Starting phenix.real_space_refine on Thu Sep 10 23:56:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ejb_48099/09_2026/9ejb_48099.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ejb_48099/09_2026/9ejb_48099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ejb_48099/09_2026/9ejb_48099.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ejb_48099/09_2026/9ejb_48099.map" model { file = "/net/cci-nas-00/data/ceres_data/9ejb_48099/09_2026/9ejb_48099.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ejb_48099/09_2026/9ejb_48099.cif" } resolution = 3.6 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= 0.014 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 Fe 4 7.16 5 P 9 5.49 5 S 35 5.16 5 C 3481 2.51 5 N 962 2.21 5 O 1032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5523 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5332 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 21, 'TRANS': 646} Chain breaks: 4 Chain: "B" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 183 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1396 SG CYS A 350 44.478 31.042 34.471 1.00101.97 S ATOM 1070 SG CYS A 310 48.114 31.387 30.775 1.00116.81 S ATOM 983 SG CYS A 298 44.975 36.213 31.346 1.00105.47 S ATOM 862 SG CYS A 283 48.590 35.012 36.268 1.00104.57 S Time building chain proxies: 1.21, per 1000 atoms: 0.22 Number of scatterers: 5523 At special positions: 0 Unit cell: (65.412, 86.112, 101.016, 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) Fe 4 26.01 S 35 16.00 P 9 15.00 O 1032 8.00 N 962 7.00 C 3481 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=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 125.9 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 350 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 310 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 298 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 283 " Number of angles added : 12 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1256 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 50.0% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 22 through 38 removed outlier: 4.230A pdb=" N ASN A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 65 removed outlier: 4.547A pdb=" N SER A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA A 62 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 4.025A pdb=" N ARG A 265 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 302 removed outlier: 3.750A pdb=" N MET A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 302 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 removed outlier: 7.430A pdb=" N ASN A 306 " --> pdb=" O ASP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.513A pdb=" N ILE A 319 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER A 320 " --> pdb=" O HIS A 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 320' Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.527A pdb=" N LYS A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 374 through 382 removed outlier: 4.128A pdb=" N SER A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 411 through 428 removed outlier: 3.940A pdb=" N VAL A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 451 removed outlier: 4.010A pdb=" N ILE A 446 " --> pdb=" O CYS A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 Processing helix chain 'A' and resid 485 through 498 removed outlier: 4.467A pdb=" N ILE A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 543 removed outlier: 6.543A pdb=" N GLN A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 546 No H-bonds generated for 'chain 'A' and resid 544 through 546' Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 669 through 687 removed outlier: 3.532A pdb=" N GLN A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 Processing helix chain 'A' and resid 712 through 721 removed outlier: 3.648A pdb=" N ASN A 716 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 749 removed outlier: 3.994A pdb=" N ILE A 746 " --> pdb=" O TYR A 742 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LYS A 747 " --> pdb=" O TYR A 743 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 809 removed outlier: 4.795A pdb=" N LYS A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 830 Processing helix chain 'A' and resid 852 through 857 Processing helix chain 'A' and resid 861 through 866 removed outlier: 3.624A pdb=" N GLN A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.776A pdb=" N LEU A 635 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 274 removed outlier: 6.316A pdb=" N ILE A 246 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 408 through 410 Processing sheet with