Starting phenix.real_space_refine on Fri Oct 23 02:45:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21rn_67945/10_2026/21rn_67945.cif Found real_map, /net/cci-nas-00/data/ceres_data/21rn_67945/10_2026/21rn_67945.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21rn_67945/10_2026/21rn_67945.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21rn_67945/10_2026/21rn_67945.map" model { file = "/net/cci-nas-00/data/ceres_data/21rn_67945/10_2026/21rn_67945.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21rn_67945/10_2026/21rn_67945.cif" } resolution = 2.95 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= 0.001 sd= 0.036 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 Ca 1 9.91 5 Fe 1 7.16 5 S 37 5.16 5 C 4998 2.51 5 N 1374 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7871 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "B" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 888 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain breaks: 1 Chain: "D" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99} Chain: "E" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 824 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 9, 'TRANS': 92} Chain: "F" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3527 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 34, 'TRANS': 405} Chain breaks: 3 Chain: "F" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {' CA': 1, 'HEM': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.66, per 1000 atoms: 0.21 Number of scatterers: 7871 At special positions: 0 Unit cell: (82.491, 96.683, 126.841, 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) Fe 1 26.01 Ca 1 19.99 S 37 16.00 O 1460 8.00 N 1374 7.00 C 4998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 361 " - pdb=" SG CYS F 372 " distance=2.03 Simple disulfide: pdb=" SG CYS F 580 " - pdb=" SG CYS F 637 " distance=2.03 Simple disulfide: pdb=" SG CYS F 678 " - pdb=" SG CYS F 704 " 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=4, symmetry=0 Links applied NAG-ASN " NAG F 802 " - " ASN F 365 " " NAG F 803 " - " ASN F 329 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 413.3 milliseconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 17 sheets defined 27.8% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.585A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.579A pdb=" N SER A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.792A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.836A pdb=" N SER C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 208 Processing helix chain 'E' and resid 212 through 216 Processing helix chain 'E' and resid 224 through 238 Processing helix chain 'F' and resid 313 through 318 Processing helix chain 'F' and resid 320 through 327 Processing helix chain 'F' and resid 377 through 382 removed outlier: 4.255A pdb=" N SER F 381 " --> pdb=" O MET F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 408 removed outlier: 3.789A pdb=" N MET F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 442 removed outlier: 5.377A pdb=" N LEU F 437 " --> pdb=" O TYR F 433 " (cutoff:3.500A) Proline residue: F 438 - end of helix Processing helix chain 'F' and resid 442 through 450 Processing helix chain 'F' and resid 467 through 472 Processing helix chain 'F' and resid 473 through 478 Processing helix chain 'F' and resid 502 through 504 No H-bonds generated for 'chain 'F' and resid 502 through 504' Processing helix chain 'F' and resid 508 through 513 Processing helix chain 'F' and resid 517 through 527 Processing helix chain 'F' and resid 539 through 545 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 572 through 580 removed outlier: 3.533A pdb=" N TRP F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 587 through 596 Processing helix chain 'F' and resid 597 through 608 Processing helix chain 'F' and resid 615 through 623 Processing helix chain 'F' and resid 632 through 649 Processing helix chain 'F' and resid 661 through 669 Processing helix chain 'F' and resid 672 through 681 Processing helix chain 'F' and resid 696 through 700 Processing helix chain 'F' and resid 712 through 716 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.495A pdb=" N GLU A 10 " --> pdb=" O THR A 115 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 57 " --> pdb=" O TYR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.495A pdb=" N GLU A 10 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.712A pdb=" N ILE B 33 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N HIS B 49 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.613A pdb=" N ILE C 34 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.874A pdb=" N VAL C 107 