Starting phenix.real_space_refine on Tue May 13 16:08:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ymo_39401/05_2025/8ymo_39401_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ymo_39401/05_2025/8ymo_39401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ymo_39401/05_2025/8ymo_39401.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ymo_39401/05_2025/8ymo_39401.map" model { file = "/net/cci-nas-00/data/ceres_data/8ymo_39401/05_2025/8ymo_39401_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ymo_39401/05_2025/8ymo_39401_neut.cif" } resolution = 2.7 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= 0.000 sd= 0.008 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 52 5.16 5 C 7088 2.51 5 N 1758 2.21 5 O 1830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10728 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5346 Classifications: {'peptide': 664} Link IDs: {'PTRANS': 35, 'TRANS': 628} Chain breaks: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-1': 2, 'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 16 Restraints were copied for chains: C Time building chain proxies: 16.23, per 1000 atoms: 1.51 Number of scatterers: 10728 At special positions: 0 Unit cell: (150.15, 82.95, 89.6, 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 52 16.00 O 1830 8.00 N 1758 7.00 C 7088 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2524 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 2 sheets defined 71.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 Processing helix chain 'A' and resid 34 through 38 Processing helix chain 'A' and resid 39 through 45 removed outlier: 3.672A pdb=" N TYR A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 83 through 91 Processing helix chain 'A' and resid 92 through 120 removed outlier: 3.929A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 160 through 195 Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 242 through 259 removed outlier: 4.525A pdb=" N LEU A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 267 removed outlier: 4.328A pdb=" N TYR A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 315 removed outlier: 6.088A pdb=" N ALA A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU A 298 " --> pdb=" O HIS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 368 through 408 removed outlier: 3.701A pdb=" N THR A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) Proline residue: A 393 - end of helix Processing helix chain 'A' and resid 428 through 439 Processing helix chain 'A' and resid 441 through 454 Processing helix chain 'A' and resid 457 through 478 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.769A pdb=" N THR A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 525 Processing helix chain 'A' and resid 526 through 535 Processing helix chain 'A' and resid 535 through 547 removed outlier: 3.602A pdb=" N ALA A 547 " --> pdb=" O HIS A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 585 Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 590 through 613 removed outlier: 4.377A pdb=" N PHE A 594 " --> pdb=" O MET A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 647 Processing helix chain 'A' and resid 655 through 660 Processing helix chain 'A' and resid 660 through 677 removed outlier: 3.989A pdb=" N VAL A 664 " --> pdb=" O ILE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 683 removed outlier: 3.510A pdb=" N VAL A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 704 through 711 removed outlier: 3.573A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'C' and resid 3 through 31 Processing helix chain 'C' and resid 34 through 38 Processing helix chain 'C' and resid 39 through 45 removed outlier: 3.672A pdb=" N TYR C 43 " --> pdb=" O PHE C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 80 Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'C' and resid 92 through 120 removed outlier: 3.929A pdb=" N TYR C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 160 through 195 Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 216 through 228 Processing helix chain 'C' and resid 242 through 259 removed outlier: 4.525A pdb=" N LEU C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 267 removed outlier: 4.328A pdb=" N TYR C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 315 removed outlier: 6.088A pdb=" N ALA C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N GLU C 298 " --> pdb=" O HIS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 339 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 368 through 408 removed outlier: 3.701A pdb=" N THR C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) Proline residue: C 393 - end of helix Processing helix chain 'C' and resid 428 through 439 Processing helix chain 'C' and resid 441 through 454 Processing helix chain 'C' and resid 457 through 478 Processing helix chain 'C' and resid 489 through 496 Processing helix chain 'C' and resid 501 through 506 removed outlier: 3.769A pdb=" N THR C 505 " --> pdb=" O GLN C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 525 Processing helix chain 'C' and resid 526 through 535 Processing helix chain 'C' and resid 535 through 547 removed outlier: 3.602A pdb=" N ALA C 547 " --> pdb=" O HIS