Starting phenix.real_space_refine on Tue Feb 11 23:18:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s1y_24812/02_2025/7s1y_24812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s1y_24812/02_2025/7s1y_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_24812/02_2025/7s1y_24812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s1y_24812/02_2025/7s1y_24812.map" model { file = "/net/cci-nas-00/data/ceres_data/7s1y_24812/02_2025/7s1y_24812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s1y_24812/02_2025/7s1y_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-5592/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: 4.70, per 1000 atoms: 0.71 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: 1.90 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: 0.56 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: 1.99 Time building geometry restraints manager: 2.15 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: 0.04 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.520 Find NCS groups from input model: 0.260 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- 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 : 0.632 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: 0.1200 time to fit residues: 27.1439 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 : 0.658 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.255822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.225613 restraints weight = 7995.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.230777 restraints weight = 4582.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.234433 restraints weight = 3156.165| |-----------------------------------------------------------------------------| r_work (final): 0.4734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 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 : 0.639 Fit side-chains REVERT: A 437 VAL cc_start: 0.8368 (m) cc_final: 0.8058 (t) REVERT: A 471 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7881 (tt0) REVERT: A 681 PHE cc_start: 0.5710 (m-80) cc_final: 0.5475 (m-80) REVERT: B 713 MET cc_start: 0.5883 (tmm) cc_final: 0.5553 (tmm) outliers start: 13 outliers final: 9 residues processed: 133 average time/residue: 0.1181 time to fit residues: 23.6442 Evaluate side-chains 115 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.8980 chunk 47 optimal weight: 8.9990 chunk 91 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.251737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.221128 restraints weight = 8036.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.226219 restraints weight = 4641.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.229611 restraints weight = 3190.122| |-----------------------------------------------------------------------------| r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6736 Z= 0.216 Angle : 0.636 11.537 9222 Z= 0.323 Chirality : 0.043 0.260 1094 Planarity : 0.004 0.069 1158 Dihedral : 6.165 41.446 1022 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.05 % Favored : 91.74 % 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: -0.35 (0.27), residues: 944 helix: 0.87 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.65 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 300 HIS 0.003 0.001 HIS B 398 PHE 0.022 0.002 PHE A 285 TYR 0.026 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 132 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.687 Fit side-chains REVERT: A 296 MET cc_start: 0.7656 (mmp) cc_final: 0.6852 (mmt) REVERT: A 437 VAL cc_start: 0.8349 (m) cc_final: 0.8052 (t) REVERT: A 471 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7947 (tt0) REVERT: A 604 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7999 (t) REVERT: B 428 MET cc_start: 0.5376 (mmp) cc_final: 0.5129 (mtm) REVERT: B 748 TYR cc_start: 0.5120 (t80) cc_final: 0.4791 (m-80) outliers start: 16 outliers final: 8 residues processed: 127 average time/residue: 0.1123 time to fit residues: 21.9691 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 : 0.730 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.243759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.211734 restraints weight = 8306.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.216755 restraints weight = 4852.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.219438 restraints weight = 3426.166| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6736 Z= 0.316 Angle : 0.700 11.765 9222 Z= 0.360 Chirality : 0.047 0.270 1094 Planarity : 0.004 0.064 1158 Dihedral : 6.916 47.346 1022 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.75 % Favored : 90.04 % Rotamer: Outliers : 5.21 % Allowed : 19.97 % Favored : 74.83 % 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: -0.82 (0.27), residues: 944 helix: 0.47 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.71 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 PHE 0.021 0.002 PHE B 285 TYR 0.020 0.002 TYR A 584 ARG 0.001 0.000 ARG B 294 *********************** 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: 30 poor density : 117 time to evaluate : 0.679 Fit side-chains REVERT: A 296 MET cc_start: 0.7745 (mmp) cc_final: 0.7195 (mmt) REVERT: A 604 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8136 (t) REVERT: B 713 MET cc_start: 0.6315 (tmm) cc_final: 0.6078 (tmm) REVERT: B 748 TYR cc_start: 0.5420 (t80) cc_final: 0.5048 (m-80) outliers start: 30 outliers final: 16 residues processed: 140 average time/residue: 0.1131 time to fit residues: 24.2684 Evaluate side-chains 122 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 415 ILE 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 292 LEU 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 740 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 65 optimal weight: 0.0470 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.250099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.219367 restraints weight = 8003.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.224160 restraints weight = 4720.