id=AA5, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.991A pdb=" N TRP A 647 " --> pdb=" O LEU A 842 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 756 through 757 removed outlier: 7.553A pdb=" N ILE A 691 " --> pdb=" O LEU A 757 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 2398 1.43 - 1.64: 3205 1.64 - 1.85: 44 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 5659 Sorted by residual: bond pdb=" N VAL A 284 " pdb=" CA VAL A 284 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.29e+00 bond pdb=" N CYS A 350 " pdb=" CA CYS A 350 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 7.77e+00 bond pdb=" N PHE A 312 " pdb=" CA PHE A 312 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.22e-02 6.72e+03 6.90e+00 bond pdb=" C3' DA B 3 " pdb=" C2' DA B 3 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.38e+00 bond pdb=" N HIS A 285 " pdb=" CA HIS A 285 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.39e-02 5.18e+03 6.30e+00 ... (remaining 5654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 7508 2.37 - 4.73: 153 4.73 - 7.10: 23 7.10 - 9.46: 5 9.46 - 11.83: 2 Bond angle restraints: 7691 Sorted by residual: angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.28 -2.38 6.00e-01 2.78e+00 1.58e+01 angle pdb=" CA ARG A 251 " pdb=" CB ARG A 251 " pdb=" CG ARG A 251 " ideal model delta sigma weight residual 114.10 122.04 -7.94 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB MET A 381 " pdb=" CG MET A 381 " pdb=" SD MET A 381 " ideal model delta sigma weight residual 112.70 124.53 -11.83 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N ILE A 377 " pdb=" CA ILE A 377 " pdb=" C ILE A 377 " ideal model delta sigma weight residual 112.96 109.36 3.60 1.00e+00 1.00e+00 1.29e+01 angle pdb=" O4 DT B 9 " pdb=" C4 DT B 9 " pdb=" C5 DT B 9 " ideal model delta sigma weight residual 124.90 122.43 2.47 7.00e-01 2.04e+00 1.25e+01 ... (remaining 7686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 2705 17.54 - 35.08: 467 35.08 - 52.62: 138 52.62 - 70.16: 49 70.16 - 87.69: 12 Dihedral angle restraints: 3371 sinusoidal: 1428 harmonic: 1943 Sorted by residual: dihedral pdb=" CA PHE A 623 " pdb=" C PHE A 623 " pdb=" N SER A 624 " pdb=" CA SER A 624 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA PRO A 18 " pdb=" C PRO A 18 " pdb=" N TYR A 19 " pdb=" CA TYR A 19 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA THR A 250 " pdb=" C THR A 250 " pdb=" N ARG A 251 " pdb=" CA ARG A 251 " ideal model delta harmonic sigma weight residual 180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.217: 855 4.217 - 8.434: 0 8.434 - 12.651: 0 12.651 - 16.869: 0 16.869 - 21.086: 4 Chirality restraints: 859 Sorted by residual: chirality pdb="FE4 SF4 A1301 " pdb=" S1 SF4 A1301 " pdb=" S2 SF4 A1301 " pdb=" S3 SF4 A1301 " both_signs ideal model delta sigma weight residual False 10.55 -10.53 21.09 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE3 SF4 A1301 " pdb=" S1 SF4 A1301 " pdb=" S2 SF4 A1301 " pdb=" S4 SF4 A1301 " both_signs ideal model delta sigma weight residual False -10.55 10.53 -21.08 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE2 SF4 A1301 " pdb=" S1 SF4 A1301 " pdb=" S3 SF4 A1301 " pdb=" S4 SF4 A1301 " both_signs ideal model delta sigma weight residual False 10.55 -10.52 21.08 2.00e-01 2.50e+01 1.11e+04 ... (remaining 856 not shown) Planarity restraints: 944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 779 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C VAL A 779 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 779 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE A 780 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 538 " -0.011 2.00e-02 2.50e+03 1.55e-02 4.18e+00 pdb=" CG PHE A 538 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 538 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 538 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 538 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 538 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 714 " -0.011 2.00e-02 2.50e+03 1.16e-02 3.35e+00 pdb=" CG TRP A 714 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 714 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 714 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 714 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 714 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 714 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 714 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 714 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 714 " 0.001 2.00e-02 2.50e+03 ... (remaining 941 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1067 2.77 - 3.30: 5177 3.30 - 