C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 585 Proline residue: C 572 - end of helix Processing helix chain 'C' and resid 590 through 613 removed outlier: 4.377A pdb=" N PHE C 594 " --> pdb=" O MET C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 647 Processing helix chain 'C' and resid 655 through 660 Processing helix chain 'C' and resid 660 through 677 removed outlier: 3.989A pdb=" N VAL C 664 " --> pdb=" O ILE C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 683 removed outlier: 3.510A pdb=" N VAL C 682 " --> pdb=" O GLU C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 700 Processing helix chain 'C' and resid 704 through 711 removed outlier: 3.573A pdb=" N TYR C 708 " --> pdb=" O ASN C 704 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP C 711 " --> pdb=" O GLY C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 714 No H-bonds generated for 'chain 'C' and resid 712 through 714' Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.398A pdb=" N TYR A 233 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER A 327 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR A 235 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A 325 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN A 237 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA A 323 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL A 239 " --> pdb=" O MET A 321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 233 through 240 removed outlier: 5.398A pdb=" N TYR C 233 " --> pdb=" O SER C 327 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER C 327 " --> pdb=" O TYR C 233 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR C 235 " --> pdb=" O PHE C 325 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE C 325 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN C 237 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA C 323 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VAL C 239 " --> pdb=" O MET C 321 " (cutoff:3.500A) 664 hydrogen bonds defined for protein. 1944 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: 3.06 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1680 1.32 - 1.44: 3066 1.44 - 1.56: 6180 1.56 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 11018 Sorted by residual: bond pdb=" CA ILE C 392 " pdb=" CB ILE C 392 " ideal model delta sigma weight residual 1.539 1.562 -0.023 5.40e-03 3.43e+04 1.81e+01 bond pdb=" CA ILE A 392 " pdb=" CB ILE A 392 " ideal model delta sigma weight residual 1.539 1.562 -0.023 5.40e-03 3.43e+04 1.81e+01 bond pdb=" CA VAL A 121 " pdb=" CB VAL A 121 " ideal model delta sigma weight residual 1.537 1.555 -0.019 5.00e-03 4.00e+04 1.38e+01 bond pdb=" CA VAL C 121 " pdb=" CB VAL C 121 " ideal model delta sigma weight residual 1.537 1.555 -0.019 5.00e-03 4.00e+04 1.38e+01 bond pdb=" C LYS A 537 " pdb=" N PRO A 538 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.36e-02 5.41e+03 1.24e+01 ... (remaining 11013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 14520 3.02 - 6.04: 384 6.04 - 9.06: 58 9.06 - 12.09: 2 12.09 - 15.11: 2 Bond angle restraints: 14966 Sorted by residual: angle pdb=" N VAL C 482 " pdb=" CA VAL C 482 " pdb=" C VAL C 482 " ideal model delta sigma weight residual 112.96 105.20 7.76 1.00e+00 1.00e+00 6.01e+01 angle pdb=" N VAL A 482 " pdb=" CA VAL A 482 " pdb=" C VAL A 482 " ideal model delta sigma weight residual 112.96 105.20 7.76 1.00e+00 1.00e+00 6.01e+01 angle pdb=" N HIS C 651 " pdb=" CA HIS C 651 " pdb=" C HIS C 651 " ideal model delta sigma weight residual 110.80 125.91 -15.11 2.13e+00 2.20e-01 5.03e+01 angle pdb=" N HIS A 651 " pdb=" CA HIS A 651 " pdb=" C HIS A 651 " ideal model delta sigma weight residual 110.80 125.91 -15.11 2.13e+00 2.20e-01 5.03e+01 angle pdb=" N ILE A 440 " pdb=" CA ILE A 440 " pdb=" C ILE A 440 " ideal model delta sigma weight residual 113.47 106.55 6.92 1.01e+00 9.80e-01 4.69e+01 ... (remaining 14961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 5088 16.71 - 33.43: 618 33.43 - 50.14: 500 50.14 - 66.85: 258 66.85 - 83.57: 34 Dihedral angle restraints: 6498 sinusoidal: 2596 harmonic: 3902 Sorted by residual: dihedral pdb=" C PHE C 390 " pdb=" N PHE C 390 " pdb=" CA PHE C 390 " pdb=" CB PHE C 390 " ideal model delta harmonic sigma weight residual -122.60 -141.33 18.73 0 2.50e+00 1.60e-01 5.61e+01 dihedral pdb=" C PHE A 390 " pdb=" N PHE A 390 " pdb=" CA PHE A 390 " pdb=" CB PHE A 390 " ideal model delta harmonic sigma weight residual -122.60 -141.33 18.73 0 2.50e+00 1.60e-01 5.61e+01 dihedral pdb=" N PHE C 390 " pdb=" C PHE C 390 " pdb=" CA PHE C 390 " pdb=" CB PHE C 390 " ideal model delta harmonic sigma weight residual 122.80 141.46 -18.66 0 2.50e+00 1.60e-01 5.57e+01 ... (remaining 6495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 1592 0.164 - 0.327: 80 0.327 - 0.491: 4 0.491 - 0.654: 0 0.654 - 0.818: 2 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA PHE C 390 " pdb=" N PHE C 390 " pdb=" C PHE C 390 " pdb=" CB PHE C 390 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" CA PHE A 390 " pdb=" N PHE A 390 " pdb=" C PHE A 390 " pdb=" CB PHE A 390 " both_signs ideal model delta sigma weight residual False 2.51 1.69 0.82 2.00e-01 2.50e+01 1.67e+01 chirality pdb=" CA TRP A 625 " pdb=" N TRP A 625 " pdb=" C TRP A 625 " pdb=" CB TRP A 625 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.22e+00 ... (remaining 1675 not shown) Planarity restraints: 1872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 649 " 0.033 2.00e-02 2.50e+03 6.35e-02 4.04e+01 pdb=" C THR A 649 " -0.110 2.00e-02 2.50e+03 pdb=" O THR A 649 " 0.040 2.00e-02 2.50e+03 pdb=" N LYS A 650 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 649 " -0.033 2.00e-02 2.50e+03 6.35e-02 4.04e+01 pdb=" C THR C 649 " 0.110 2.00e-02 2.50e+03 pdb=" O THR C 649 " -0.040 2.00e-02 2.50e+03 pdb=" N LYS C 650 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 389 " 0.023 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C PHE C 389 " -0.078 2.00e-02 2.50e+03 pdb=" O PHE C 389 " 0.028 2.00e-02 2.50e+03 pdb=" N PHE C 390 " 0.026 2.00e-02 2.50e+03 ... (remaining 1869 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 143 2.63 - 3.20: 9659 3.20 - 3.76: 19153 3.76 - 4.33: 27150 4.33 - 4.90: 41068 Nonbonded interactions: 97173 Sorted by model distance: nonbonded pdb=" O GLY C 648 " pdb=" NE2 HIS C 651 " model vdw 2.060 3.120 nonbonded pdb=" O GLY A 648 " pdb=" NE2 HIS A 651 " model vdw 2.060 3.120 nonbonded pdb=" CG2 ILE C 483 " pdb=" CD1 PHE C 494 " model vdw 2.070 3.760 nonbonded pdb=" CG2 ILE A 483 " pdb=" CD1 PHE A 494 " model vdw 2.070 3.760 nonbonded pdb=" OD1 ASN A 241 " pdb=" CB ALA A 366 " model vdw 2.119 3.460 ... (remaining 97168 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 27.030 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: 1.910 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 34.920 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 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 : 0.007 0.048 11018 Z= 0.502 Angle : 1.186 15.107 14966 Z= 0.796 Chirality : 0.081 0.818 1678 Planarity : 0.006 0.064 1872 Dihedral : 24.230 83.566 3974 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 1.22 % Allowed : 9.73 % Favored : 89.06 % Rotamer: Outliers : 33.45 % Allowed : 13.91 % Favored : 52.64 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.93 (0.20), residues: 1316 helix: -1.03 (0.15), residues: 860 sheet: -3.43 (0.58), residues: 50 loop : -3.61 (0.26), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 625 HIS 0.004 0.001 HIS C 651 PHE 0.011 0.002 PHE C 383 TYR 0.010 0.001 TYR C 618 ARG 0.002 0.000 ARG C 331 Details of bonding type rmsd hydrogen bonds : bond 0.18123 ( 664) hydrogen bonds : angle 7.48021 ( 1944) covalent geometry : bond 0.00665 (11018) covalent geometry : angle 1.18612 (14966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 380 poor density : 216 time to evaluate : 1.206 Fit side-chains REVERT: A 41 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7647 (tptt) REVERT: A 61 PHE cc_start: 0.2961 (OUTLIER) cc_final: 0.1594 (t80) REVERT: A 159 PHE cc_start: 0.3455 (OUTLIER) cc_final: 0.3231 (t80) REVERT: A 278 LYS cc_start: 0.2467 (OUTLIER) cc_final: 0.0449 (ttmt) REVERT: A 353 TRP cc_start: 0.6656 (m100) cc_final: 0.6257 (t60) REVERT: A 555 ASP cc_start: 0.0128 (OUTLIER) cc_final: -0.0221 (t0) REVERT: A 639 SER cc_start: 0.6352 (OUTLIER) cc_final: 0.6012 (p) REVERT: A 654 SER cc_start: 0.4772 (OUTLIER) cc_final: 0.4185 (t) REVERT: A 676 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7670 (tpt90) REVERT: A 692 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.6855 (tttt) REVERT: C 41 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7635 (tptt) REVERT: C 61 PHE cc_start: 0.2929 (OUTLIER) cc_final: 0.1578 (t80) REVERT: C 159 PHE cc_start: 0.3486 (OUTLIER) cc_final: 0.3225 (t80) REVERT: C 278 LYS cc_start: 0.2460 (OUTLIER) cc_final: 0.0456 (ttmt) REVERT: C 353 TRP cc_start: 0.6650 (m100) cc_final: 0.6258 (t60) REVERT: C 555 ASP cc_start: 0.0134 (OUTLIER) cc_final: -0.0210 (t0) REVERT: C 639 SER cc_start: 0.6373 (OUTLIER) cc_final: 0.6031 (p) REVERT: C 654 SER cc_start: 0.4786 (OUTLIER) cc_final: 0.4181 (t) REVERT: C 676 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7667 (tpt90) REVERT: C 692 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.6865 (tttt) outliers start: 380 outliers final: 18 residues processed: 500 average time/residue: 1.0803 time to fit residues: 584.1489 Evaluate side-chains 158 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 295 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 639 SER Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 295 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 439 LEU Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 639 SER Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 676 ARG Chi-restraints excluded: chain C residue 692 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 103 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 31 GLN A 63 ASN A 90 HIS A 190 GLN A 228 ASN A 339 GLN A 501 GLN A 543 HIS A 573 GLN A 609 GLN A 615 ASN A 616 GLN A 640 GLN A 687 GLN A 704 ASN A 715 HIS C 14 ASN C 31 GLN C 63 ASN C 90 HIS C 190 GLN C 228 ASN C 339 GLN C 501 GLN C 543 HIS C 573 GLN C 609 GLN C 615 ASN C 616 GLN C 640 GLN C 687 GLN C 704 ASN C 715 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.192436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.121945 restraints weight = 11002.321| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.09 r_work: 0.3202 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11018 Z= 0.185 Angle : 0.777 16.559 14966 Z= 0.387 Chirality : 0.046 0.217 1678 Planarity : 0.006 0.043 1872 Dihedral : 9.079 59.264 1542 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.21 % Favored : 91.64 % Rotamer: Outliers : 8.63 % Allowed : 24.65 % Favored : 66.