Starting phenix.real_space_refine on Fri Dec 27 21:58:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s1y_24812/12_2024/7s1y_24812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s1y_24812/12_2024/7s1y_24812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s1y_24812/12_2024/7s1y_24812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s1y_24812/12_2024/7s1y_24812.map" model { file = "/net/cci-nas-00/data/ceres_data/7s1y_24812/12_2024/7s1y_24812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s1y_24812/12_2024/7s1y_24812.cif" } resolution = 3.6 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= 0.008 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 34 5.16 5 Cl 2 4.86 5 C 4338 2.51 5 N 1054 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6580 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3263 Classifications: {'peptide': 474} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 78} Link IDs: {'PTRANS': 16, 'TRANS': 457} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3263 Classifications: {'peptide': 474} Incomplete info: {'backbone_only': 21, 'truncation_to_alanine': 78} Link IDs: {'PTRANS': 16, 'TRANS': 457} Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 9, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {' K': 1, ' CL': 1, '82U': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 27 Unusual residues: {' K': 1, ' CL': 1, '82U': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.86, per 1000 atoms: 0.74 Number of scatterers: 6580 At special positions: 0 Unit cell: (107.06, 66.78, 86.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 2 17.00 S 34 16.00 O 1150 8.00 N 1054 7.00 C 4338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 577 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 568 " distance=2.04 Simple disulfide: pdb=" SG CYS B 577 " - pdb=" SG CYS B 582 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 82U A1303 " pdb=" CB 82U B1303 " Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 74.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 286 through 300 removed outlier: 3.742A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 4.033A pdb=" N TRP A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 343 removed outlier: 4.321A pdb=" N LEU A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 361 removed outlier: 3.760A pdb=" N LEU A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 399 removed outlier: 3.743A pdb=" N ALA A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 425 removed outlier: 4.241A pdb=" N ILE A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 455 removed outlier: 4.320A pdb=" N TRP A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.657A pdb=" N LYS A 460 " --> pdb=" O LEU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 486 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 502 through 507 removed outlier: 3.516A pdb=" N ILE A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 511 removed outlier: 3.688A pdb=" N LEU A 511 " --> pdb=" O SER A 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 508 through 511' Processing helix chain 'A' and resid 516 through 544 removed outlier: 4.436A pdb=" N LYS A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 524 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 571 removed outlier: 4.530A pdb=" N LYS A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 599 through 632 removed outlier: 3.512A pdb=" N ILE A 603 " --> pdb=" O PHE A 599 " (cutoff:3.500A) Proline residue: A 623 - end of helix removed outlier: 3.825A pdb=" N ASP A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 669 Processing helix chain 'A' and resid 674 through 699 removed outlier: 4.476A pdb=" N ASN A 680 " --> pdb=" O PRO A 676 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE A 682 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 730 removed outlier: 3.831A pdb=" N LEU A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 752 Processing helix chain 'B' and resid 286 through 300 removed outlier: 3.680A pdb=" N GLY B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 4.056A pdb=" N TRP B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 343 removed outlier: 4.364A pdb=" N LEU B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 361 removed outlier: 3.752A pdb=" N LEU B 355 " --> pdb=" O GLY B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 399 removed outlier: 3.631A pdb=" N ALA B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 4.173A pdb=" N ILE B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 