3.84: 9160 3.84 - 4.37: 10269 4.37 - 4.90: 17786 Nonbonded interactions: 43459 Sorted by model distance: nonbonded pdb=" O ARG A 543 " pdb=" NH1 ARG A 543 " model vdw 2.239 3.120 nonbonded pdb=" O ALA A 406 " pdb=" OH TYR A 548 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O GLU A 394 " model vdw 2.262 3.040 nonbonded pdb=" O ALA A 678 " pdb=" OG SER A 682 " model vdw 2.301 3.040 nonbonded pdb=" NH2 ARG A 539 " pdb=" OG SER A 601 " model vdw 2.303 3.120 ... (remaining 43454 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: 4.190 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.280 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 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 0.391 5663 Z= 0.334 Angle : 0.917 21.871 7703 Z= 0.464 Chirality : 1.439 21.086 859 Planarity : 0.005 0.044 944 Dihedral : 20.192 87.694 2115 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 4.77 % Allowed : 33.73 % Favored : 61.50 % 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: -2.03 (0.33), residues: 658 helix: -0.29 (0.30), residues: 298 sheet: -1.62 (0.77), residues: 55 loop : -2.40 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 831 TYR 0.013 0.002 TYR A 268 PHE 0.035 0.002 PHE A 538 TRP 0.029 0.002 TRP A 714 HIS 0.019 0.002 HIS A 639 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.26 ( 5659) covalent geometry : angle 0.82696 / 0.46 ( 7691) hydrogen bonds : bond 0.16690 / 10.58 ( 221) hydrogen bonds : angle 7.55895 / 5.21 ( 645) metal coordination : bond 0.26508 / 13.14 ( 4) metal coordination : angle 10.09374 / 4.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 65 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7090 (p-80) REVERT: A 526 MET cc_start: 0.8072 (tmm) cc_final: 0.7815 (tmm) REVERT: A 660 LEU cc_start: 0.6767 (mt) cc_final: 0.5843 (tt) REVERT: A 672 PHE cc_start: 0.5629 (OUTLIER) cc_final: 0.4376 (t80) REVERT: A 746 ILE cc_start: 0.0343 (OUTLIER) cc_final: -0.0162 (tp) REVERT: A 751 GLU cc_start: -0.1141 (OUTLIER) cc_final: -0.1807 (tp30) REVERT: A 790 LYS cc_start: 0.6841 (mtmp) cc_final: 0.6366 (mttm) REVERT: A 867 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6295 (mp10) outliers start: 28 outliers final: 16 residues processed: 90 average time/residue: 0.0790 time to fit residues: 9.3039 Evaluate side-chains 85 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 639 HIS Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 786 PHE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 867 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.0070 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4823 r_free = 0.4823 target = 0.243213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.211034 restraints weight = 6488.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.214024 restraints weight = 5155.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.214151 restraints weight = 4318.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.214969 restraints weight = 4050.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.215234 restraints weight = 3684.229| |-----------------------------------------------------------------------------| r_work (final): 0.4577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6362 moved from start: 0.0800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.265 5663 Z= 0.402 Angle : 2.485 50.575 7703 Z= 1.422 Chirality : 0.433 6.424 859 Planarity : 0.004 0.037 944 Dihedral : 14.328 65.551 864 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 5.96 % Allowed : 30.32 % Favored : 63.71 % 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: -1.72 (0.33), residues: 658 helix: 0.05 (0.30), residues: 303 sheet: -0.31 (0.93), residues: 43 loop : -2.56 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 543 TYR 0.009 0.001 TYR A 548 PHE 0.029 0.002 PHE A 538 TRP 0.011 0.001 TRP A 647 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.01166 / 0.40 ( 5659) covalent geometry : angle 2.16169 / 1.42 ( 7691) hydrogen bonds : bond 0.03938 / 2.49 ( 221) hydrogen bonds : angle 5.72045 / 4.05 ( 645) metal coordination : bond 0.03921 / 1.93 ( 4) metal coordination : angle 31.13408 / 16.