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.00 (0.23), residues: 1316 helix: 0.79 (0.18), residues: 862 sheet: -3.86 (0.49), residues: 46 loop : -3.55 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 625 HIS 0.004 0.001 HIS C 651 PHE 0.018 0.002 PHE A 494 TYR 0.027 0.002 TYR C 43 ARG 0.007 0.001 ARG A 60 Details of bonding type rmsd hydrogen bonds : bond 0.05231 ( 664) hydrogen bonds : angle 5.33515 ( 1944) covalent geometry : bond 0.00401 (11018) covalent geometry : angle 0.77652 (14966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 126 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.5997 (OUTLIER) cc_final: 0.5665 (mttp) REVERT: A 278 LYS cc_start: 0.0630 (OUTLIER) cc_final: 0.0083 (ttmt) REVERT: A 318 LYS cc_start: 0.7978 (pttp) cc_final: 0.7765 (pmtt) REVERT: A 353 TRP cc_start: 0.8235 (m100) cc_final: 0.7172 (t60) REVERT: A 508 MET cc_start: 0.2929 (OUTLIER) cc_final: 0.1737 (mmp) REVERT: A 555 ASP cc_start: 0.3685 (OUTLIER) cc_final: 0.2780 (t0) REVERT: A 671 ARG cc_start: 0.7215 (mtp-110) cc_final: 0.6787 (mmm160) REVERT: A 676 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8045 (tpt90) REVERT: C 254 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5674 (mttp) REVERT: C 278 LYS cc_start: 0.0631 (OUTLIER) cc_final: 0.0085 (ttmt) REVERT: C 318 LYS cc_start: 0.7970 (pttp) cc_final: 0.7759 (pmtt) REVERT: C 353 TRP cc_start: 0.8231 (m100) cc_final: 0.7175 (t60) REVERT: C 508 MET cc_start: 0.2932 (OUTLIER) cc_final: 0.1735 (mmp) REVERT: C 555 ASP cc_start: 0.3687 (OUTLIER) cc_final: 0.2779 (t0) REVERT: C 671 ARG cc_start: 0.7199 (mtp-110) cc_final: 0.6774 (mmm160) REVERT: C 676 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8045 (tpt90) outliers start: 98 outliers final: 32 residues processed: 208 average time/residue: 1.0606 time to fit residues: 240.3234 Evaluate side-chains 156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 165 MET Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 676 ARG Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 VAL Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 676 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 124 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 272 GLN A 575 GLN A 616 GLN C 63 ASN C 272 GLN C 575 GLN C 616 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120069 restraints weight = 11607.284| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.11 r_work: 0.3218 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11018 Z= 0.162 Angle : 0.705 16.761 14966 Z= 0.339 Chirality : 0.044 0.175 1678 Planarity : 0.005 0.039 1872 Dihedral : 7.219 58.608 1500 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.66 % Favored : 91.19 % Rotamer: Outliers : 7.57 % Allowed : 23.94 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.53 (0.23), residues: 1316 helix: 1.22 (0.18), residues: 850 sheet: -3.68 (0.52), residues: 46 loop : -3.40 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 625 HIS 0.004 0.001 HIS C 651 PHE 0.012 0.001 PHE C 548 TYR 0.008 0.001 TYR C 361 ARG 0.005 0.001 ARG C 376 Details of bonding type rmsd hydrogen bonds : bond 0.04634 ( 664) hydrogen bonds : angle 4.83130 ( 1944) covalent geometry : bond 0.00357 (11018) covalent geometry : angle 0.70507 (14966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 124 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 LYS cc_start: 0.5916 (OUTLIER) cc_final: 0.5596 (mttp) REVERT: A 258 TRP cc_start: 0.4038 (OUTLIER) cc_final: 0.3273 (t60) REVERT: A 278 LYS cc_start: 0.0394 (OUTLIER) cc_final: 0.0011 (ttmt) REVERT: A 287 GLN cc_start: 0.5574 (OUTLIER) cc_final: 0.5015 (pm20) REVERT: A 348 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8293 (mt-10) REVERT: A 353 TRP cc_start: 0.8142 (m100) cc_final: 0.6999 (t60) REVERT: A 555 ASP cc_start: 0.3223 (OUTLIER) cc_final: 0.2665 (t0) REVERT: A 646 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5813 (tp) REVERT: C 254 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5603 (mttp) REVERT: C 258 TRP cc_start: 0.4039 (OUTLIER) cc_final: 0.3274 (t60) REVERT: C 278 LYS cc_start: 0.0396 (OUTLIER) cc_final: 0.0010 (ttmt) REVERT: C 287 GLN cc_start: 0.5567 (OUTLIER) cc_final: 0.5008 (pm20) REVERT: C 348 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8294 (mt-10) REVERT: C 353 TRP cc_start: 0.8126 (m100) cc_final: 0.6984 (t60) REVERT: C 555 ASP cc_start: 0.3218 (OUTLIER) cc_final: 0.2659 (t0) REVERT: C 646 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5840 (tp) outliers start: 86 outliers final: 32 residues processed: 202 average time/residue: 1.1891 time to fit residues: 259.9190 Evaluate side-chains 156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 112 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 281 CYS Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 646 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 616 GLN C 190 GLN C 616 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.119068 