final: 0.7973 (t0) REVERT: A 794 GLN cc_start: 0.7287 (OUTLIER) cc_final: 0.6954 (pp30) REVERT: A 816 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8689 (tp) outliers start: 20 outliers final: 12 residues processed: 87 average time/residue: 0.0624 time to fit residues: 7.4005 Evaluate side-chains 85 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 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 489 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.152148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122995 restraints weight = 6461.113| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.85 r_work: 0.3164 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5762 Z= 0.129 Angle : 0.550 8.809 7872 Z= 0.264 Chirality : 0.041 0.196 893 Planarity : 0.003 0.037 924 Dihedral : 6.622 96.217 936 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.33 % Allowed : 19.09 % Favored : 77.58 % 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: 0.05 (0.35), residues: 627 helix: 2.20 (0.30), residues: 295 sheet: -2.30 (0.56), residues: 79 loop : -1.90 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 811 TYR 0.008 0.001 TYR A 390 PHE 0.021 0.001 PHE A 616 TRP 0.004 0.001 TRP A 512 HIS 0.001 0.000 HIS A 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 5758) covalent geometry : angle 0.55016 / 0.26 ( 7872) hydrogen bonds : bond 0.03517 / 2.35 ( 269) hydrogen bonds : angle 3.64688 / 2.45 ( 764) metal coordination : bond 0.00156 / 0.08 ( 3) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.213 Fit side-chains REVERT: A 460 PHE cc_start: 0.8452 (m-80) cc_final: 0.8244 (m-80) REVERT: A 487 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7865 (mttp) REVERT: A 492 ASP cc_start: 0.7281 (m-30) cc_final: 0.6082 (t0) REVERT: A 521 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: A 526 PRO cc_start: 0.8005 (Cg_endo) cc_final: 0.7729 (Cg_exo) REVERT: A 632 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 653 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8044 (pp) REVERT: A 759 LYS cc_start: 0.8070 (mtmt) cc_final: 0.7614 (ttpp) REVERT: A 763 ASP cc_start: 0.8239 (t70) cc_final: 0.7959 (t0) REVERT: A 794 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6970 (pp30) outliers start: 19 outliers final: 12 residues processed: 86 average time/residue: 0.0585 time to fit residues: 7.0309 Evaluate side-chains 83 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 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 489 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 46 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126163 restraints weight = 6469.894| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.93 r_work: 0.3154 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5762 Z= 0.119 Angle : 0.543 8.603 7872 Z= 0.261 Chirality : 0.041 0.195 893 Planarity : 0.003 0.039 924 Dihedral : 6.600 96.354 936 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 2.80 % Allowed : 19.61 % Favored : 77.58 % 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: 0.02 (0.35), residues: 627 helix: 2.22 (0.30), residues: 296 sheet: -2.49 (0.52), residues: 85 loop : -1.88 (0.38), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 811 TYR 0.009 0.001 TYR A 390 PHE 0.025 0.001 PHE A 616 TRP 0.004 0.001 TRP A 512 HIS 0.001 0.000 HIS A 847 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 5758) covalent geometry : angle 0.54313 / 0.26 ( 7872) hydrogen bonds : bond 0.03443 / 2.30 ( 269) hydrogen bonds : angle 3.63693 / 2.44 ( 764) metal coordination : bond 0.00148 / 0.07 ( 3) Misc. bond : bond 0.00052 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 487 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7876 (mttp) REVERT: A 492 ASP cc_start: 0.7286 (m-30) cc_final: 0.6058 (t0) REVERT: A 521 MET cc_start: 0.7860 (OUTLIER) cc_final: 0.7626 (mtp) REVERT: A 526 PRO cc_start: 0.8056 (Cg_endo) cc_final: 0.7780 (Cg_exo) REVERT: A 632 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8326 (tt) REVERT: A 647 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8573 (mp) REVERT: A 653 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7956 (pp) REVERT: A 759 LYS cc_start: 0.8187 (mtmt) cc_final: 0.7718 (ttpp) REVERT: A 763 ASP cc_start: 0.8263 (t70) cc_final: 0.8002 (t0) REVERT: A 794 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6975 (pp30) outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 0.0568 time to fit residues: 6.7302 Evaluate side-chains 87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 794 GLN Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 8 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 41 optimal weight: 0.0000 chunk 43 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.161856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132830 restraints weight = 6522.838| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.86 r_work: 0.3227 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5762 Z= 0.092 Angle : 0.513 7.809 7872 Z= 0.247 Chirality : 0.040 0.188 893 Planarity : 0.003 0.037 924 Dihedral : 6.384 93.655 936 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.28 % Allowed : 20.32 % Favored : 77.41 % 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: 0.26 (0.35), residues: 627 helix: 2.38 (0.30), residues: 294 sheet: -2.19 (0.57), residues: 79 loop : -1.78 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 811 TYR 0.011 0.001 TYR A 390 PHE 0.025 0.001 PHE A 616 TRP 0.004 0.001 TRP A 771 HIS 0.007 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 5758) covalent geometry : angle 0.51284 / 0.25 ( 7872) hydrogen bonds : bond 0.03161 / 2.12 ( 269) hydrogen bonds : angle 3.49443 / 2.37 ( 764) metal coordination : bond 0.00068 / 0.03 ( 3) Misc. bond : bond 0.00053 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.197 Fit side-chains revert: symmetry clash REVERT: A 411 SER cc_start: 0.8881 (p) cc_final: 0.8633 (m) REVERT: A 495 ASN cc_start: 0.7657 (m-40) cc_final: 0.7339 (p0) REVERT: A 526 PRO cc_start: 0.8032 (Cg_endo) cc_final: 0.7767 (Cg_exo) REVERT: A 632 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8263 (tt) REVERT: A 647 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8360 (mp) REVERT: A 653 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7919 (pp) REVERT: A 759 LYS cc_start: 0.8088 (mtmt) cc_final: 0.7701 (ttpp) REVERT: A 763 ASP cc_start: 0.8209 (t70) cc_final: 0.7985 (t0) REVERT: A 872 ASP cc_start: 0.8315 (t0) cc_final: 0.8073 (t0) outliers start: 13 outliers final: 8 residues processed: 81 average time/residue: 0.0665 time to fit residues: 7.3048 Evaluate side-chains 79 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 531 GLU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 903 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 0.0020 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 573 ASN A 786 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.121775 restraints weight = 6457.620| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.79 r_work: 0.3138 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5762 Z= 0.111 Angle : 0.532 8.515 7872 Z= 0.257 Chirality : 0.040 0.183 893 Planarity : 0.003 0.037 924 Dihedral : 6.467 94.807 936 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.10 % Allowed : 20.67 % Favored : 77.23 % 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: 0.28 (0.35), residues: 627 helix: 2.35 (0.30), residues: 295 sheet: -2.10 (0.58), residues: 79 loop : -1.74 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 811 TYR 0.011 0.001 TYR A 390 PHE 0.028 0.001 PHE A 616 TRP 0.008 0.001 TRP A 512 HIS 0.009 0.001 HIS A 786 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 5758) covalent geometry : angle 0.53164 / 0.26 ( 7872) hydrogen bonds : bond 0.03348 / 2.24 ( 269) hydrogen bonds : angle 3.58483 / 2.42 ( 764) metal coordination : bond 0.00111 / 0.06 ( 3) Misc. bond : bond 0.00053 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1233.34 seconds wall clock time: 21 minutes 57.57 seconds (1317.57 seconds total)