Starting phenix.real_space_refine on Sun Dec 29 13:16:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vt0_32117/12_2024/7vt0_32117.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vt0_32117/12_2024/7vt0_32117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vt0_32117/12_2024/7vt0_32117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vt0_32117/12_2024/7vt0_32117.map" model { file = "/net/cci-nas-00/data/ceres_data/7vt0_32117/12_2024/7vt0_32117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vt0_32117/12_2024/7vt0_32117.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 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: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 6690 2.51 5 N 1796 2.21 5 O 2006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10536 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5268 Classifications: {'peptide': 663} Link IDs: {'PTRANS': 29, 'TRANS': 633} Chain: "B" Number of atoms: 5268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5268 Classifications: {'peptide': 663} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 632} Time building chain proxies: 6.43, per 1000 atoms: 0.61 Number of scatterers: 10536 At special positions: 0 Unit cell: (156.02, 100.068, 107.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 2006 8.00 N 1796 7.00 C 6690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 625 " - pdb=" SG CYS A 660 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 736 " distance=2.02 Simple disulfide: pdb=" SG CYS A 684 " - pdb=" SG CYS A 699 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 473 " distance=2.02 Simple disulfide: pdb=" SG CYS B 625 " - pdb=" SG CYS B 660 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 736 " distance=2.05 Simple disulfide: pdb=" SG CYS B 684 " - pdb=" SG CYS B 699 " distance=2.02 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: 2.45 Conformation dependent library (CDL) restraints added in 1.3 seconds 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 28 sheets defined 3.8% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 617 through 622 removed outlier: 3.527A pdb=" N ALA A 620 " --> pdb=" O ALA A 617 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 622 " --> pdb=" O ASP A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 removed outlier: 3.955A pdb=" N TYR A 630 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 706 Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.679A pdb=" N TYR B 258 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 259 " --> pdb=" O ASP B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 259' Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.564A pdb=" N ASN B 368 " --> pdb=" O HIS B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 621 removed outlier: 3.521A pdb=" N ALA B 620 " --> pdb=" O ALA B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 702 through 706 Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 97 removed outlier: 5.717A pdb=" N GLN A 614 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 95 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILE A 612 " --> pdb=" O GLN A 95 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 599 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLY A 585 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 removed outlier: 4.398A pdb=" N VAL A 116 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 137 Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.818A pdb=" N TYR A 177 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR A 190 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP A 188 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 211 removed outlier: 3.613A pdb=" N ASP A 208 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 210 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 220 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 232 " --> pdb=" O GLY A 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 248 through 252 removed outlier: 