restraints weight = 11384.048| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.10 r_work: 0.3209 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11018 Z= 0.156 Angle : 0.661 14.285 14966 Z= 0.319 Chirality : 0.043 0.155 1678 Planarity : 0.005 0.041 1872 Dihedral : 6.481 50.723 1490 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 6.34 % Allowed : 25.00 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.38 (0.23), residues: 1316 helix: 1.30 (0.18), residues: 852 sheet: -3.50 (0.55), residues: 46 loop : -3.28 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 625 HIS 0.003 0.001 HIS C 651 PHE 0.010 0.001 PHE A 72 TYR 0.009 0.001 TYR A 361 ARG 0.005 0.001 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 664) hydrogen bonds : angle 4.63253 ( 1944) covalent geometry : bond 0.00348 (11018) covalent geometry : angle 0.66113 (14966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 128 time to evaluate : 1.197 Fit side-chains REVERT: A 61 PHE cc_start: 0.2373 (OUTLIER) cc_final: 0.0222 (t80) REVERT: A 278 LYS cc_start: 0.0388 (OUTLIER) cc_final: 0.0043 (ttmt) REVERT: A 287 GLN cc_start: 0.5658 (OUTLIER) cc_final: 0.5088 (pm20) REVERT: A 288 LYS cc_start: 0.3435 (OUTLIER) cc_final: 0.2865 (pptt) REVERT: A 292 ILE cc_start: 0.0680 (OUTLIER) cc_final: 0.0028 (pp) REVERT: A 296 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5967 (mt) REVERT: A 348 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 353 TRP cc_start: 0.8135 (m100) cc_final: 0.7003 (t60) REVERT: A 508 MET cc_start: 0.3243 (tpt) cc_final: 0.1987 (mmp) REVERT: A 555 ASP cc_start: 0.3192 (OUTLIER) cc_final: 0.2752 (t0) REVERT: A 646 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5942 (tp) REVERT: A 711 ASP cc_start: 0.8373 (p0) cc_final: 0.7842 (m-30) REVERT: C 61 PHE cc_start: 0.2385 (OUTLIER) cc_final: 0.0222 (t80) REVERT: C 278 LYS cc_start: 0.0388 (OUTLIER) cc_final: 0.0044 (ttmt) REVERT: C 287 GLN cc_start: 0.5653 (OUTLIER) cc_final: 0.5084 (pm20) REVERT: C 288 LYS cc_start: 0.3443 (OUTLIER) cc_final: 0.2874 (pptt) REVERT: C 292 ILE cc_start: 0.0681 (OUTLIER) cc_final: 0.0032 (pp) REVERT: C 296 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5963 (mt) REVERT: C 348 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8270 (mt-10) REVERT: C 353 TRP cc_start: 0.8131 (m100) cc_final: 0.7004 (t60) REVERT: C 508 MET cc_start: 0.3226 (tpt) cc_final: 0.1973 (mmp) REVERT: C 555 ASP cc_start: 0.3190 (OUTLIER) cc_final: 0.2753 (t0) REVERT: C 646 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5962 (tp) REVERT: C 711 ASP cc_start: 0.8358 (p0) cc_final: 0.7828 (m-30) outliers start: 72 outliers final: 22 residues processed: 184 average time/residue: 1.1922 time to fit residues: 237.0636 Evaluate side-chains 152 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 510 ILE Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 114 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 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 31 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 272 GLN A 575 GLN A 616 GLN C 31 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 272 GLN C 575 GLN C 616 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118937 restraints weight = 11370.887| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.08 r_work: 0.3220 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11018 Z= 0.146 Angle : 0.631 13.099 14966 Z= 0.306 Chirality : 0.043 0.155 1678 Planarity : 0.005 0.041 1872 Dihedral : 6.049 45.964 1488 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 6.16 % Allowed : 25.53 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.30 (0.23), residues: 1316 helix: 1.36 (0.18), residues: 852 sheet: -3.44 (0.57), residues: 46 loop : -3.28 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 625 HIS 0.003 0.001 HIS C 651 PHE 0.009 0.001 PHE A 33 TYR 0.009 0.001 TYR C 361 ARG 0.004 0.000 ARG A 376 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 664) hydrogen bonds : angle 4.46590 ( 1944) covalent geometry : bond 0.00323 (11018) covalent geometry : angle 0.63142 (14966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 124 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.2378 (OUTLIER) cc_final: 0.0161 (t80) REVERT: A 254 LYS cc_start: 0.5956 (OUTLIER) cc_final: 0.5589 (mttp) REVERT: A 278 LYS cc_start: 0.0314 (OUTLIER) cc_final: 0.0026 (ttmt) REVERT: A 287 GLN cc_start: 0.5686 (OUTLIER) cc_final: 0.5111 (pm20) REVERT: A 288 LYS cc_start: 0.3214 (OUTLIER) cc_final: 0.2702 (pptt) REVERT: A 292 ILE cc_start: 0.0667 (OUTLIER) cc_final: 0.0015 (pp) REVERT: A 348 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8207 (mt-10) REVERT: A 508 MET cc_start: 0.3334 (tpt) cc_final: 0.2055 (mmp) REVERT: A 551 LYS cc_start: 0.4460 (OUTLIER) cc_final: 0.4257 (mmtt) REVERT: A 555 ASP cc_start: 0.3178 (OUTLIER) cc_final: 0.2803 (t0) REVERT: A 646 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.6038 (tp) REVERT: A 711 ASP cc_start: 0.8352 (p0) cc_final: 0.7823 (m-30) REVERT: C 61 PHE cc_start: 0.2388 (OUTLIER) cc_final: 0.0163 (t80) REVERT: C 254 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.5617 (mttp) REVERT: C 278 LYS cc_start: 0.0314 (OUTLIER) cc_final: 0.0028 (ttmt) REVERT: C 287 GLN