Starting phenix.real_space_refine on Thu Jul 2 04:59:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s1y_24812/07_2026/7s1y_24812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s1y_24812/07_2026/7s1y_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 { model { file = "/net/cci-nas-00/data/ceres_data/7s1y_24812/07_2026/7s1y_24812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s1y_24812/07_2026/7s1y_24812.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7s1y_24812/07_2026/7s1y_24812.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s1y_24812/07_2026/7s1y_24812.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s1y_24812/07_2026/7s1y_24812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s1y_24812/07_2026/7s1y_24812.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: {'ASN:plan1': 9, 'PHE:plan': 4, 'ARG:plan': 3, 'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1} 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: {'ASN:plan1': 9, 'PHE:plan': 4, 'ARG:plan': 3, 'GLU:plan': 12, 'ASP:plan': 8, 'GLN:plan1': 3, 'TYR:plan': 1} 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: 1.82, per 1000 atoms: 0.28 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: 0.69 Conformation dependent library (CDL) restraints added in 434.9 milliseconds 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: 0.11 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: 0.97 Time building geometry restraints manager: 0.90 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: 0.02 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: 1.130 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 8.430 Find NCS groups from input model: 0.140 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5541 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 6742 Z= 0.198 Angle : 0.773 15.702 9230 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 : 13.33 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.001 0.000 ARG A 358 TYR 0.016 0.001 TYR B 739 PHE 0.025 0.001 PHE A 608 TRP 0.017 0.001 TRP A 287 HIS 0.004 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 ( 6736) covalent geometry : angle 0.77208 / 0.42 ( 9222) SS BOND : bond 0.00439 / 0.18 ( 4) SS BOND : angle 1.59179 / 0.88 ( 8) hydrogen bonds : bond 0.10765 / 7.45 ( 490) hydrogen bonds : angle 5.22050 / 3.85 ( 1464) Misc. bond : bond 0.00079 / 0.04 ( 2) *********************** 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 : 0.224 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: 0.3590 (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: 0.3868 (p) REVERT: B 677 ILE cc_start: 0.7567 (mm) cc_final: 0.7212 (mm) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0441 time to fit residues: 10.4858 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 : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4885 r_free = 0.4885 target = 0.253544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.222968 restraints weight = 8077.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.228140 restraints weight = 4603.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.231708 restraints weight = 3149.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.233833 restraints weight = 2435.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4744 r_free = 0.4744 target = 0.235705 restraints weight = 2050.792| |-----------------------------------------------------------------------------| r_work (final): 0.4748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6742 Z= 0.155 Angle : 0.658 10.723 9230 Z= 0.336 Chirality : 0.043 0.305 1094 Planarity : 0.005 0.084 1158 Dihedral : 6.127 39.141 1022 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.79 % Favored : 91.00 % Rotamer: Outliers : 2.43 % Allowed : 12.85 % Favored : 84.72 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.27), residues: 944 helix: 0.83 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -2.61 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 546 TYR 0.028 0.002 TYR A 739 PHE 0.023 0.002 PHE B 477 TRP 0.009 0.001 TRP B 287 HIS 0.006 0.002 HIS B 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 6736) covalent geometry : angle 0.65711 / 0.34 ( 9222) SS BOND : bond 0.00069 / 0.03 ( 4) SS BOND : angle 1.27837 / 0.72 ( 8) hydrogen bonds : bond 0.04309 / 2.93 ( 490) hydrogen bonds : angle 4.51406 / 3.34 ( 1464) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** 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 140 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.225 Fit side-chains REVERT: A 437 VAL cc_start: 0.8368 (m) cc_final: 0.8058 (t) REVERT: A 471 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7909 (tt0) REVERT: A 604 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7748 (t) REVERT: B 677 ILE cc_start: 0.7354 (mm) cc_final: 0.7096 (mm) outliers start: 14 outliers final: 9 residues processed: 137 average time/residue: 0.0439 time to fit residues: 9.2821 Evaluate side-chains 116 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 740 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 1 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 435 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.249830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.218925 restraints weight = 8077.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.224045 restraints weight = 4632.