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 247 TYR cc_start: 0.5281 (m-10) cc_final: 0.4814 (m-10) REVERT: A 432 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8278 (mtmm) REVERT: A 499 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6595 (pm20) REVERT: A 526 MET cc_start: 0.8125 (tmm) cc_final: 0.7862 (tmm) REVERT: A 660 LEU cc_start: 0.6587 (mt) cc_final: 0.5807 (tt) REVERT: A 672 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.4448 (t80) REVERT: A 746 ILE cc_start: 0.0376 (OUTLIER) cc_final: -0.0255 (tp) REVERT: A 790 LYS cc_start: 0.6671 (mtmp) cc_final: 0.6203 (mttm) REVERT: A 798 ARG cc_start: 0.7031 (mtm180) cc_final: 0.6474 (ttm110) outliers start: 35 outliers final: 17 residues processed: 104 average time/residue: 0.0820 time to fit residues: 11.0815 Evaluate side-chains 88 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 432 LYS Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 835 HIS Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 881 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 639 HIS A 815 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.241459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.210492 restraints weight = 6403.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.212001 restraints weight = 5100.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.212671 restraints weight = 4601.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.213639 restraints weight = 3977.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.214259 restraints weight = 3633.341| |-----------------------------------------------------------------------------| r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.247 5663 Z= 0.398 Angle : 2.491 50.454 7703 Z= 1.421 Chirality : 0.432 6.359 859 Planarity : 0.004 0.039 944 Dihedral : 13.583 65.992 843 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 6.30 % Allowed : 29.47 % Favored : 64.22 % 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: -1.68 (0.34), residues: 658 helix: 0.16 (0.30), residues: 304 sheet: -1.37 (0.80), residues: 56 loop : -2.47 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 543 TYR 0.010 0.001 TYR A 268 PHE 0.014 0.002 PHE A 591 TRP 0.012 0.001 TRP A 714 HIS 0.006 0.001 HIS A 639 Details of bonding type rmsd/Z covalent geometry : bond 0.01154 / 0.40 ( 5659) covalent geometry : angle 2.16178 / 1.42 ( 7691) hydrogen bonds : bond 0.03722 / 2.30 ( 221) hydrogen bonds : angle 5.56101 / 3.92 ( 645) metal coordination : bond 0.03569 / 1.78 ( 4) metal coordination : angle 31.40912 / 16.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 74 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 247 TYR cc_start: 0.5435 (m-10) cc_final: 0.4977 (m-10) REVERT: A 369 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.4888 (m-80) REVERT: A 499 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: A 660 LEU cc_start: 0.6711 (mt) cc_final: 0.5789 (tt) REVERT: A 672 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.4365 (t80) REVERT: A 790 LYS cc_start: 0.6729 (mtmp) cc_final: 0.6214 (mttm) REVERT: A 798 ARG cc_start: 0.6915 (mtm180) cc_final: 0.6419 (ttm170) outliers start: 37 outliers final: 24 residues processed: 103 average time/residue: 0.0789 time to fit residues: 10.5311 Evaluate side-chains 97 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 881 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 58 optimal weight: 0.2980 chunk 8 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 0.0000 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4811 r_free = 0.4811 target = 0.242462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.209790 restraints weight = 6399.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.212492 restraints weight = 5026.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.214232 restraints weight = 4038.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.215003 restraints weight = 3712.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.218295 restraints weight = 3429.722| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 5663 Z= 0.392 Angle : 2.489 50.425 7703 Z= 1.419 Chirality : 0.432 6.339 859 Planarity : 0.004 0.039 944 Dihedral : 13.311 66.412 838 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 5.45 % Allowed : 30.49 % Favored : 64.05 % 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: -1.49 (0.33), residues: 658 helix: 0.27 (0.30), residues: 301 sheet: -0.29 (0.92), residues: 43 loop : -2.45 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 543 TYR 0.008 0.001 TYR A 268 PHE 0.013 0.001 PHE A 591 TRP 0.009 0.001 TRP A 592 HIS 0.004 0.001 HIS A 639 Details of bonding type rmsd/Z covalent geometry : bond 0.01144 / 0.39 ( 5659) covalent geometry : angle 2.15631 / 1.42 ( 7691) hydrogen bonds : bond 0.03374 / 2.08 ( 221) hydrogen bonds : angle 5.42614 / 3.83 ( 645) metal coordination : bond 0.02678 / 1.33 ( 4) metal coordination : angle 31.58288 / 16.48 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.206 Fit side-chains REVERT: A 14 LYS cc_start: 0.6751 (OUTLIER) cc_final: 0.6393 (mmmt) REVERT: A 247 TYR cc_start: 0.5468 (m-10) cc_final: 0.5050 (m-10) REVERT: A 369 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.4892 (m-80) REVERT: A 499 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6649 (pm20) REVERT: A 526 MET cc_start: 0.8217 (tmm) cc_final: 0.7987 (tmm) REVERT: A 672 PHE cc_start: 0.5687 (OUTLIER) cc_final: 0.4230 (t80) REVERT: A 746 ILE cc_start: 0.0618 (OUTLIER) cc_final: 0.0052 (tp) REVERT: A 790 LYS cc_start: 0.6742 (mtmp) cc_final: 0.6228 (mttm) REVERT: A 798 ARG cc_start: 0.6876 (mtm180) cc_final: 0.6414 (ttm170) outliers start: 32 outliers final: 21 residues processed: 98 average time/residue: 0.0813 time to fit residues: 10.4825 Evaluate side-chains 95 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 69 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 881 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4800 r_free = 0.4800 target = 0.240699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.207723 restraints weight = 6513.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.210649 restraints weight = 4956.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.213377 restraints weight = 4112.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.214919 restraints weight = 3541.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.216328 restraints weight = 3187.393| |-----------------------------------------------------------------------------| r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 5663 Z= 0.400 Angle : 2.499 50.404 7703 Z= 1.423 Chirality : 0.432 6.325 859 Planarity : 0.004 0.040 944 Dihedral : 13.156 66.821 835 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 6.47 % Allowed : 30.49 % Favored : 63.03 % 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: -1.59 (0.33), residues: 658 helix: 0.34 (0.30), residues: 296 sheet: -1.49 (0.80), residues: 57 loop : -2.46 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 543 TYR 0.012 0.001 TYR A 268 PHE 0.017 0.002 PHE A 631 TRP 0.013 0.001 TRP A 647 HIS 0.004 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.01159 / 0.40 ( 5659) covalent geometry : angle 2.16685 / 1.42 ( 7691) hydrogen bonds : bond 0.03412 / 2.09 ( 221) hydrogen bonds : angle 5.43224 / 3.83 ( 645) metal coordination : bond 0.02456 / 1.22 ( 4) metal coordination : angle 31.63362 / 16.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 70 time to evaluate : 0.276 Fit side-chains REVERT: A 14 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6452 (mmtt) REVERT: A 247 TYR cc_start: 0.5546 (m-10) cc_final: 0.5307 (m-10) REVERT: A 369 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.4848 (m-80) REVERT: A 499 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6630 (pm20) REVERT: A 538 PHE cc_start: 0.5568 (m-80) cc_final: 0.5177 (m-80) REVERT: A 672 PHE cc_start: 0.5798 (OUTLIER) cc_final: 0.4425 (t80) REVERT: A 746 ILE cc_start: 0.0560 (OUTLIER) cc_final: 0.0071 (tp) REVERT: A 790 LYS cc_start: 0.6820 (mtmp) cc_final: 0.6290 (mttm) REVERT: A 798 ARG cc_start: 0.6870 (mtm180) cc_final: 0.6403 (ttm170) outliers start: 38 outliers final: 21 residues processed: 103 average time/residue: 0.0788 time to fit residues: 10.6964 Evaluate side-chains 93 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 881 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 14 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4788 r_free = 0.4788 target = 0.239214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.208730 restraints weight = 6257.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.210780 restraints weight = 5012.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.214987 restraints weight = 3998.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.215223 restraints weight = 3339.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.215593 restraints weight = 2898.754| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 5663 Z= 0.400 Angle : 2.506 50.424 7703 Z= 1.424 Chirality : 0.432 6.325 859 Planarity : 0.004 0.039 944 Dihedral : 13.118 67.190 835 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 6.81 % Allowed : 30.32 % Favored : 62.86 % 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: -1.56 (0.33), residues: 658 helix: 0.35 (0.30), residues: 290 sheet: -0.67 (0.90), residues: 45 loop : -2.50 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.011 0.001 TYR A 268 PHE 0.016 0.002 PHE A 631 TRP 0.013 0.001 TRP A 592 HIS 0.004 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.01160 / 0.40 ( 5659) covalent geometry : angle 2.17343 / 1.42 ( 7691) hydrogen bonds : bond 0.03413 / 2.11 ( 221) hydrogen bonds : angle 5.42925 / 3.83 ( 645) metal coordination : bond 0.02209 / 1.10 ( 4) metal coordination : angle 31.67542 / 16.56 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 71 time