3.547A pdb=" N SER A 252 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A 277 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.819A pdb=" N MET A 307 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362 removed outlier: 3.696A pdb=" N TYR A 373 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 372 " --> pdb=" O SER A 385 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AB1, first strand: chain 'A' and resid 504 through 507 removed outlier: 3.645A pdb=" N ALA A 506 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 534 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 560 through 561 Processing sheet with id=AB4, first strand: chain 'A' and resid 623 through 624 removed outlier: 7.171A pdb=" N VAL A 623 " --> pdb=" O PHE A 661 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 688 through 689 Processing sheet with id=AB6, first strand: chain 'A' and resid 722 through 724 Processing sheet with id=AB7, first strand: chain 'B' and resid 91 through 97 removed outlier: 5.018A pdb=" N VAL B 92 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASN B 616 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 94 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 585 " --> pdb=" O PHE B 600 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 106 through 110 removed outlier: 4.203A pdb=" N VAL B 116 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 134 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.817A pdb=" N TYR B 177 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 189 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 219 through 222 removed outlier: 4.049A pdb=" N GLN B 245 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 248 through 252 removed outlier: 4.252A pdb=" N SER B 250 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 280 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 276 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL B 277 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 299 through 303 Processing sheet with id=AC4, first strand: chain 'B' and resid 350 through 353 removed outlier: 6.824A pdb=" N PHE B 360 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN B 371 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU B 372 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 414 through 416 Processing sheet with id=AC6, first strand: chain 'B' and resid 475 through 477 removed outlier: 3.767A pdb=" N ALA B 506 " --> pdb=" O TYR B 521 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 534 " --> pdb=" O VAL B 520 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 560 through 561 Processing sheet with id=AC9, first strand: chain 'B' and resid 623 through 624 removed outlier: 6.982A pdb=" N VAL B 623 " --> pdb=" O PHE B 661 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 722 through 724 162 hydrogen bonds defined for protein. 357 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: 2.81 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1759 1.27 - 1.41: 2909 1.41 - 1.55: 6071 1.55 - 1.69: 9 1.69 - 1.83: 62 Bond restraints: 10810 Sorted by residual: bond pdb=" CA CYS A 362 " pdb=" C CYS A 362 " ideal model delta sigma weight residual 1.533 1.353 0.180 9.60e-03 1.09e+04 3.53e+02 bond pdb=" CA VAL A 363 " pdb=" C VAL A 363 " ideal model delta sigma weight residual 1.523 1.372 0.151 1.27e-02 6.20e+03 1.41e+02 bond pdb=" CA ASN B 662 " pdb=" C ASN B 662 " ideal model delta sigma weight residual 1.522 1.385 0.137 1.38e-02 5.25e+03 9.88e+01 bond pdb=" CA ASP B 667 " pdb=" C ASP B 667 " ideal model delta sigma weight residual 1.523 1.392 0.132 1.34e-02 5.57e+03 9.65e+01 bond pdb=" CA LEU A 386 " pdb=" C LEU A 386 " ideal model delta sigma weight residual 1.521 1.393 0.127 1.30e-02 5.92e+03 9.59e+01 ... (remaining 10805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.62: 14522 5.62 - 11.24: 118 11.24 - 16.86: 14 16.86 - 22.48: 1 22.48 - 28.09: 1 Bond angle restraints: 14656 Sorted by residual: angle pdb=" N HIS A 365 " pdb=" CA HIS A 365 " pdb=" C HIS A 365 " ideal model delta sigma weight residual 111.52 83.43 28.09 1.40e+00 5.10e-01 4.03e+02 angle pdb=" N ASP B 629 " pdb=" CA ASP B 629 " pdb=" C ASP B 629 " ideal model delta sigma weight residual 114.56 100.19 14.37 1.27e+00 6.20e-01 1.28e+02 angle pdb=" C ARG B 668 " pdb=" N PRO B 669 " pdb=" CA PRO B 669 " ideal model delta sigma weight residual 119.84 105.74 14.10 1.25e+00 6.40e-01 1.27e+02 angle pdb=" CA GLU B 592 " pdb=" C GLU B 592 " pdb=" N LYS B 593 " ideal model delta sigma weight residual 116.08 103.97 12.11 1.29e+00 6.01e-01 8.82e+01 angle pdb=" N PHE B 666 " pdb=" CA PHE B 666 " pdb=" C PHE B 666 " ideal model delta sigma weight residual 110.80 129.83 -19.03 2.13e+00 2.20e-01 7.98e+01 ... (remaining 14651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5681 17.65 - 35.30: 566 35.30 - 52.95: 109 52.95 - 70.59: 37 70.59 - 88.24: 4 Dihedral angle restraints: 6397 sinusoidal: 2557 harmonic: 3840 Sorted by residual: dihedral pdb=" CB CYS B 684 " pdb=" SG CYS B 684 " pdb=" SG CYS B 699 " pdb=" CB CYS B 699 " ideal model delta sinusoidal sigma weight residual -86.00 -19.23 -66.77 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 736 " pdb=" CB CYS A 736 " ideal model delta sinusoidal sigma weight residual 93.00 36.45 56.55 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 736 " pdb=" CB CYS B 736 " ideal model delta sinusoidal sigma weight residual -86.00 -32.48 -53.52 1 1.00e+01 1.00e-02 3.89e+01 ... (remaining 6394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1329 0.078 - 0.155: 188 0.155 - 0.233: 23 0.233 - 0.311: 8 0.311 - 0.388: 6 Chirality restraints: 1554 Sorted by residual: chirality pdb=" CA ASN A 388 " pdb=" N ASN A 388 " pdb=" C ASN A 388 " pdb=" CB ASN A 388 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CA SER A 364 " pdb=" N SER A 364 " pdb=" C SER A 364 " pdb=" CB SER A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA LEU B 645 " pdb=" N LEU B 645 " pdb=" C LEU B 645 " pdb=" CB LEU B 645 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1551 not shown) Planarity restraints: 1910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 674 " -0.033 2.00e-02 2.50e+03 6.62e-02 4.38e+01 pdb=" C ASN B 674 " 0.114 2.00e-02 2.50e+03 pdb=" O ASN B 674 " -0.043 2.00e-02 2.50e+03 pdb=" N CYS B 675 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 592 " -0.018 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C GLU B 592 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU B 592 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS B 593 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 673 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER A 673 " 0.068 2.00e-02 2.50e+03 pdb=" O SER A 673 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN A 674 " -0.023 2.00e-02 2.50e+03 ... (remaining 1907 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 485 2.68 - 3.24: 9871 3.24 - 3.79: 14869 3.79 - 4.35: 20121 4.35 - 4.90: 33649 Nonbonded interactions: 78995 Sorted by model distance: nonbonded pdb=" CB VAL A 363 " pdb=" N SER A 364 " model vdw 2.126 2.840 nonbonded pdb=" OE2 GLU B 356 " pdb=" OH TYR B 424 " model vdw 2.196 3.040 nonbonded pdb=" OG SER B 170 " pdb=" O ASP B 173 " model vdw 2.206 3.040 nonbonded pdb=" O LYS A 260 " pdb=" OG1 THR A 263 " model vdw 2.227 3.040 nonbonded pdb=" O GLU A 697 " pdb=" OH TYR A 728 " model vdw 2.229 3.040 ... (remaining 78990 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.690 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.011 0.180 10810 Z= 0.733 Angle : 1.309 28.095 14656 Z= 0.802 Chirality : 0.061 0.388 1554 Planarity : 0.007 0.090 1910 Dihedral : 14.914 88.243 3920 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 3.10 % Allowed : 14.30 % Favored : 82.60 % Rotamer: Outliers : 3.65 % Allowed : 3.13 % Favored : 93.22 % Cbeta Deviations : 1.