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.227493 restraints weight = 3213.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.229434 restraints weight = 2504.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.230877 restraints weight = 2132.196| |-----------------------------------------------------------------------------| r_work (final): 0.4701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6742 Z= 0.154 Angle : 0.647 11.646 9230 Z= 0.330 Chirality : 0.044 0.268 1094 Planarity : 0.004 0.070 1158 Dihedral : 6.324 42.438 1022 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.94 % Favored : 91.84 % Rotamer: Outliers : 3.47 % Allowed : 18.58 % Favored : 77.95 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.27), residues: 944 helix: 0.77 (0.21), residues: 632 sheet: None (None), residues: 0 loop : -2.68 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.025 0.002 TYR A 739 PHE 0.028 0.002 PHE A 608 TRP 0.016 0.001 TRP A 300 HIS 0.004 0.001 HIS B 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 6736) covalent geometry : angle 0.64684 / 0.33 ( 9222) SS BOND : bond 0.00100 / 0.05 ( 4) SS BOND : angle 1.05383 / 0.59 ( 8) hydrogen bonds : bond 0.04370 / 2.94 ( 490) hydrogen bonds : angle 4.52228 / 3.36 ( 1464) Misc. bond : bond 0.00141 / 0.07 ( 2) *********************** 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 135 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.145 Fit side-chains REVERT: A 296 MET cc_start: 0.7648 (mmp) cc_final: 0.6849 (mmt) REVERT: A 437 VAL cc_start: 0.8266 (m) cc_final: 0.7977 (t) REVERT: A 604 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7933 (t) REVERT: A 681 PHE cc_start: 0.5941 (m-80) cc_final: 0.5713 (m-80) REVERT: B 748 TYR cc_start: 0.5129 (t80) cc_final: 0.4838 (m-80) outliers start: 20 outliers final: 11 residues processed: 130 average time/residue: 0.0459 time to fit residues: 9.4216 Evaluate side-chains 118 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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 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 364 PHE Chi-restraints excluded: chain B residue 486 THR 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 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 0.0470 chunk 40 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 40.0000 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 314 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4852 r_free = 0.4852 target = 0.250725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.220169 restraints weight = 8150.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.225109 restraints weight = 4790.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.228461 restraints weight = 3376.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.230425 restraints weight = 2661.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.231297 restraints weight = 2273.716| |-----------------------------------------------------------------------------| r_work (final): 0.4691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6742 Z= 0.145 Angle : 0.633 11.337 9230 Z= 0.323 Chirality : 0.044 0.254 1094 Planarity : 0.004 0.063 1158 Dihedral : 6.266 42.216 1022 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.26 % Favored : 91.53 % Rotamer: Outliers : 4.51 % Allowed : 20.14 % Favored : 75.35 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.27), residues: 944 helix: 0.82 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.67 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.020 0.002 TYR A 584 PHE 0.021 0.001 PHE A 608 TRP 0.007 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6736) covalent geometry : angle 0.63234 / 0.32 ( 9222) SS BOND : bond 0.00097 / 0.05 ( 4) SS BOND : angle 0.96560 / 0.54 ( 8) hydrogen bonds : bond 0.04200 / 2.82 ( 490) hydrogen bonds : angle 4.47147 / 3.31 ( 1464) Misc. bond : bond 0.00140 / 0.07 ( 2) *********************** 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 143 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.165 Fit side-chains REVERT: A 296 MET cc_start: 0.7717 (mmp) cc_final: 0.7054 (mmt) REVERT: A 437 VAL cc_start: 0.8329 (m) cc_final: 0.8002 (t) REVERT: A 604 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.8015 (t) REVERT: A 713 MET cc_start: 0.6513 (tmm) cc_final: 0.6262 (tmm) REVERT: B 748 TYR cc_start: 0.5187 (t80) cc_final: 0.4933 (m-80) outliers start: 26 outliers final: 13 residues processed: 136 average time/residue: 0.0403 time to fit residues: 8.6160 Evaluate side-chains 126 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL 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 B residue 288 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 486 THR 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 52 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 27 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4864 r_free = 0.4864 target = 0.252055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.221376 restraints weight = 8285.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.225988 restraints weight = 4798.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.229688 restraints weight = 3385.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.232018 restraints weight = 2632.