cc_start: 0.5680 (OUTLIER) cc_final: 0.5109 (pm20) REVERT: C 288 LYS cc_start: 0.3236 (OUTLIER) cc_final: 0.2726 (pptt) REVERT: C 292 ILE cc_start: 0.0669 (OUTLIER) cc_final: 0.0022 (pp) REVERT: C 348 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8225 (mt-10) REVERT: C 508 MET cc_start: 0.3312 (tpt) cc_final: 0.2043 (mmp) REVERT: C 551 LYS cc_start: 0.4459 (OUTLIER) cc_final: 0.4254 (mmtt) REVERT: C 555 ASP cc_start: 0.3196 (OUTLIER) cc_final: 0.2820 (t0) REVERT: C 646 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.6054 (tp) REVERT: C 711 ASP cc_start: 0.8341 (p0) cc_final: 0.7814 (m-30) outliers start: 70 outliers final: 22 residues processed: 180 average time/residue: 1.1822 time to fit residues: 230.4133 Evaluate side-chains 150 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 39 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 616 GLN C 31 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN ** C 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 ASN C 616 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118090 restraints weight = 11423.639| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.10 r_work: 0.3163 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11018 Z= 0.152 Angle : 0.630 12.540 14966 Z= 0.307 Chirality : 0.042 0.163 1678 Planarity : 0.005 0.042 1872 Dihedral : 5.695 46.264 1484 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.55 % Allowed : 26.41 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.22 (0.23), residues: 1316 helix: 1.39 (0.18), residues: 854 sheet: -3.35 (0.58), residues: 46 loop : -3.20 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.003 0.001 HIS C 651 PHE 0.009 0.001 PHE C 225 TYR 0.009 0.001 TYR A 361 ARG 0.005 0.000 ARG C 671 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 664) hydrogen bonds : angle 4.46295 ( 1944) covalent geometry : bond 0.00337 (11018) covalent geometry : angle 0.63004 (14966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 122 time to evaluate : 1.132 Fit side-chains REVERT: A 61 PHE cc_start: 0.2390 (OUTLIER) cc_final: 0.0177 (t80) REVERT: A 78 GLU cc_start: 0.7586 (tt0) cc_final: 0.7200 (mm-30) REVERT: A 159 PHE cc_start: 0.5301 (t80) cc_final: 0.5080 (t80) REVERT: A 278 LYS cc_start: 0.0370 (OUTLIER) cc_final: 0.0117 (ttmt) REVERT: A 287 GLN cc_start: 0.5659 (OUTLIER) cc_final: 0.5091 (pm20) REVERT: A 288 LYS cc_start: 0.3075 (OUTLIER) cc_final: 0.2579 (pptt) REVERT: A 348 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8197 (mt-10) REVERT: A 508 MET cc_start: 0.3359 (tpt) cc_final: 0.2054 (mmp) REVERT: A 551 LYS cc_start: 0.4444 (OUTLIER) cc_final: 0.4211 (mmtt) REVERT: A 555 ASP cc_start: 0.3165 (OUTLIER) cc_final: 0.2854 (t0) REVERT: A 646 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6105 (tp) REVERT: A 711 ASP cc_start: 0.8391 (p0) cc_final: 0.7864 (m-30) REVERT: C 61 PHE cc_start: 0.2393 (OUTLIER) cc_final: 0.0177 (t80) REVERT: C 78 GLU cc_start: 0.7595 (tt0) cc_final: 0.7209 (mm-30) REVERT: C 159 PHE cc_start: 0.5310 (t80) cc_final: 0.5101 (t80) REVERT: C 278 LYS cc_start: 0.0368 (OUTLIER) cc_final: 0.0117 (ttmt) REVERT: C 287 GLN cc_start: 0.5650 (OUTLIER) cc_final: 0.5086 (pm20) REVERT: C 288 LYS cc_start: 0.3081 (OUTLIER) cc_final: 0.2587 (pptt) REVERT: C 348 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8206 (mt-10) REVERT: C 508 MET cc_start: 0.3340 (tpt) cc_final: 0.2046 (mmp) REVERT: C 551 LYS cc_start: 0.4441 (OUTLIER) cc_final: 0.4207 (mmtt) REVERT: C 555 ASP cc_start: 0.3170 (OUTLIER) cc_final: 0.2857 (t0) REVERT: C 646 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.6108 (tp) REVERT: C 711 ASP cc_start: 0.8375 (p0) cc_final: 0.7850 (m-30) outliers start: 63 outliers final: 26 residues processed: 175 average time/residue: 1.1465 time to fit residues: 217.3258 Evaluate side-chains 156 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 555 ASP Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 555 ASP Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 646 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 272 GLN A 546 ASN A 616 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 272 GLN C 616 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116045 restraints weight = 11542.132| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.10 r_work: 0.3147 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11018 Z= 0.175 Angle : 0.670 16.159 14966 Z= 0.323 Chirality : 0.044 0.203 1678 Planarity : 0.005 0.042 1872 Dihedral : 5.703 48.301 1484 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.49 % Allowed : 27.55 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.24 (0.23), residues: 1316 helix: 1.35 (0.17), residues: 854 sheet: -3.41 (0.58), residues: 46 loop : -3.11 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 625 HIS 0.003 0.001 HIS A 90 PHE 0.010 0.001 PHE C 225 TYR 0.011 0.001 TYR C 361 ARG 0.006 0.000 ARG C 671 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 664) hydrogen bonds : angle 4.45648 ( 1944) covalent geometry : bond 0.00404 (11018) covalent geometry : angle 0.66973 (14966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.2410 (OUTLIER) cc_final: 0.0305 (t80) REVERT: A 78 GLU cc_start: 0.7586 (tt0) cc_final: 0.7176 (mm-30) REVERT: A 278 LYS cc_start: 