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.21), residues: 1322 helix: -5.13 (0.27), residues: 6 sheet: -2.70 (0.28), residues: 327 loop : -2.99 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 542 HIS 0.011 0.001 HIS B 545 PHE 0.043 0.002 PHE B 661 TYR 0.024 0.002 TYR B 630 ARG 0.008 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 1.332 Fit side-chains revert: symmetry clash REVERT: A 279 ARG cc_start: 0.7161 (ttp-110) cc_final: 0.6924 (ttp-110) REVERT: A 304 ASP cc_start: 0.7700 (t0) cc_final: 0.7480 (t0) REVERT: A 348 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: A 394 PRO cc_start: 0.6890 (Cg_endo) cc_final: 0.6518 (Cg_exo) REVERT: A 438 MET cc_start: 0.7938 (mmt) cc_final: 0.5777 (ptm) REVERT: A 690 MET cc_start: -0.1204 (mmp) cc_final: -0.3495 (ttm) REVERT: A 730 LYS cc_start: 0.3115 (OUTLIER) cc_final: 0.2839 (pttt) REVERT: B 593 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6857 (mtmm) REVERT: B 638 GLU cc_start: 0.5393 (OUTLIER) cc_final: 0.4930 (tp30) REVERT: B 647 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.7129 (m90) outliers start: 42 outliers final: 17 residues processed: 164 average time/residue: 0.2727 time to fit residues: 63.1748 Evaluate side-chains 127 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 362 CYS Chi-restraints excluded: chain A residue 367 ASN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 637 ASP Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 647 HIS Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 675 CYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain B residue 690 MET Chi-restraints excluded: chain B residue 700 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 77 optimal weight: 0.0370 chunk 119 optimal weight: 0.7980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 388 ASN ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN B 269 HIS B 566 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10810 Z= 0.235 Angle : 0.735 7.914 14656 Z= 0.392 Chirality : 0.047 0.183 1554 Planarity : 0.005 0.091 1910 Dihedral : 8.018 69.780 1494 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 1.13 % Allowed : 14.45 % Favored : 84.42 % Rotamer: Outliers : 1.91 % Allowed : 10.17 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.21), residues: 1322 helix: None (None), residues: 0 sheet: -2.23 (0.28), residues: 329 loop : -2.74 (0.18), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 542 HIS 0.007 0.001 HIS B 608 PHE 0.017 0.002 PHE B 661 TYR 0.019 0.002 TYR B 392 ARG 0.005 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 304 ASP cc_start: 0.7574 (t0) cc_final: 0.7311 (t0) REVERT: A 392 TYR cc_start: 0.6800 (t80) cc_final: 0.6385 (t80) REVERT: A 394 PRO cc_start: 0.7387 (Cg_endo) cc_final: 0.6909 (Cg_exo) REVERT: A 690 MET cc_start: -0.0991 (mmp) cc_final: -0.3386 (ttm) REVERT: B 630 TYR cc_start: 0.8779 (m-80) cc_final: 0.8489 (m-80) REVERT: B 682 TYR cc_start: 0.4478 (OUTLIER) cc_final: 0.2536 (m-80) REVERT: B 683 GLU cc_start: -0.0702 (OUTLIER) cc_final: -0.0936 (pt0) outliers start: 22 outliers final: 14 residues processed: 142 average time/residue: 0.2112 time to fit residues: 44.8145 Evaluate side-chains 117 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 467 CYS Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 649 THR Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 675 CYS Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain B residue 700 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS B 476 HIS B 647 HIS B 662 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10810 Z= 0.228 Angle : 0.698 8.884 14656 Z= 0.369 Chirality : 0.046 0.154 1554 Planarity : 0.005 0.086 1910 Dihedral : 6.610 58.276 1469 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 1.21 % Allowed : 13.31 % Favored : 85.48 % Rotamer: Outliers : 1.74 % Allowed : 12.26 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -2.03 (0.28), residues: 341 loop : -2.58 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 542 HIS 0.006 0.001 HIS B 647 PHE 0.015 0.001 PHE B 200 TYR 0.015 0.001 TYR B 186 ARG 0.005 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 