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.233369 restraints weight = 2207.730| |-----------------------------------------------------------------------------| r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6742 Z= 0.135 Angle : 0.632 11.238 9230 Z= 0.320 Chirality : 0.043 0.276 1094 Planarity : 0.004 0.060 1158 Dihedral : 6.164 41.563 1022 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.52 % Favored : 92.27 % Rotamer: Outliers : 4.51 % Allowed : 22.74 % Favored : 72.74 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.27), residues: 944 helix: 0.88 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.72 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 546 TYR 0.020 0.001 TYR B 584 PHE 0.021 0.001 PHE A 495 TRP 0.006 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 6736) covalent geometry : angle 0.63195 / 0.32 ( 9222) SS BOND : bond 0.00096 / 0.05 ( 4) SS BOND : angle 0.92452 / 0.52 ( 8) hydrogen bonds : bond 0.04110 / 2.77 ( 490) hydrogen bonds : angle 4.38891 / 3.25 ( 1464) Misc. bond : bond 0.00122 / 0.06 ( 2) *********************** 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 134 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.194 Fit side-chains REVERT: A 296 MET cc_start: 0.7798 (mmp) cc_final: 0.7407 (mmt) REVERT: A 437 VAL cc_start: 0.8315 (m) cc_final: 0.7986 (t) REVERT: A 713 MET cc_start: 0.6354 (tmm) cc_final: 0.6084 (tmm) REVERT: B 288 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7329 (mp) REVERT: B 748 TYR cc_start: 0.5152 (t80) cc_final: 0.4878 (m-80) outliers start: 26 outliers final: 17 residues processed: 129 average time/residue: 0.0452 time to fit residues: 9.2086 Evaluate side-chains 128 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 364 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 THR 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 B residue 288 ILE Chi-restraints excluded: chain B residue 312 VAL 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 717 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 57 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4835 r_free = 0.4835 target = 0.249365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.218676 restraints weight = 8128.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.223798 restraints weight = 4687.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.227113 restraints weight = 3241.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.229115 restraints weight = 2543.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.229953 restraints weight = 2164.860| |-----------------------------------------------------------------------------| r_work (final): 0.4685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6742 Z= 0.155 Angle : 0.647 11.533 9230 Z= 0.329 Chirality : 0.044 0.319 1094 Planarity : 0.004 0.057 1158 Dihedral : 6.332 43.844 1022 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.84 % Favored : 91.95 % Rotamer: Outliers : 4.69 % Allowed : 21.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.27), residues: 944 helix: 0.78 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.74 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 294 TYR 0.016 0.001 TYR A 584 PHE 0.025 0.002 PHE A 495 TRP 0.006 0.001 TRP A 733 HIS 0.003 0.001 HIS B 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 6736) covalent geometry : angle 0.64639 / 0.33 ( 9222) SS BOND : bond 0.00103 / 0.05 ( 4) SS BOND : angle 0.87335 / 0.50 ( 8) hydrogen bonds : bond 0.04345 / 2.89 ( 490) hydrogen bonds : angle 4.41219 / 3.27 ( 1464) Misc. bond : bond 0.00144 / 0.07 ( 2) *********************** 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 138 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.273 Fit side-chains REVERT: A 296 MET cc_start: 0.7584 (mmp) cc_final: 0.7109 (mmt) REVERT: A 604 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7951 (t) REVERT: A 681 PHE cc_start: 0.5923 (m-80) cc_final: 0.5691 (m-80) REVERT: A 713 MET cc_start: 0.6396 (tmm) cc_final: 0.6142 (tmm) REVERT: B 681 PHE cc_start: 0.5784 (m-80) cc_final: 0.5400 (m-80) REVERT: B 748 TYR cc_start: 0.5289 (t80) cc_final: 0.5010 (m-80) outliers start: 27 outliers final: 19 residues processed: 131 average time/residue: 0.0437 time to fit residues: 9.0148 Evaluate side-chains 129 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.159 ------------------------------------------------------------------------------- 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 364 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 531 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 288 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 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 717 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.250477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.219805 restraints weight = 8012.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.224886 restraints weight = 4633.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.227852 restraints weight = 3218.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.230487 restraints weight = 2556.