0.0330 (OUTLIER) cc_final: 0.0105 (ttmt) REVERT: A 287 GLN cc_start: 0.5660 (OUTLIER) cc_final: 0.5115 (pm20) REVERT: A 288 LYS cc_start: 0.3100 (OUTLIER) cc_final: 0.2612 (pptt) REVERT: A 348 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 508 MET cc_start: 0.3440 (tpt) cc_final: 0.2136 (mmp) REVERT: A 551 LYS cc_start: 0.4443 (OUTLIER) cc_final: 0.4199 (mmtt) REVERT: A 711 ASP cc_start: 0.8399 (p0) cc_final: 0.7846 (m-30) REVERT: C 61 PHE cc_start: 0.2414 (OUTLIER) cc_final: 0.0307 (t80) REVERT: C 78 GLU cc_start: 0.7583 (tt0) cc_final: 0.7172 (mm-30) REVERT: C 278 LYS cc_start: 0.0325 (OUTLIER) cc_final: 0.0101 (ttmt) REVERT: C 287 GLN cc_start: 0.5653 (OUTLIER) cc_final: 0.5109 (pm20) REVERT: C 288 LYS cc_start: 0.3099 (OUTLIER) cc_final: 0.2608 (pptt) REVERT: C 348 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8181 (mt-10) REVERT: C 508 MET cc_start: 0.3419 (tpt) cc_final: 0.2125 (mmp) REVERT: C 551 LYS cc_start: 0.4450 (OUTLIER) cc_final: 0.4204 (mmtt) REVERT: C 711 ASP cc_start: 0.8383 (p0) cc_final: 0.7834 (m-30) outliers start: 51 outliers final: 30 residues processed: 173 average time/residue: 1.1432 time to fit residues: 214.4856 Evaluate side-chains 160 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 392 ILE Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 569 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 2 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 272 GLN A 616 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 272 GLN C 616 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.188929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118537 restraints weight = 11286.882| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.08 r_work: 0.3177 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11018 Z= 0.136 Angle : 0.641 16.144 14966 Z= 0.307 Chirality : 0.042 0.179 1678 Planarity : 0.005 0.042 1872 Dihedral : 5.397 45.874 1480 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 4.14 % Allowed : 28.61 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.10 (0.24), residues: 1316 helix: 1.44 (0.18), residues: 858 sheet: -3.41 (0.58), residues: 46 loop : -3.06 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 625 HIS 0.003 0.001 HIS C 651 PHE 0.010 0.001 PHE C 72 TYR 0.008 0.001 TYR C 361 ARG 0.007 0.000 ARG C 671 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 664) hydrogen bonds : angle 4.34774 ( 1944) covalent geometry : bond 0.00296 (11018) covalent geometry : angle 0.64071 (14966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.2422 (OUTLIER) cc_final: 0.0334 (t80) REVERT: A 78 GLU cc_start: 0.7556 (tt0) cc_final: 0.7128 (mm-30) REVERT: A 287 GLN cc_start: 0.5667 (OUTLIER) cc_final: 0.5128 (pm20) REVERT: A 288 LYS cc_start: 0.3098 (OUTLIER) cc_final: 0.2574 (pptt) REVERT: A 348 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8161 (mt-10) REVERT: A 508 MET cc_start: 0.3421 (tpt) cc_final: 0.2146 (mmp) REVERT: A 551 LYS cc_start: 0.4461 (OUTLIER) cc_final: 0.4216 (mmtt) REVERT: A 711 ASP cc_start: 0.8384 (p0) cc_final: 0.7849 (m-30) REVERT: C 61 PHE cc_start: 0.2427 (OUTLIER) cc_final: 0.0332 (t80) REVERT: C 78 GLU cc_start: 0.7554 (tt0) cc_final: 0.7124 (mm-30) REVERT: C 287 GLN cc_start: 0.5659 (OUTLIER) cc_final: 0.5121 (pm20) REVERT: C 288 LYS cc_start: 0.3102 (OUTLIER) cc_final: 0.2578 (pptt) REVERT: C 348 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8161 (mt-10) REVERT: C 508 MET cc_start: 0.3431 (tpt) cc_final: 0.2145 (mmp) REVERT: C 551 LYS cc_start: 0.4469 (OUTLIER) cc_final: 0.4224 (mmtt) REVERT: C 711 ASP cc_start: 0.8374 (p0) cc_final: 0.7841 (m-30) outliers start: 47 outliers final: 22 residues processed: 173 average time/residue: 1.1830 time to fit residues: 221.7713 Evaluate side-chains 154 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 565 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 86 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 56 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 272 GLN A 616 GLN C 190 GLN C 272 GLN C 616 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.189175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119175 restraints weight = 11450.904| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.08 r_work: 0.3184 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11018 Z= 0.136 Angle : 0.637 15.551 14966 Z= 0.306 Chirality : 0.042 0.173 1678 Planarity : 0.005 0.041 1872 Dihedral : 5.132 45.552 1468 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.52 % Allowed : 28.96 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.02 (0.24), residues: 1316 helix: 1.50 (0.18), residues: 858 sheet: -3.41 (0.58), residues: 46 loop : -3.03 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 625 HIS 0.003 0.001 HIS C 651 PHE 0.010 0.001 PHE C 72 TYR 0.007 0.001 TYR C 361 ARG 0.006 0.000 ARG C 671 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 664) hydrogen bonds : angle 4.30918 ( 1944) covalent geometry : bond 0.00298 (11018) covalent geometry : angle 0.63744 (14966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 PHE cc_start: 0.2445 (OUTLIER) cc_final: 0.0353 (t80) REVERT: A 78 GLU cc_start: 0.7532 (tt0) cc_final: 0.7127 (mm-30) REVERT: A 287 GLN cc_start: 0.5662 (OUTLIER) cc_final: 0.5136 (pm20) REVERT: A 288 LYS cc_start: 0.3077 (OUTLIER) cc_final: 0.2521 (pptt) REVERT: A 348 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 551 LYS cc_start: 0.4493 (OUTLIER) cc_final: 0.4237 (mmtt) REVERT: A 711 ASP cc_start: 0.8370 (p0) cc_final: 0.7850 (m-30) REVERT: C 61 PHE cc_start: 0.2434 (OUTLIER) cc_final: 0.0347 (t80) REVERT: C 78 GLU cc_start: 0.7521 (tt0) cc_final: 0.7112 (mm-30) REVERT: C 287 GLN cc_start: 0.5652 (OUTLIER) cc_final: 0.5131 (pm20) REVERT: C 288 LYS cc_start: 0.3081 (OUTLIER) cc_final: 0.2526 (pptt) REVERT: C 348 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8180 (mt-10) REVERT: C 551 LYS cc_start: 0.4481 (OUTLIER) cc_final: 0.4224 (mmtt) REVERT: C 711 ASP cc_start: 0.8360 (p0) cc_final: 0.7843 (m-30) outliers start: 40 outliers final: 24 residues processed: 168 average time/residue: 1.1354 time to fit residues: 207.0930 Evaluate side-chains 164 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 565 ILE Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 272 GLN Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 569 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 79 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 108 optimal weight: 0.0870 chunk 116 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 616 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 616 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.188503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119503 restraints weight = 11565.004| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.08 r_work: 0.3179 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11018 Z= 0.141 Angle : 0.636 14.984 14966 Z= 0.305 Chirality : 0.043 0.168 1678 Planarity : 0.005 0.041 1872 Dihedral : 5.126 45.995 1468 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 2.90 % Allowed : 29.40 % Favored : 67.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.03 (0.24), residues: 1316 helix: 1.54 (0.17), residues: 858 sheet: -3.38 (0.59), residues: 46 loop : -3.00 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 625 HIS 0.003 0.001 HIS C 651 PHE 0.010 0.001 PHE A 27 TYR 0.006 0.001 TYR C 361 ARG 0.006 0.000 ARG C 671 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 664) hydrogen bonds : angle 4.28696 ( 1944) covalent geometry : bond 0.00315 (11018) covalent geometry : angle 0.63593 (14966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.055 Fit side-chains REVERT: A 61 PHE cc_start: 0.2392 (OUTLIER) cc_final: 0.0323 (t80) REVERT: A 78 GLU cc_start: 0.7389 (tt0) cc_final: 0.6969 (mm-30) REVERT: A 287 GLN cc_start: 0.5655 (OUTLIER) cc_final: 0.5144 (pm20) REVERT: A 288 LYS cc_start: 0.3077 (OUTLIER) cc_final: 0.2527 (pptt) REVERT: A 348 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 371 SER cc_start: 0.7914 (m) cc_final: 0.7486 (p) REVERT: A 711 ASP cc_start: 0.8291 (p0) cc_final: 0.7777 (m-30) REVERT: C 61 PHE cc_start: 0.2398 (OUTLIER) cc_final: 0.0322 (t80) REVERT: C 78 GLU cc_start: 0.7385 (tt0) cc_final: 0.6962 (mm-30) REVERT: C 287 GLN cc_start: 0.5650 (OUTLIER) cc_final: 0.5139 (pm20) REVERT: C 288 LYS cc_start: 0.3078 (OUTLIER) cc_final: 0.2525 (pptt) REVERT: C 348 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8051 (mt-10) REVERT: C 371 SER cc_start: 0.7910 (m) cc_final: 0.7478 (p) REVERT: C 551 LYS cc_start: 0.4530 (OUTLIER) cc_final: 0.4271 (mmtt) REVERT: C 711 ASP cc_start: 0.8288 (p0) cc_final: 0.7779 (m-30) outliers start: 33 outliers final: 18 residues processed: 167 average time/residue: 1.0222 time to fit residues: 186.7785 Evaluate side-chains 153 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 287 GLN Chi-restraints excluded: chain A residue 288 LYS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 569 THR Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 232 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 551 LYS Chi-restraints excluded: chain C residue 569 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 129 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 128 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 190 GLN A 616 GLN ** C 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 GLN C 616 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.188437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119652 restraints weight = 11426.182| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.06 r_work: 0.3179 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11018 Z= 0.141 Angle : 0.627 13.768 14966 Z= 0.302 Chirality : 0.043 0.157 1678 Planarity : 0.005 0.041 1872 Dihedral : 5.089 46.690 1468 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.90 % Allowed : 29.58 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.06 (0.23), residues: 1316 helix: 1.53 (0.17), residues: 860 sheet: -3.41 (0.59), residues: 46 loop : -2.94 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.003 0.001 HIS C 651 PHE 0.010 0.001 PHE C 72 TYR 0.008 0.001 TYR A 577 ARG 0.006 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 664) hydrogen bonds : angle 4.26931 ( 1944) covalent geometry : bond 0.00314 (11018) covalent geometry : angle 0.62654 (14966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11077.52 seconds wall clock time: 192 minutes 41.67 seconds (11561.67 seconds total)