455 removed outlier: 4.324A pdb=" N TRP B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.647A pdb=" N LYS B 460 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 removed outlier: 3.515A pdb=" N PHE B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 499 Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 508 through 511 removed outlier: 3.670A pdb=" N LEU B 511 " --> pdb=" O SER B 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 508 through 511' Processing helix chain 'B' and resid 516 through 544 removed outlier: 4.373A pdb=" N LYS B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU B 524 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 571 removed outlier: 4.120A pdb=" N LYS B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 599 through 632 removed outlier: 3.612A pdb=" N ILE B 603 " --> pdb=" O PHE B 599 " (cutoff:3.500A) Proline residue: B 623 - end of helix removed outlier: 3.844A pdb=" N ASP B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 669 Processing helix chain 'B' and resid 674 through 699 removed outlier: 4.145A pdb=" N ASN B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 681 " --> pdb=" O ILE B 677 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE B 682 " --> pdb=" O ILE B 678 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B 683 " --> pdb=" O SER B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 730 removed outlier: 4.036A pdb=" N LEU B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 752 490 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2040 1.34 - 1.46: 1702 1.46 - 1.58: 2942 1.58 - 1.70: 2 1.70 - 1.81: 50 Bond restraints: 6736 Sorted by residual: bond pdb=" CG PRO A 676 " pdb=" CD PRO A 676 " ideal model delta sigma weight residual 1.503 1.346 0.157 3.40e-02 8.65e+02 2.15e+01 bond pdb=" N 82U A1303 " pdb=" CA 82U A1303 " ideal model delta sigma weight residual 1.366 1.442 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" N 82U B1303 " pdb=" CA 82U B1303 " ideal model delta sigma weight residual 1.366 1.439 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CB PRO A 676 " pdb=" CG PRO A 676 " ideal model delta sigma weight residual 1.492 1.658 -0.166 5.00e-02 4.00e+02 1.11e+01 bond pdb=" N PRO A 676 " pdb=" CD PRO A 676 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.51e+00 ... (remaining 6731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 9126 3.14 - 6.28: 84 6.28 - 9.42: 10 9.42 - 12.56: 1 12.56 - 15.70: 1 Bond angle restraints: 9222 Sorted by residual: angle pdb=" CA PRO A 676 " pdb=" N PRO A 676 " pdb=" CD PRO A 676 " ideal model delta sigma weight residual 112.00 96.30 15.70 1.40e+00 5.10e-01 1.26e+02 angle pdb=" N PRO A 676 " pdb=" CD PRO A 676 " pdb=" CG PRO A 676 " ideal model delta sigma weight residual 103.20 92.75 10.45 1.50e+00 4.44e-01 4.85e+01 angle pdb=" CA PRO A 636 " pdb=" N PRO A 636 " pdb=" CD PRO A 636 " ideal model delta sigma weight residual 112.00 104.41 7.59 1.40e+00 5.10e-01 2.94e+01 angle pdb=" CA PRO A 676 " pdb=" CB PRO A 676 " pdb=" CG PRO A 676 " ideal model delta sigma weight residual 104.50 97.20 7.30 1.90e+00 2.77e-01 1.48e+01 angle pdb=" C PRO A 676 " pdb=" CA PRO A 676 " pdb=" CB PRO A 676 " ideal model delta sigma weight residual 110.88 115.84 -4.96 1.41e+00 5.03e-01 1.24e+01 ... (remaining 9217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 3427 17.69 - 35.39: 286 35.39 - 53.08: 37 53.08 - 70.77: 5 70.77 - 88.47: 3 Dihedral angle restraints: 3758 sinusoidal: 1134 harmonic: 2624 Sorted by residual: dihedral pdb=" CB CYS B 563 " pdb=" SG CYS B 563 " pdb=" SG CYS B 568 " pdb=" CB CYS B 568 " ideal model delta sinusoidal sigma weight residual 93.00 168.61 -75.61 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS A 563 " pdb=" SG CYS A 563 " pdb=" SG CYS A 568 " pdb=" CB CYS A 568 " ideal model delta sinusoidal sigma weight residual 93.00 148.54 -55.54 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CA TYR B 711 " pdb=" C TYR B 711 " pdb=" N ASN B 712 " pdb=" CA ASN B 712 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 862 0.053 - 0.106: 214 0.106 - 0.159: 15 0.159 - 0.212: 0 0.212 - 0.265: 3 Chirality restraints: 1094 Sorted by residual: chirality pdb=" CA TYR A 711 " pdb=" N TYR A 711 " pdb=" C TYR A 711 " pdb=" CB TYR A 711 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA TYR B 711 " pdb=" N TYR B 711 " pdb=" C TYR B 711 " pdb=" CB TYR B 711 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA PRO A 676 " pdb=" N PRO A 676 " pdb=" C PRO A 676 " pdb=" CB PRO A 676 