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.231830 restraints weight = 2144.218| |-----------------------------------------------------------------------------| r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6446 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6742 Z= 0.142 Angle : 0.643 11.419 9230 Z= 0.326 Chirality : 0.044 0.333 1094 Planarity : 0.004 0.055 1158 Dihedral : 6.245 42.975 1022 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.63 % Favored : 92.16 % Rotamer: Outliers : 5.03 % Allowed : 21.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.27), residues: 944 helix: 0.81 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -2.77 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 294 TYR 0.016 0.001 TYR B 584 PHE 0.024 0.001 PHE A 495 TRP 0.006 0.001 TRP A 733 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 6736) covalent geometry : angle 0.64237 / 0.33 ( 9222) SS BOND : bond 0.00170 / 0.09 ( 4) SS BOND : angle 0.95729 / 0.55 ( 8) hydrogen bonds : bond 0.04194 / 2.80 ( 490) hydrogen bonds : angle 4.38689 / 3.25 ( 1464) Misc. bond : bond 0.00137 / 0.07 ( 2) *********************** 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 147 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.235 Fit side-chains REVERT: A 296 MET cc_start: 0.7552 (mmp) cc_final: 0.7170 (mmt) REVERT: A 713 MET cc_start: 0.6225 (tmm) cc_final: 0.6013 (tmm) REVERT: B 681 PHE cc_start: 0.5811 (m-80) cc_final: 0.5606 (m-80) REVERT: B 748 TYR cc_start: 0.5259 (t80) cc_final: 0.4912 (m-80) outliers start: 29 outliers final: 19 residues processed: 138 average time/residue: 0.0482 time to fit residues: 10.3173 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 : 0.215 ------------------------------------------------------------------------------- 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 364 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 486 THR 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 288 ILE Chi-restraints excluded: chain B residue 312 VAL 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 692 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.250388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.218592 restraints weight = 8134.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.223738 restraints weight = 4712.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.227209 restraints weight = 3300.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.229062 restraints weight = 2605.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.230982 restraints weight = 2245.598| |-----------------------------------------------------------------------------| r_work (final): 0.4688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6742 Z= 0.150 Angle : 0.682 11.369 9230 Z= 0.342 Chirality : 0.047 0.401 1094 Planarity : 0.004 0.054 1158 Dihedral : 6.307 43.953 1022 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.63 % Favored : 92.16 % Rotamer: Outliers : 3.99 % Allowed : 23.26 % Favored : 72.74 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.27), residues: 944 helix: 0.72 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.85 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 294 TYR 0.020 0.001 TYR A 739 PHE 0.023 0.002 PHE A 495 TRP 0.006 0.001 TRP A 733 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 6736) covalent geometry : angle 0.68210 / 0.34 ( 9222) SS BOND : bond 0.00123 / 0.06 ( 4) SS BOND : angle 0.86825 / 0.50 ( 8) hydrogen bonds : bond 0.04337 / 2.91 ( 490) hydrogen bonds : angle 4.49753 / 3.35 ( 1464) Misc. bond : bond 0.00142 / 0.07 ( 2) *********************** 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 137 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.206 Fit side-chains REVERT: B 681 PHE cc_start: 0.5937 (m-80) cc_final: 0.5725 (m-80) REVERT: B 748 TYR cc_start: 0.5283 (t80) cc_final: 0.4906 (m-80) outliers start: 23 outliers final: 21 residues processed: 129 average time/residue: 0.0443 time to fit residues: 9.0349 Evaluate side-chains 134 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 364 PHE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 486 THR 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 531 LEU 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 692 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 18 optimal weight: 0.1980 chunk 42 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 65 optimal weight: 10.0000 chunk 19 optimal weight: 0.0670 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.252842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.222288 restraints weight = 8133.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.227416 restraints weight = 4718.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.230998 restraints weight = 3272.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.233012 restraints weight = 2547.