1.241 Fit side-chains REVERT: A 365 HIS cc_start: 0.6510 (t-170) cc_final: 0.6273 (t-90) REVERT: A 392 TYR cc_start: 0.6858 (t80) cc_final: 0.6250 (t80) REVERT: A 394 PRO cc_start: 0.7414 (Cg_endo) cc_final: 0.6825 (Cg_exo) REVERT: A 690 MET cc_start: -0.1227 (mmp) cc_final: -0.3620 (ttm) REVERT: B 438 MET cc_start: 0.7210 (mmt) cc_final: 0.6990 (mmt) REVERT: B 644 LEU cc_start: 0.5125 (OUTLIER) cc_final: 0.4895 (tp) outliers start: 20 outliers final: 11 residues processed: 127 average time/residue: 0.2097 time to fit residues: 40.1913 Evaluate side-chains 111 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 662 ASN Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 700 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 62 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 57 optimal weight: 0.0170 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 127 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS A 365 HIS ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10810 Z= 0.176 Angle : 0.667 9.808 14656 Z= 0.352 Chirality : 0.046 0.225 1554 Planarity : 0.004 0.085 1910 Dihedral : 5.718 44.900 1458 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 1.13 % Allowed : 12.18 % Favored : 86.69 % Rotamer: Outliers : 2.35 % Allowed : 13.57 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.79 (0.29), residues: 328 loop : -2.43 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 542 HIS 0.004 0.001 HIS A 365 PHE 0.011 0.001 PHE B 200 TYR 0.019 0.001 TYR A 349 ARG 0.003 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.252 Fit side-chains REVERT: A 93 TYR cc_start: 0.8105 (p90) cc_final: 0.7803 (p90) REVERT: A 304 ASP cc_start: 0.7685 (t0) cc_final: 0.7464 (t0) REVERT: A 392 TYR cc_start: 0.6773 (t80) cc_final: 0.6141 (t80) REVERT: A 394 PRO cc_start: 0.7213 (Cg_endo) cc_final: 0.6593 (Cg_exo) REVERT: A 690 MET cc_start: -0.1127 (mmp) cc_final: -0.3521 (ttm) outliers start: 27 outliers final: 14 residues processed: 133 average time/residue: 0.2146 time to fit residues: 42.5326 Evaluate side-chains 114 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 421 GLN Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS A 269 HIS A 476 HIS ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN B 269 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 10810 Z= 0.617 Angle : 0.893 10.340 14656 Z= 0.471 Chirality : 0.053 0.195 1554 Planarity : 0.006 0.082 1910 Dihedral : 6.856 58.132 1455 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 1.13 % Allowed : 18.31 % Favored : 80.56 % Rotamer: Outliers : 2.70 % Allowed : 15.57 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -2.20 (0.28), residues: 340 loop : -2.63 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 542 HIS 0.009 0.002 HIS A 169 PHE 0.024 0.003 PHE B 576 TYR 0.032 0.003 TYR A 563 ARG 0.005 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 374 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 394 PRO cc_start: 0.7462 (Cg_endo) cc_final: 0.7140 (Cg_exo) REVERT: A 690 MET cc_start: -0.0608 (mmp) cc_final: -0.3272 (ttm) REVERT: A 730 LYS cc_start: 0.2281 (OUTLIER) cc_final: 0.1995 (pttt) REVERT: B 189 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8798 (mt) REVERT: B 480 ARG cc_start: 0.6488 (mmm160) cc_final: 0.6125 (mmm160) outliers start: 31 outliers final: 19 residues processed: 137 average time/residue: 0.2346 time to fit residues: 46.7553 Evaluate side-chains 119 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 474 SER Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 74 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 554 GLN B 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10810 Z= 0.238 Angle : 0.707 10.688 14656 Z= 0.375 Chirality : 0.046 0.168 1554 Planarity : 0.005 0.079 1910 Dihedral : 6.127 44.917 1455 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 1.13 % Allowed : 12.71 % Favored : 86.16 % Rotamer: Outliers : 2.43 % Allowed : 16.87 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -2.12 (0.28), residues: 332 loop : -2.49 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 542 HIS 0.003 0.001 HIS A 169 PHE 0.024 0.002 PHE A 382 TYR 0.018 0.001 TYR A 349 ARG 0.006 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 103 time to evaluate : 1.201 Fit side-chains REVERT: A 307 MET cc_start: 0.8442 (ttt) cc_final: 0.7998 (tpp) REVERT: A 394 PRO cc_start: 0.7310 (Cg_endo) cc_final: 0.7013 (Cg_exo) REVERT: A 690 MET cc_start: -0.1042 (mmp) cc_final: -0.3483 (ttm) REVERT: B 480 ARG cc_start: 0.6260 (mmm160) cc_final: 0.5998 (mmm160) REVERT: B 644 LEU cc_start: 0.5664 (OUTLIER) cc_final: 0.5366 (tt) outliers start: 28 outliers final: 23 residues processed: 128 average time/residue: 0.2187 time to fit residues: 41.0067 Evaluate side-chains 123 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 127 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10810 Z= 0.252 Angle : 0.700 9.370 14656 Z= 0.369 Chirality : 0.046 0.161 1554 Planarity : 0.005 0.077 1910 Dihedral : 5.968 45.374 1455 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 1.06 % Allowed : 14.37 % Favored : 84.57 % Rotamer: Outliers : 2.70 % Allowed : 16.26 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -2.00 (0.29), residues: 324 loop : -2.44 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 542 HIS 0.004 0.001 HIS A 169 PHE 0.016 0.002 PHE B 200 TYR 0.017 0.001 TYR A 349 ARG 0.006 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 99 time to evaluate : 1.328 Fit side-chains REVERT: A 304 ASP cc_start: 0.7664 (t0) cc_final: 0.7372 (t0) REVERT: A 307 MET cc_start: 0.8427 (ttt) cc_final: 0.8129 (tpp) REVERT: A 392 TYR cc_start: 0.6889 (t80) cc_final: 0.6347 (t80) REVERT: A 394 PRO cc_start: 0.7286 (Cg_endo) cc_final: 0.6706 (Cg_exo) REVERT: A 690 MET cc_start: -0.1093 (mmp) cc_final: -0.3503 (ttm) REVERT: A 730 LYS cc_start: 0.1889 (OUTLIER) cc_final: 0.1655 (pttt) REVERT: B 243 MET cc_start: 0.8111 (tpp) cc_final: 0.7517 (tpt) REVERT: B 644 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.5273 (tt) outliers start: 31 outliers final: 25 residues processed: 125 average time/residue: 0.2246 time to fit residues: 41.1332 Evaluate side-chains 124 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 97 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 115 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10810 Z= 0.236 Angle : 0.686 8.661 14656 Z= 0.362 Chirality : 0.046 0.155 1554 Planarity : 0.005 0.076 1910 Dihedral : 5.837 43.922 1455 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 1.06 % Allowed : 12.71 % Favored : 86.23 % Rotamer: Outliers : 2.96 % Allowed : 16.78 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.88 (0.29), residues: 322 loop : -2.41 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 542 HIS 0.004 0.001 HIS A 169 PHE 0.018 0.001 PHE B 200 TYR 0.015 0.001 TYR B 93 ARG 0.005 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.082 Fit side-chains REVERT: A 304 ASP cc_start: 0.7620 (t0) cc_final: 0.7331 (t0) REVERT: A 307 MET cc_start: 0.8413 (ttt) cc_final: 0.8111 (tpp) REVERT: A 392 TYR cc_start: 0.6891 (t80) cc_final: 0.6376 (t80) REVERT: A 394 PRO cc_start: 0.7286 (Cg_endo) cc_final: 0.6741 (Cg_exo) REVERT: A 438 MET cc_start: 0.7932 (mmm) cc_final: 0.5954 (ptp) REVERT: A 690 MET cc_start: -0.0996 (mmp) cc_final: -0.3410 (ttm) REVERT: A 730 LYS cc_start: 0.1872 (OUTLIER) cc_final: 0.1639 (pttt) REVERT: B 243 MET cc_start: 0.8068 (tpp) cc_final: 0.7456 (tpt) REVERT: B 644 LEU cc_start: 0.5566 (OUTLIER) cc_final: 0.5250 (tt) outliers start: 34 outliers final: 26 residues processed: 140 average time/residue: 0.2281 time to fit residues: 46.1444 Evaluate side-chains 127 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 2.9990 chunk 121 optimal weight: 0.0040 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10810 Z= 0.223 Angle : 0.700 12.875 14656 Z= 0.368 Chirality : 0.046 0.240 1554 Planarity : 0.005 0.075 1910 Dihedral : 5.766 43.779 1455 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.98 % Allowed : 13.09 % Favored : 85.93 % Rotamer: Outliers : 2.52 % Allowed : 17.30 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.80 (0.29), residues: 322 loop : -2.38 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 542 HIS 0.004 0.001 HIS A 169 PHE 0.016 0.001 PHE B 200 TYR 0.032 0.001 TYR A 349 ARG 0.005 0.000 ARG B 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 1.180 Fit side-chains REVERT: A 246 GLU cc_start: 0.7201 (tp30) cc_final: 0.6930 (tp30) REVERT: A 304 ASP cc_start: 0.7612 (t0) cc_final: 0.7327 (t0) REVERT: A 307 MET cc_start: 0.8375 (ttt) cc_final: 0.8083 (tpp) REVERT: A 392 TYR cc_start: 0.6879 (t80) cc_final: 0.6365 (t80) REVERT: A 394 PRO cc_start: 0.7292 (Cg_endo) cc_final: 0.6708 (Cg_exo) REVERT: A 690 MET cc_start: -0.0976 (mmp) cc_final: -0.3414 (ttm) REVERT: A 730 LYS cc_start: 0.1883 (OUTLIER) cc_final: 0.1654 (pttt) REVERT: B 243 MET cc_start: 0.8029 (tpp) cc_final: 0.7414 (tpt) REVERT: B 514 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7172 (tt) REVERT: B 644 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.5005 (tt) outliers start: 29 outliers final: 25 residues processed: 129 average time/residue: 0.2448 time to fit residues: 45.7027 Evaluate side-chains 127 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 131 optimal weight: 0.0470 chunk 121 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10810 Z= 0.228 Angle : 0.702 12.393 14656 Z= 0.367 Chirality : 0.046 0.254 1554 Planarity : 0.004 0.074 1910 Dihedral : 5.750 43.493 1455 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.91 % Allowed : 12.48 % Favored : 86.61 % Rotamer: Outliers : 2.70 % Allowed : 17.65 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.82 (0.29), residues: 330 loop : -2.37 (0.19), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 542 HIS 0.004 0.001 HIS A 169 PHE 0.026 0.001 PHE B 200 TYR 0.027 0.001 TYR A 349 ARG 0.005 0.000 ARG B 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2644 Ramachandran restraints generated. 1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7222 (tp30) cc_final: 0.6933 (tp30) REVERT: A 304 ASP cc_start: 0.7620 (t0) cc_final: 0.7329 (t0) REVERT: A 307 MET cc_start: 0.8389 (ttt) cc_final: 0.8124 (tpp) REVERT: A 392 TYR cc_start: 0.6803 (t80) cc_final: 0.6315 (t80) REVERT: A 394 PRO cc_start: 0.7315 (Cg_endo) cc_final: 0.6731 (Cg_exo) REVERT: A 690 MET cc_start: -0.0999 (mmp) cc_final: -0.3414 (ttm) REVERT: A 730 LYS cc_start: 0.1908 (OUTLIER) cc_final: 0.1674 (pttt) REVERT: B 243 MET cc_start: 0.8065 (tpp) cc_final: 0.7498 (tpt) REVERT: B 644 LEU cc_start: 0.5337 (OUTLIER) cc_final: 0.5017 (tt) outliers start: 31 outliers final: 25 residues processed: 133 average time/residue: 0.2350 time to fit residues: 45.1507 Evaluate side-chains 127 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 566 ASN Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain B residue 682 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 0.0670 chunk 43 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.203394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141453 restraints weight = 11810.792| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.44 r_work: 0.3449 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10810 Z= 0.298 Angle : 0.728 10.409 14656 Z= 0.381 Chirality : 0.047 0.231 1554 Planarity : 0.005 0.074 1910 Dihedral : 5.982 48.970 1455 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.91 % Allowed : 14.45 % Favored : 84.64 % Rotamer: Outliers : 2.61 % Allowed : 18.26 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.22), residues: 1322 helix: None (None), residues: 0 sheet: -1.94 (0.29), residues: 332 loop : -2.41 (0.19), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 542 HIS 0.005 0.001 HIS A 169 PHE 0.031 0.002 PHE B 200 TYR 0.028 0.002 TYR A 349 ARG 0.005 0.000 ARG B 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2278.60 seconds wall clock time: 43 minutes 4.93 seconds (2584.93 seconds total)