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.227566 restraints weight = 3348.608| |-----------------------------------------------------------------------------| r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6736 Z= 0.201 Angle : 0.630 11.703 9222 Z= 0.324 Chirality : 0.043 0.275 1094 Planarity : 0.004 0.060 1158 Dihedral : 6.250 42.349 1022 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.84 % Favored : 91.95 % Rotamer: Outliers : 3.65 % Allowed : 23.78 % Favored : 72.57 % 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: -0.52 (0.27), residues: 944 helix: 0.79 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.80 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 287 HIS 0.003 0.001 HIS B 398 PHE 0.020 0.002 PHE A 495 TYR 0.019 0.002 TYR A 584 ARG 0.003 0.000 ARG A 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 137 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.692 Fit side-chains REVERT: A 296 MET cc_start: 0.7624 (mmp) cc_final: 0.7136 (mmt) REVERT: A 681 PHE cc_start: 0.5900 (m-80) cc_final: 0.5509 (m-80) REVERT: B 285 PHE cc_start: 0.6752 (p90) cc_final: 0.6541 (p90) REVERT: B 713 MET cc_start: 0.6047 (tmm) cc_final: 0.5765 (tmm) REVERT: B 748 TYR cc_start: 0.5406 (t80) cc_final: 0.5095 (m-80) outliers start: 21 outliers final: 13 residues processed: 131 average time/residue: 0.1149 time to fit residues: 23.0707 Evaluate side-chains 128 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 611 THR Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 677 ILE 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 611 THR Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 717 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 50 optimal weight: 0.0770 chunk 60 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 0.0010 overall best weight: 0.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.254662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4635 r_free = 0.4635 target = 0.224585 restraints weight = 7966.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.229607 restraints weight = 4670.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.233157 restraints weight = 3257.718| |-----------------------------------------------------------------------------| r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.3120 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= 0.175 Angle : 0.636 11.057 9222 Z= 0.322 Chirality : 0.045 0.310 1094 Planarity : 0.004 0.057 1158 Dihedral : 5.992 39.584 1022 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.31 % Favored : 92.48 % Rotamer: Outliers : 3.47 % Allowed : 24.65 % 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: -0.34 (0.27), residues: 944 helix: 0.92 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.72 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 287 HIS 0.002 0.001 HIS B 398 PHE 0.021 0.001 PHE A 473 TYR 0.017 0.001 TYR B 584 ARG 0.003 0.000 ARG B 546 *********************** 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 141 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.669 Fit side-chains REVERT: A 298 ASN cc_start: 0.6411 (OUTLIER) cc_final: 0.6189 (t0) REVERT: B 748 TYR cc_start: 0.5207 (t80) cc_final: 0.4916 (m-80) outliers start: 20 outliers final: 12 residues processed: 136 average time/residue: 0.1273 time to fit residues: 25.7277 Evaluate side-chains 121 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASN 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 677 ILE 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 611 THR Chi-restraints excluded: chain B residue 677 ILE Chi-restraints excluded: chain B residue 717 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 74 optimal weight: 40.0000 chunk 73 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.252014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.221603 restraints weight = 7970.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.226566 restraints weight = 4674.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.229952 restraints weight = 3285.866| |-----------------------------------------------------------------------------| r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6378 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6736 Z= 0.216 Angle : 0.666 14.507 9222 Z= 0.334 Chirality : 0.045 0.276 1094 Planarity : 0.004 0.055 1158 Dihedral : 6.104 41.358 1022 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.31 % Favored : 92.48 % Rotamer: Outliers : 4.17 % Allowed : 24.31 % 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: -0.42 (0.27), residues: 944 helix: 0.86 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.74 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 732 HIS 0.003 0.001 HIS B 398 PHE 0.021 0.002 PHE B 708 TYR 0.019 0.001 TYR A 739 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 135 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.706 Fit side-chains REVERT: A 298 ASN cc_start: 0.6557 (OUTLIER) cc_final: 0.6336 (t0) REVERT: A 681 PHE cc_start: 0.5457 (m-80) cc_final: 0.5234 (m-80) REVERT: B 296 MET cc_start: 0.7421 (mmp) cc_final: 0.7078 (mmt) REVERT: B 748 TYR cc_start: 0.5269 (t80) cc_final: 0.4890 (m-80) outliers start: 24 outliers final: 16 residues processed: 130 average time/residue: 0.1147 time to fit residues: 22.6815 Evaluate side-chains 125 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASN 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 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 717 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 22 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 89 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.251578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.221113 restraints weight = 7986.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.226161 restraints weight = 4711.