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1091 not shown) Planarity restraints: 1158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 635 " 0.090 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO A 636 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO A 636 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 636 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 675 " 0.084 5.00e-02 4.00e+02 1.14e-01 2.10e+01 pdb=" N PRO A 676 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 288 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C ILE B 288 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE B 288 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 289 " -0.010 2.00e-02 2.50e+03 ... (remaining 1155 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.28: 4 2.28 - 3.00: 3840 3.00 - 3.71: 12513 3.71 - 4.43: 17616 4.43 - 5.14: 28763 Nonbonded interactions: 62736 Sorted by model distance: nonbonded pdb=" K K A1301 " pdb=" O5 82U A1303 " model vdw 1.566 2.850 nonbonded pdb=" K K B1301 " pdb=" O5 82U B1303 " model vdw 1.614 2.850 nonbonded pdb=" OG SER A 339 " pdb=" OH TYR A 711 " model vdw 2.133 3.040 nonbonded pdb=" OG SER B 339 " pdb=" OH TYR B 711 " model vdw 2.142 3.040 nonbonded pdb=" OE1 GLU B 485 " pdb=" OG SER B 489 " model vdw 2.313 3.040 ... (remaining 62731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.220 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 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 : 0.005 0.166 6736 Z= 0.323 Angle : 0.772 15.702 9222 Z= 0.417 Chirality : 0.044 0.265 1094 Planarity : 0.006 0.131 1158 Dihedral : 12.892 88.467 2098 Min Nonbonded Distance : 1.566 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.20 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.24 % 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: -0.33 (0.28), residues: 944 helix: 0.96 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -2.61 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 287 HIS 0.004 0.001 HIS A 398 PHE 0.025 0.001 PHE A 608 TYR 0.016 0.001 TYR B 739 ARG 0.001 0.000 ARG A 358 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.725 Fit side-chains REVERT: A 389 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7227 (mt-10) REVERT: A 465 PHE cc_start: 0.7882 (t80) cc_final: 0.7521 (t80) REVERT: A 471 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7788 (tt0) REVERT: A 630 CYS cc_start: 0.3999 (m) cc_final: 0.3591 (p) REVERT: A 676 PRO cc_start: 0.7727 (Cg_endo) cc_final: 0.7511 (Cg_exo) REVERT: A 725 ILE cc_start: 0.8035 (mm) cc_final: 0.7791 (mt) REVERT: B 630 CYS cc_start: 0.4421 (m) cc_final: 0.3869 (p) REVERT: B 677 ILE cc_start: 0.7566 (mm) cc_final: 0.7212 (mm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1250 time to fit residues: 28.6038 Evaluate side-chains 112 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN B 298 ASN B 435 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6736 Z= 0.218 Angle : 0.646 10.505 9222 Z= 0.330 Chirality : 0.043 0.307 1094 Planarity : 0.005 0.083 1158 Dihedral : 6.044 38.573 1022 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.58 % Favored : 91.21 % Rotamer: Outliers : 2.26 % Allowed : 12.33 % Favored : 85.42 % Cbeta Deviations : 0.24 % 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: -0.31 (0.27), residues: 944 helix: 0.88 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.58 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 287 HIS 0.005 0.002 HIS B 398 PHE 0.023 0.002 PHE B 477 TYR 0.029 0.002 TYR A 739 ARG 0.004 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.523 Fit side-chains REVERT: A 389 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7307 (mt-10) REVERT: A 471 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7690 (tt0) REVERT: A 681 PHE cc_start: 0.5784 (m-80) cc_final: 0.5493 (m-80) REVERT: A 725 ILE cc_start: 0.8161 (mm) cc_final: 0.7899 (mt) REVERT: B 389 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7388 (mt-10) REVERT: B 713 MET cc_start: 0.5563 (tmm) cc_final: 0.5240 (tmm) outliers start: 13 outliers final: 9 residues processed: 133 average time/residue: 0.1206 time to fit residues: 23.7849 Evaluate side-chains 116 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 621 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 30.0000 chunk 84 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 chunk 68 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6736 Z= 0.209 Angle : 0.629 11.466 9222 Z= 0.318 Chirality : 0.043 0.261 1094 Planarity : 0.004 