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.234519 restraints weight = 2158.852| |-----------------------------------------------------------------------------| r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6742 Z= 0.138 Angle : 0.686 11.662 9230 Z= 0.343 Chirality : 0.047 0.352 1094 Planarity : 0.004 0.053 1158 Dihedral : 6.096 40.966 1022 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.63 % Favored : 92.16 % Rotamer: Outliers : 3.30 % Allowed : 24.48 % Favored : 72.22 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.27), residues: 944 helix: 0.79 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.83 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 294 TYR 0.021 0.001 TYR A 739 PHE 0.022 0.001 PHE A 495 TRP 0.009 0.001 TRP A 287 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6736) covalent geometry : angle 0.68535 / 0.34 ( 9222) SS BOND : bond 0.00126 / 0.06 ( 4) SS BOND : angle 0.91711 / 0.53 ( 8) hydrogen bonds : bond 0.04196 / 2.83 ( 490) hydrogen bonds : angle 4.50148 / 3.33 ( 1464) Misc. bond : bond 0.00117 / 0.06 ( 2) *********************** 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 130 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.285 Fit side-chains REVERT: B 384 VAL cc_start: 0.6448 (OUTLIER) cc_final: 0.6223 (t) REVERT: B 681 PHE cc_start: 0.5857 (m-80) cc_final: 0.5613 (m-80) REVERT: B 748 TYR cc_start: 0.5245 (t80) cc_final: 0.4883 (m-80) outliers start: 19 outliers final: 17 residues processed: 125 average time/residue: 0.0488 time to fit residues: 9.7018 Evaluate side-chains 123 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 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 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 531 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 692 SER 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 55 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 0.0870 chunk 11 optimal weight: 0.0980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 0.0020 chunk 40 optimal weight: 1.9990 overall best weight: 0.3766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.254357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.223752 restraints weight = 8022.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.228957 restraints weight = 4647.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.232603 restraints weight = 3229.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.234767 restraints weight = 2505.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.236058 restraints weight = 2115.656| |-----------------------------------------------------------------------------| r_work (final): 0.4741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6742 Z= 0.139 Angle : 0.716 15.834 9230 Z= 0.349 Chirality : 0.048 0.352 1094 Planarity : 0.004 0.054 1158 Dihedral : 6.011 39.925 1022 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.89 % Favored : 92.90 % Rotamer: Outliers : 3.47 % Allowed : 25.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.27), residues: 944 helix: 0.79 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.81 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 294 TYR 0.021 0.001 TYR A 739 PHE 0.023 0.001 PHE A 495 TRP 0.010 0.001 TRP B 732 HIS 0.002 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6736) covalent geometry : angle 0.71542 / 0.35 ( 9222) SS BOND : bond 0.00136 / 0.07 ( 4) SS BOND : angle 0.89182 / 0.51 ( 8) hydrogen bonds : bond 0.04180 / 2.84 ( 490) hydrogen bonds : angle 4.52533 / 3.36 ( 1464) Misc. bond : bond 0.00120 / 0.06 ( 2) ********************** 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 132 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.223 Fit side-chains REVERT: A 713 MET cc_start: 0.6357 (tmm) cc_final: 0.5996 (tmm) REVERT: B 384 VAL cc_start: 0.6440 (OUTLIER) cc_final: 0.6171 (t) REVERT: B 748 TYR cc_start: 0.5205 (t80) cc_final: 0.4857 (m-80) outliers start: 20 outliers final: 15 residues processed: 128 average time/residue: 0.0471 time to fit residues: 9.3974 Evaluate side-chains 122 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 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 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 611 THR Chi-restraints excluded: chain B residue 621 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 14 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.252801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.222038 restraints weight = 8199.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.227007 restraints weight = 4890.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.229831 restraints weight = 3454.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.232329 restraints weight = 2782.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.233080 restraints weight = 2361.582| |-----------------------------------------------------------------------------| r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6461 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6742 Z= 0.155 Angle : 0.738 16.553 9230 Z= 0.362 Chirality : 0.049 0.354 1094 Planarity : 0.004 0.053 1158 Dihedral : 6.199 42.380 1022 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.20 % Favored : 92.58 % Rotamer: Outliers : 3.30 % Allowed : 26.39 % Favored : 70.31 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.27), residues: 944 helix: 0.73 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.80 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 294 TYR 0.019 0.001 TYR A 739 PHE 0.025 0.002 PHE B 466 TRP 0.009 0.001 TRP B 732 HIS 0.003 0.001 HIS A 398 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 6736) covalent geometry : angle 0.73735 / 0.36 ( 9222) SS BOND : bond 0.00309 / 0.12 ( 4) SS BOND : angle 1.18123 / 0.68 ( 8) hydrogen bonds : bond 0.04366 / 2.96 ( 490) hydrogen bonds : angle 4.57248 / 3.40 ( 1464) Misc. bond : bond 0.00140 / 0.07 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1059.43 seconds wall clock time: 19 minutes 3.90 seconds (1143.90 seconds total)