to evaluate : 0.371 Fit side-chains REVERT: A 247 TYR cc_start: 0.5601 (m-10) cc_final: 0.5318 (m-10) REVERT: A 331 MET cc_start: -0.0805 (ttt) cc_final: -0.1091 (ttt) REVERT: A 369 TYR cc_start: 0.6554 (OUTLIER) cc_final: 0.4896 (m-80) REVERT: A 398 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6275 (tp) REVERT: A 499 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6649 (pm20) REVERT: A 620 MET cc_start: 0.3150 (mmm) cc_final: 0.2178 (mtp) REVERT: A 672 PHE cc_start: 0.5733 (OUTLIER) cc_final: 0.4387 (t80) REVERT: A 746 ILE cc_start: 0.0595 (OUTLIER) cc_final: 0.0108 (tp) REVERT: A 790 LYS cc_start: 0.6840 (mtmp) cc_final: 0.6292 (mttm) REVERT: A 798 ARG cc_start: 0.6899 (mtm180) cc_final: 0.6412 (ttm170) outliers start: 40 outliers final: 28 residues processed: 106 average time/residue: 0.0755 time to fit residues: 10.7570 Evaluate side-chains 100 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 835 HIS Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 881 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 53 optimal weight: 0.1980 chunk 21 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4811 r_free = 0.4811 target = 0.241528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.209095 restraints weight = 6446.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.212415 restraints weight = 4921.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.214898 restraints weight = 4023.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.216708 restraints weight = 3470.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.217749 restraints weight = 3106.078| |-----------------------------------------------------------------------------| r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 5663 Z= 0.391 Angle : 2.503 50.416 7703 Z= 1.422 Chirality : 0.432 6.323 859 Planarity : 0.004 0.039 944 Dihedral : 13.012 67.136 835 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 6.64 % Allowed : 29.98 % Favored : 63.37 % 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: -1.49 (0.33), residues: 658 helix: 0.41 (0.31), residues: 296 sheet: -0.62 (0.90), residues: 45 loop : -2.52 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 762 TYR 0.009 0.001 TYR A 268 PHE 0.060 0.002 PHE A 538 TRP 0.017 0.001 TRP A 714 HIS 0.004 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.01144 / 0.39 ( 5659) covalent geometry : angle 2.16904 / 1.42 ( 7691) hydrogen bonds : bond 0.03169 / 1.95 ( 221) hydrogen bonds : angle 5.36144 / 3.80 ( 645) metal coordination : bond 0.02207 / 1.09 ( 4) metal coordination : angle 31.69980 / 16.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 0.223 Fit side-chains REVERT: A 247 TYR cc_start: 0.5521 (m-10) cc_final: 0.5223 (m-10) REVERT: A 331 MET cc_start: -0.0638 (ttt) cc_final: -0.0920 (ttt) REVERT: A 369 TYR cc_start: 0.6488 (OUTLIER) cc_final: 0.4864 (m-80) REVERT: A 398 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6029 (tp) REVERT: A 499 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6647 (pm20) REVERT: A 620 MET cc_start: 0.3183 (mmm) cc_final: 0.2148 (mtp) REVERT: A 672 PHE cc_start: 0.5783 (OUTLIER) cc_final: 0.4379 (t80) REVERT: A 751 GLU cc_start: -0.0863 (OUTLIER) cc_final: -0.1528 (tp30) REVERT: A 790 LYS cc_start: 0.6810 (mtmp) cc_final: 0.6280 (mttm) REVERT: A 798 ARG cc_start: 0.6814 (mtm180) cc_final: 0.6385 (ttm170) outliers start: 39 outliers final: 26 residues processed: 107 average time/residue: 0.0892 time to fit residues: 12.3695 Evaluate side-chains 101 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 70 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 881 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 15 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 32 optimal weight: 0.0980 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4805 r_free = 0.4805 target = 0.240936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.208828 restraints weight = 6368.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.212215 restraints weight = 4829.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.214297 restraints weight = 3937.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.216370 restraints weight = 3413.