0.069 1158 Dihedral : 6.108 40.907 1022 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.84 % Favored : 91.95 % Rotamer: Outliers : 2.78 % Allowed : 18.23 % Favored : 78.99 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.32 (0.27), residues: 944 helix: 0.90 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.64 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 300 HIS 0.003 0.001 HIS B 398 PHE 0.021 0.002 PHE A 285 TYR 0.025 0.002 TYR A 739 ARG 0.004 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.695 Fit side-chains REVERT: A 296 MET cc_start: 0.7359 (mmp) cc_final: 0.6592 (mmt) REVERT: A 389 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 471 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7749 (tt0) REVERT: A 604 SER cc_start: 0.6733 (OUTLIER) cc_final: 0.6507 (t) REVERT: A 725 ILE cc_start: 0.8204 (mm) cc_final: 0.7965 (mt) REVERT: A 728 PHE cc_start: 0.6643 (m-80) cc_final: 0.6339 (m-10) REVERT: B 285 PHE cc_start: 0.7300 (p90) cc_final: 0.7087 (p90) REVERT: B 428 MET cc_start: 0.6732 (mmp) cc_final: 0.5981 (mtm) REVERT: B 748 TYR cc_start: 0.4212 (t80) cc_final: 0.3746 (m-80) outliers start: 16 outliers final: 8 residues processed: 131 average time/residue: 0.1171 time to fit residues: 23.7121 Evaluate side-chains 119 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 604 SER Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 740 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6736 Z= 0.202 Angle : 0.633 12.922 9222 Z= 0.318 Chirality : 0.042 0.245 1094 Planarity : 0.004 0.063 1158 Dihedral : 6.073 40.437 1022 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.73 % Favored : 92.06 % Rotamer: Outliers : 4.34 % Allowed : 21.18 % Favored : 74.48 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.34 (0.27), residues: 944 helix: 0.90 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.65 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 732 HIS 0.003 0.001 HIS A 398 PHE 0.028 0.002 PHE A 608 TYR 0.020 0.002 TYR A 584 ARG 0.003 0.000 ARG A 546 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.672 Fit side-chains REVERT: A 296 MET cc_start: 0.7446 (mmp) cc_final: 0.7142 (mmp) REVERT: A 389 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7401 (mt-10) REVERT: A 465 PHE cc_start: 0.7944 (t80) cc_final: 0.7642 (t80) REVERT: A 471 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7689 (tt0) REVERT: A 681 PHE cc_start: 0.5760 (m-80) cc_final: 0.5508 (m-80) REVERT: A 725 ILE cc_start: 0.8216 (mm) cc_final: 0.7953 (mt) REVERT: A 728 PHE cc_start: 0.6551 (m-80) cc_final: 0.6234 (m-80) REVERT: B 285 PHE cc_start: 0.7314 (p90) cc_final: 0.7015 (p90) REVERT: B 443 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7811 (mm) REVERT: B 465 PHE cc_start: 0.7767 (t80) cc_final: 0.7467 (t80) REVERT: B 748 TYR cc_start: 0.4216 (t80) cc_final: 0.3829 (m-80) outliers start: 25 outliers final: 12 residues processed: 139 average time/residue: 0.1124 time to fit residues: 23.8796 Evaluate side-chains 126 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 740 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 30 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5550 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6736 Z= 0.191 Angle : 0.631 12.080 9222 Z= 0.316 Chirality : 0.043 0.279 1094 Planarity : 0.004 0.059 1158 Dihedral : 6.006 40.533 1022 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.16 % Favored : 91.63 % Rotamer: Outliers : 3.99 % Allowed : 22.22 % Favored : 73.78 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.27 (0.27), residues: 944 helix: 0.96 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.70 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 PHE 0.026 0.001 PHE A 608 TYR 0.019 0.001 TYR B 584 ARG 0.003 0.000 ARG B 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.683 Fit side-chains REVERT: A 296 MET cc_start: 0.7464 (mmp) cc_final: 0.7229 (mmt) REVERT: A 389 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7386 (mt-10) REVERT: A 465 PHE cc_start: 0.7848 (t80) cc_final: 0.7602 (t80) REVERT: A 681 PHE cc_start: 0.6029 (m-80) cc_final: 0.5772 (m-80) REVERT: A 713 MET cc_start: 0.5379 (tmm) cc_final: 0.5161 (tmm) REVERT: A 725 ILE cc_start: 0.8210 (mm) cc_final: 0.7947 (mt) REVERT: A 728 PHE cc_start: 0.6368 (m-80) cc_final: 0.6074 (m-80) REVERT: B 285 PHE cc_start: 0.7094 (p90) cc_final: 0.6799 (p90) REVERT: B 428 MET cc_start: 0.6707 (mmp) cc_final: 0.6033 (mtt) REVERT: B 443 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7960 (mm) REVERT: B 465 PHE