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.229129 restraints weight = 3296.617| |-----------------------------------------------------------------------------| r_work (final): 0.4670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 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 : 0.003 0.056 6736 Z= 0.223 Angle : 0.675 14.904 9222 Z= 0.336 Chirality : 0.045 0.315 1094 Planarity : 0.004 0.053 1158 Dihedral : 6.142 42.950 1022 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.52 % Favored : 92.27 % Rotamer: Outliers : 3.65 % Allowed : 24.83 % 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: -0.44 (0.27), residues: 944 helix: 0.83 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -2.82 (0.31), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 287 HIS 0.002 0.001 HIS B 398 PHE 0.024 0.002 PHE A 495 TYR 0.019 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 132 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.762 Fit side-chains REVERT: A 298 ASN cc_start: 0.6528 (OUTLIER) cc_final: 0.6300 (t0) REVERT: B 384 VAL cc_start: 0.6604 (OUTLIER) cc_final: 0.6330 (t) REVERT: B 681 PHE cc_start: 0.5881 (m-80) cc_final: 0.5645 (m-80) REVERT: B 748 TYR cc_start: 0.5281 (t80) cc_final: 0.4885 (m-80) outliers start: 21 outliers final: 16 residues processed: 127 average time/residue: 0.1177 time to fit residues: 23.0254 Evaluate side-chains 127 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASN 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 B residue 312 VAL Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 415 ILE 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 677 ILE Chi-restraints excluded: chain B residue 692 SER 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 12 optimal weight: 10.0000 chunk 84 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.252294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.221795 restraints weight = 8119.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.226950 restraints weight = 4729.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.230388 restraints weight = 3285.223| |-----------------------------------------------------------------------------| r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6736 Z= 0.216 Angle : 0.674 15.263 9222 Z= 0.335 Chirality : 0.045 0.335 1094 Planarity : 0.004 0.053 1158 Dihedral : 6.095 42.316 1022 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.20 % Favored : 92.58 % Rotamer: Outliers : 3.99 % Allowed : 24.83 % Favored : 71.18 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.40 (0.27), residues: 944 helix: 0.87 (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 0.007 0.001 TRP B 287 HIS 0.003 0.001 HIS B 398 PHE 0.023 0.002 PHE A 495 TYR 0.019 0.001 TYR A 739 ARG 0.003 0.001 ARG A 546 *********************** 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 134 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.669 Fit side-chains REVERT: A 296 MET cc_start: 0.7482 (mmp) cc_final: 0.7024 (mmt) REVERT: A 298 ASN cc_start: 0.6504 (OUTLIER) cc_final: 0.6258 (t0) REVERT: A 384 VAL cc_start: 0.6599 (OUTLIER) cc_final: 0.6361 (t) REVERT: A 713 MET cc_start: 0.6442 (tmm) cc_final: 0.6135 (tmm) REVERT: B 296 MET cc_start: 0.7613 (mmt) cc_final: 0.7391 (mmt) REVERT: B 384 VAL cc_start: 0.6597 (OUTLIER) cc_final: 0.6328 (t) REVERT: B 748 TYR cc_start: 0.5273 (t80) cc_final: 0.4874 (m-80) outliers start: 23 outliers final: 17 residues processed: 129 average time/residue: 0.1197 time to fit residues: 23.7634 Evaluate side-chains 126 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 384 VAL 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 677 ILE Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 531 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 677 ILE Chi-restraints excluded: chain B residue 692 SER 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 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.250933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.219868 restraints weight = 8091.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.224992 restraints weight = 4767.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.228148 restraints weight = 3330.393| |-----------------------------------------------------------------------------| r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6736 Z= 0.240 Angle : 0.702 15.653 9222 Z= 0.349 Chirality : 0.047 0.354 1094 Planarity : 0.004 0.053 1158 Dihedral : 6.219 42.975 1022 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.63 % Favored : 92.16 % Rotamer: Outliers : 3.65 % Allowed : 25.35 % Favored : 71.01 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.42 (0.27), residues: 944 helix: 0.83 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.76 (0.31), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 287 HIS 0.002 0.001 HIS B 398 PHE 0.025 0.002 PHE B 466 TYR 0.020 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 129 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.634 Fit side-chains REVERT: A 298 ASN cc_start: 0.6556 (OUTLIER) cc_final: 0.6341 (t0) REVERT: A 384 VAL cc_start: 0.6736 (OUTLIER) cc_final: 0.6507 (t) REVERT: A 713 MET cc_start: 0.6520 (tmm) cc_final: 0.6223 (tmm) REVERT: B 384 VAL cc_start: 0.6590 (OUTLIER) cc_final: 0.6308 (t) REVERT: B 681 PHE cc_start: 0.5873 (m-80) cc_final: 0.5610 (m-80) outliers start: 21 outliers final: 17 residues processed: 124 average time/residue: 0.1156 time to fit residues: 22.0886 Evaluate side-chains 126 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 ASN Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 384 VAL 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 B residue 353 TYR Chi-restraints excluded: chain B residue 364 PHE Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 531 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 677 ILE Chi-restraints excluded: chain B residue 692 SER 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 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 0.0370 chunk 71 optimal weight: 0.9980 chunk 89 optimal weight: 0.0050 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.255595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.225147 restraints weight = 8218.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.230261 restraints weight = 4837.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.233734 restraints weight = 3386.246| |-----------------------------------------------------------------------------| r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6736 Z= 0.208 Angle : 0.689 15.900 9222 Z= 0.340 Chirality : 0.046 0.375 1094 Planarity : 0.004 0.053 1158 Dihedral : 6.018 39.950 1022 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.31 % Favored : 92.48 % Rotamer: Outliers : 3.30 % Allowed : 26.04 % Favored : 70.66 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.26 (0.27), residues: 944 helix: 0.96 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.61 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 287 HIS 0.003 0.001 HIS B 398 PHE 0.021 0.002 PHE A 495 TYR 0.021 0.001 TYR A 739 ARG 0.007 0.001 ARG B 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.38 seconds wall clock time: 35 minutes 57.89 seconds (2157.89 seconds total)