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.217728 restraints weight = 3046.171| |-----------------------------------------------------------------------------| r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 5663 Z= 0.393 Angle : 2.510 50.427 7703 Z= 1.424 Chirality : 0.432 6.323 859 Planarity : 0.004 0.040 944 Dihedral : 12.977 67.011 833 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 6.13 % Allowed : 30.15 % Favored : 63.71 % 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: -1.53 (0.33), residues: 658 helix: 0.43 (0.30), residues: 296 sheet: -1.50 (0.80), residues: 57 loop : -2.45 (0.34), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 658 TYR 0.010 0.001 TYR A 268 PHE 0.046 0.002 PHE A 538 TRP 0.016 0.001 TRP A 714 HIS 0.003 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.01148 / 0.39 ( 5659) covalent geometry : angle 2.17721 / 1.42 ( 7691) hydrogen bonds : bond 0.03201 / 1.97 ( 221) hydrogen bonds : angle 5.30964 / 3.75 ( 645) metal coordination : bond 0.02145 / 1.06 ( 4) metal coordination : angle 31.71255 / 16.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 71 time to evaluate : 0.198 Fit side-chains REVERT: A 29 MET cc_start: 0.6330 (mmt) cc_final: 0.4084 (mmt) REVERT: A 247 TYR cc_start: 0.5630 (m-10) cc_final: 0.5419 (m-10) REVERT: A 331 MET cc_start: -0.0607 (ttt) cc_final: -0.0878 (ttt) REVERT: A 369 TYR cc_start: 0.6537 (OUTLIER) cc_final: 0.4884 (m-80) REVERT: A 398 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6033 (tp) REVERT: A 499 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: A 620 MET cc_start: 0.3222 (mmm) cc_final: 0.2210 (mtp) REVERT: A 672 PHE cc_start: 0.5695 (OUTLIER) cc_final: 0.4306 (t80) REVERT: A 746 ILE cc_start: 0.0587 (OUTLIER) cc_final: 0.0187 (tp) REVERT: A 751 GLU cc_start: -0.0573 (OUTLIER) cc_final: -0.1299 (tp30) REVERT: A 790 LYS cc_start: 0.6803 (mtmp) cc_final: 0.6257 (mttm) REVERT: A 798 ARG cc_start: 0.6821 (mtm180) cc_final: 0.6369 (ttm170) REVERT: A 866 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7332 (mt0) outliers start: 36 outliers final: 25 residues processed: 101 average time/residue: 0.0714 time to fit residues: 9.8134 Evaluate side-chains 101 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 881 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 0.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 = 0.4794 r_free = 0.4794 target = 0.239610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.207572 restraints weight = 6473.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.210682 restraints weight = 4915.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.213143 restraints weight = 4049.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.214537 restraints weight = 3497.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.216122 restraints weight = 3161.181| |-----------------------------------------------------------------------------| r_work (final): 0.4579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 5663 Z= 0.397 Angle : 2.518 50.449 7703 Z= 1.427 Chirality : 0.432 6.326 859 Planarity : 0.004 0.042 944 Dihedral : 12.995 67.154 833 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 5.96 % Allowed : 30.83 % Favored : 63.20 % 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: -1.54 (0.33), residues: 658 helix: 0.37 (0.30), residues: 296 sheet: -1.27 (0.84), residues: 50 loop : -2.45 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 762 TYR 0.012 0.001 TYR A 268 PHE 0.047 0.002 PHE A 538 TRP 0.018 0.001 TRP A 714 HIS 0.004 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.01156 / 0.40 ( 5659) covalent geometry : angle 2.18624 / 1.42 ( 7691) hydrogen bonds : bond 0.03250 / 2.01 ( 221) hydrogen bonds : angle 5.33575 / 3.77 ( 645) metal coordination : bond 0.02140 / 1.06 ( 4) metal coordination : angle 31.71805 / 16.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 70 time to evaluate : 0.215 Fit side-chains REVERT: A 41 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.7355 (p90) REVERT: A 331 MET cc_start: -0.0527 (ttt) cc_final: -0.0763 (ttt) REVERT: A 369 TYR cc_start: 0.6525 (OUTLIER) cc_final: 0.4951 (m-80) REVERT: A 398 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6049 (tp) REVERT: A 499 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6662 (pm20) REVERT: A 672 PHE cc_start: 0.5748 (OUTLIER) cc_final: 0.4322 (t80) REVERT: A 746 ILE cc_start: 0.0694 (OUTLIER) cc_final: 0.0150 (tp) REVERT: A 790 LYS cc_start: 0.6818 (mtmp) cc_final: 0.6261 (mttm) REVERT: A 798 ARG cc_start: 0.6827 (mtm180) cc_final: 0.6334 (ttm170) outliers start: 35 outliers final: 26 residues processed: 99 average time/residue: 0.0770 time to fit residues: 10.0899 Evaluate side-chains 102 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 881 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 54 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 32 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 815 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.239792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.209170 restraints weight = 6283.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.212582 restraints weight = 4593.