cc_start: 0.7744 (t80) cc_final: 0.7438 (t80) REVERT: B 748 TYR cc_start: 0.4296 (t80) cc_final: 0.3912 (m-80) outliers start: 23 outliers final: 13 residues processed: 131 average time/residue: 0.1115 time to fit residues: 22.4661 Evaluate side-chains 127 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 740 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5658 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6736 Z= 0.308 Angle : 0.703 12.838 9222 Z= 0.357 Chirality : 0.046 0.342 1094 Planarity : 0.004 0.057 1158 Dihedral : 6.894 48.304 1022 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.90 % Favored : 90.89 % Rotamer: Outliers : 5.90 % Allowed : 20.66 % Favored : 73.44 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.81 (0.27), residues: 944 helix: 0.49 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.74 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 PHE 0.024 0.002 PHE A 495 TYR 0.017 0.002 TYR A 711 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 0.661 Fit side-chains REVERT: A 296 MET cc_start: 0.7437 (mmp) cc_final: 0.7111 (mmt) REVERT: A 389 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7567 (mt-10) REVERT: A 465 PHE cc_start: 0.7973 (t80) cc_final: 0.7709 (t80) REVERT: A 725 ILE cc_start: 0.8260 (mm) cc_final: 0.8011 (mt) REVERT: B 285 PHE cc_start: 0.7284 (p90) cc_final: 0.6979 (p90) REVERT: B 428 MET cc_start: 0.6900 (mmp) cc_final: 0.6565 (mtt) REVERT: B 485 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6662 (mm-30) REVERT: B 748 TYR cc_start: 0.4608 (t80) cc_final: 0.4062 (m-80) outliers start: 34 outliers final: 21 residues processed: 135 average time/residue: 0.1135 time to fit residues: 23.6509 Evaluate side-chains 129 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 740 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5603 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6736 Z= 0.228 Angle : 0.678 16.421 9222 Z= 0.340 Chirality : 0.046 0.365 1094 Planarity : 0.004 0.055 1158 Dihedral : 6.386 43.093 1022 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.84 % Favored : 91.95 % Rotamer: Outliers : 5.03 % Allowed : 22.05 % Favored : 72.92 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.65 (0.27), residues: 944 helix: 0.63 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -2.72 (0.31), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 PHE 0.020 0.002 PHE A 608 TYR 0.016 0.002 TYR B 584 ARG 0.003 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.665 Fit side-chains REVERT: A 389 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 725 ILE cc_start: 0.8183 (mm) cc_final: 0.7930 (mt) REVERT: B 285 PHE cc_start: 0.7281 (p90) cc_final: 0.6996 (p90) REVERT: B 296 MET cc_start: 0.7570 (mmp) cc_final: 0.7053 (mmt) REVERT: B 428 MET cc_start: 0.6897 (mmp) cc_final: 0.6574 (mtt) REVERT: B 465 PHE cc_start: 0.7902 (t80) cc_final: 0.7637 (t80) REVERT: B 485 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6646 (mm-30) REVERT: B 748 TYR cc_start: 0.4566 (t80) cc_final: 0.4065 (m-80) outliers start: 29 outliers final: 20 residues processed: 134 average time/residue: 0.1166 time to fit residues: 23.8949 Evaluate side-chains 132 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 717 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.0030 chunk 8 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5580 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6736 Z= 0.222 Angle : 0.707 15.445 9222 Z= 0.349 Chirality : 0.048 0.398 1094 Planarity : 0.004 0.055 1158 Dihedral : 6.316 42.317 1022 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.73 % Favored : 92.06 % Rotamer: Outliers : 4.17 % Allowed : 23.96 % Favored : 71.88 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.64 (0.27), residues: 944 helix: 0.67 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.83 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 PHE 0.018 0.002 PHE A 495 TYR 0.020 0.001 TYR A 739 ARG 0.004 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.633 Fit side-chains REVERT: A 389 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7449 (mt-10) REVERT: A 465 PHE cc_start: 0.7946 (t80) cc_final: 0.7726 (t80) REVERT: A 725 ILE cc_start: 0.8241 (mm) cc_final: 0.7995 (mt) REVERT: B 428 MET cc_start: 0.7012 (mmp) cc_final: 0.6651 (mtt) REVERT: B 465 PHE cc_start: 0.7944 (t80) cc_final: 0.7692 (t80) REVERT: B 485 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6575 (mm-30) REVERT: B 681 PHE cc_start: 0.6020 (m-80) cc_final: 0.5798 (m-80) REVERT: B 748 TYR cc_start: 0.4552 (t80) cc_final: 0.4042 (m-80) outliers start: 24 outliers final: 18 residues processed: 130 average time/residue: 0.1230 time to fit residues: 23.7449 Evaluate side-chains 125 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 692 SER Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 717 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 89 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6736 Z= 0.238 Angle : 0.710 15.018 9222 Z= 0.351 Chirality : 0.046 0.352 1094 Planarity : 0.004 0.054 1158 Dihedral : 6.306 43.084 1022 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.84 % Favored : 91.95 % Rotamer: Outliers : 3.30 % Allowed : 25.17 % Favored : 71.53 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.61 (0.27), residues: 944 helix: 0.68 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.83 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 PHE 0.023 0.002 PHE A 495 TYR 0.019 0.001 TYR A 739 ARG 0.004 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.745 Fit side-chains REVERT: A 389 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7450 (mt-10) REVERT: A 465 PHE cc_start: 0.7979 (t80) cc_final: 0.7701 (t80) REVERT: A 713 MET cc_start: 0.6026 (tmm) cc_final: 0.5704 (tmm) REVERT: A 725 ILE cc_start: 0.8281 (mm) cc_final: 0.8041 (mt) REVERT: B 296 MET cc_start: 0.7361 (mmt) cc_final: 0.6969 (mmt) REVERT: B 428 MET cc_start: 0.6925 (mmp) cc_final: 0.6683 (mtt) REVERT: B 485 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6601 (mm-30) REVERT: B 748 TYR cc_start: 0.4571 (t80) cc_final: 0.4030 (m-80) outliers start: 19 outliers final: 18 residues processed: 123 average time/residue: 0.1156 time to fit residues: 21.8413 Evaluate side-chains 125 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 717 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 74 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 6736 Z= 0.254 Angle : 0.740 15.960 9222 Z= 0.363 Chirality : 0.047 0.334 1094 Planarity : 0.004 0.054 1158 Dihedral : 6.408 44.305 1022 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.63 % Favored : 92.16 % Rotamer: Outliers : 3.47 % Allowed : 25.17 % Favored : 71.35 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.64 (0.27), residues: 944 helix: 0.65 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.81 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 PHE 0.028 0.002 PHE A 495 TYR 0.019 0.001 TYR A 739 ARG 0.004 0.001 ARG B 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1888 Ramachandran restraints generated. 944 Oldfield, 0 Emsley, 944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.925 Fit side-chains REVERT: A 389 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 465 PHE cc_start: 0.7984 (t80) cc_final: 0.7724 (t80) REVERT: A 725 ILE cc_start: 0.8266 (mm) cc_final: 0.8012 (mt) REVERT: B 296 MET cc_start: 0.7340 (mmt) cc_final: 0.6973 (mmt) REVERT: B 485 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 681 PHE cc_start: 0.5981 (m-80) cc_final: 0.5680 (m-80) REVERT: B 748 TYR cc_start: 0.4581 (t80) cc_final: 0.4016 (m-80) outliers start: 20 outliers final: 19 residues processed: 121 average time/residue: 0.1314 time to fit residues: 24.6060 Evaluate side-chains 126 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 677 ILE Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 533 TYR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 740 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.249004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.218036 restraints weight = 8026.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.223070 restraints weight = 4690.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.226033 restraints weight = 3287.641| |-----------------------------------------------------------------------------| r_work (final): 0.4655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6736 Z= 0.256 Angle : 0.743 16.109 9222 Z= 0.365 Chirality : 0.047 0.312 1094 Planarity : 0.004 0.054 1158 Dihedral : 6.475 44.853 1022 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.94 % Favored : 91.84 % Rotamer: Outliers : 3.82 % Allowed : 25.17 % Favored : 71.01 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.64 (0.27), residues: 944 helix: 0.65 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.80 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 PHE 0.027 0.002 PHE B 466 TYR 0.019 0.001 TYR A 739 ARG 0.004 0.001 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1427.33 seconds wall clock time: 27 minutes 24.12 seconds (1644.12 seconds total)