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.215187 restraints weight = 3661.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.217031 restraints weight = 3090.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.218087 restraints weight = 2715.671| |-----------------------------------------------------------------------------| r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.242 5663 Z= 0.391 Angle : 2.513 50.452 7703 Z= 1.425 Chirality : 0.432 6.329 859 Planarity : 0.004 0.042 944 Dihedral : 12.944 66.970 833 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 6.13 % Allowed : 30.83 % Favored : 63.03 % 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: -1.44 (0.33), residues: 658 helix: 0.45 (0.30), residues: 296 sheet: -1.21 (0.84), residues: 50 loop : -2.39 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 762 TYR 0.009 0.001 TYR A 268 PHE 0.041 0.002 PHE A 538 TRP 0.017 0.001 TRP A 714 HIS 0.004 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.01145 / 0.39 ( 5659) covalent geometry : angle 2.18059 / 1.42 ( 7691) hydrogen bonds : bond 0.03079 / 1.90 ( 221) hydrogen bonds : angle 5.25445 / 3.72 ( 645) metal coordination : bond 0.02203 / 1.09 ( 4) metal coordination : angle 31.69819 / 16.60 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1316 Ramachandran restraints generated. 658 Oldfield, 0 Emsley, 658 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 0.189 Fit side-chains REVERT: A 29 MET cc_start: 0.6337 (mmt) cc_final: 0.4048 (mmt) REVERT: A 41 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7425 (p90) REVERT: A 331 MET cc_start: -0.0423 (ttt) cc_final: -0.0651 (ttt) REVERT: A 369 TYR cc_start: 0.6506 (OUTLIER) cc_final: 0.4928 (m-80) REVERT: A 398 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6049 (tp) REVERT: A 499 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6594 (pm20) REVERT: A 620 MET cc_start: 0.2869 (mmm) cc_final: 0.1962 (mtp) REVERT: A 672 PHE cc_start: 0.5703 (OUTLIER) cc_final: 0.4446 (t80) REVERT: A 746 ILE cc_start: 0.0594 (OUTLIER) cc_final: 0.0028 (tp) REVERT: A 790 LYS cc_start: 0.6862 (mtmp) cc_final: 0.6321 (mttm) REVERT: A 798 ARG cc_start: 0.6823 (mtm180) cc_final: 0.6365 (ttm170) REVERT: A 866 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7317 (mt0) outliers start: 36 outliers final: 28 residues processed: 99 average time/residue: 0.0780 time to fit residues: 10.2334 Evaluate side-chains 102 residues out of total 587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 67 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 499 GLN Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 661 CYS Chi-restraints excluded: chain A residue 672 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 784 ILE Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 845 VAL Chi-restraints excluded: chain A residue 847 ASP Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 881 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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 = 0.4732 r_free = 0.4732 target = 0.233490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.200439 restraints weight = 6458.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.204460 restraints weight = 4563.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.207452 restraints weight = 3550.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.209534 restraints weight = 2940.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.210828 restraints weight = 2555.884| |-----------------------------------------------------------------------------| r_work (final): 0.4535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.242 5663 Z= 0.395 Angle : 2.516 50.457 7703 Z= 1.427 Chirality : 0.432 6.327 859 Planarity : 0.004 0.042 944 Dihedral : 12.953 66.862 833 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 6.30 % Allowed : 30.49 % Favored : 63.20 % 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: -1.44 (0.33), residues: 658 helix: 0.44 (0.30), residues: 296 sheet: -1.25 (0.85), residues: 50 loop : -2.38 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 762 TYR 0.011 0.001 TYR A 268 PHE 0.043 0.002 PHE A 538 TRP 0.026 0.002 TRP A 714 HIS 0.003 0.001 HIS A 804 Details of bonding type rmsd/Z covalent geometry : bond 0.01151 / 0.39 ( 5659) covalent geometry : angle 2.18477 / 1.42 ( 7691) hydrogen bonds : bond 0.03202 / 1.97 ( 221) hydrogen bonds : angle 5.22802 / 3.69 ( 645) metal coordination : bond 0.02131 / 1.06 ( 4) metal coordination : angle 31.71261 / 16.61 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1113.83 seconds wall clock time: 20 minutes 0.12 seconds (1200.12 seconds total)