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.387A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.387A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N HIS D 49 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 33 " --> pdb=" O HIS D 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 167 through 168 Processing sheet with id=AB5, first strand: chain 'E' and resid 218 through 223 removed outlier: 4.413A pdb=" N ALA F 529 " --> pdb=" O ASP E 219 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 328 through 329 removed outlier: 4.536A pdb=" N LEU F 336 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 482 through 484 Processing sheet with id=AB8, first strand: chain 'F' and resid 685 through 687 323 hydrogen bonds defined for protein. 822 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: 1.22 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 2711 1.37 - 1.53: 4437 1.53 - 1.68: 860 1.68 - 1.83: 56 1.83 - 1.99: 4 Bond restraints: 8068 Sorted by residual: bond pdb=" C3C HEM F 801 " pdb=" CAC HEM F 801 " ideal model delta sigma weight residual 1.544 1.463 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" CAB HEM F 801 " pdb=" CBB HEM F 801 " ideal model delta sigma weight residual 1.337 1.409 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C3B HEM F 801 " pdb=" CAB HEM F 801 " ideal model delta sigma weight residual 1.544 1.480 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C2B HEM F 801 " pdb=" C3B HEM F 801 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" C2C HEM F 801 " pdb=" CMC HEM F 801 " ideal model delta sigma weight residual 1.544 1.493 0.051 2.00e-02 2.50e+03 6.47e+00 ... (remaining 8063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 10919 3.36 - 6.72: 30 6.72 - 10.07: 0 10.07 - 13.43: 1 13.43 - 16.79: 2 Bond angle restraints: 10952 Sorted by residual: angle pdb=" C3B HEM F 801 " pdb=" CAB HEM F 801 " pdb=" CBB HEM F 801 " ideal model delta sigma weight residual 120.00 136.79 -16.79 3.00e+00 1.11e-01 3.13e+01 angle pdb=" C3C HEM F 801 " pdb=" CAC HEM F 801 " pdb=" CBC HEM F 801 " ideal model delta sigma weight residual 120.00 130.45 -10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N ALA A 103 " pdb=" CA ALA A 103 " pdb=" C ALA A 103 " ideal model delta sigma weight residual 110.80 116.99 -6.19 2.13e+00 2.20e-01 8.44e+00 angle pdb=" C THR F 308 " pdb=" CA THR F 308 " pdb=" CB THR F 308 " ideal model delta sigma weight residual 110.22 105.43 4.79 1.67e+00 3.59e-01 8.23e+00 angle pdb=" C TYR A 101 " pdb=" N ASP A 102 " pdb=" CA ASP A 102 " ideal model delta sigma weight residual 121.87 117.35 4.52 1.83e+00 2.99e-01 6.10e+00 ... (remaining 10947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4184 17.77 - 35.54: 489 35.54 - 53.31: 136 53.31 - 71.08: 25 71.08 - 88.85: 17 Dihedral angle restraints: 4851 sinusoidal: 2012 harmonic: 2839 Sorted by residual: dihedral pdb=" C2C HEM F 801 " pdb=" C3C HEM F 801 " pdb=" CAC HEM F 801 " pdb=" CBC HEM F 801 " ideal model delta sinusoidal sigma weight residual 180.00 103.94 76.06 2 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CA CYS F 704 " pdb=" C CYS F 704 " pdb=" N ASN F 705 " pdb=" CA ASN F 705 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA THR C 101 " pdb=" C THR C 101 " pdb=" N THR C 102 " pdb=" CA THR C 102 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 646 0.028 - 0.056: 349 0.056 - 0.084: 102 0.084 - 0.112: 66 0.112 - 0.140: 16 Chirality restraints: 1179 Sorted by residual: chirality pdb=" CA ILE B 21 " pdb=" N ILE B 21 " pdb=" C ILE B 21 " pdb=" CB ILE B 21 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE F 284 " pdb=" N ILE F 284 " pdb=" C ILE F 284 " pdb=" CB ILE F 284 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE D 21 " pdb=" N ILE D 21 " pdb=" C ILE D 21 " pdb=" CB ILE D 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 1176 not shown) Planarity restraints: 1407 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 802 " -0.323 2.00e-02 2.50e+03 2.74e-01 9.37e+02 pdb=" C7 NAG F 802 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 802 " -0.184 2.00e-02 2.50e+03 pdb=" N2 NAG F 802 " 0.476 2.00e-02 2.50e+03 pdb=" O7 NAG F 802 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM F 801 " -0.219 2.00e-02 2.50e+03 1.59e-01 5.69e+02 pdb=" C1B HEM F 801 " 0.025 2.00e-02 2.50e+03 pdb=" C2B HEM F 801 " -0.046 2.00e-02 2.50e+03 pdb=" C3B HEM F 801 " 0.057 2.00e-02 2.50e+03 pdb=" C4B HEM F 801 " -0.043 2.00e-02 2.50e+03 pdb=" CAB HEM F 801 " 0.204 2.00e-02 2.50e+03 pdb=" CHB HEM F 801 " 0.274 2.00e-02 2.50e+03 pdb=" CHC HEM F 801 " -0.020 2.00e-02 2.50e+03 pdb=" CMB HEM F 801 " -0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM F 801 " -0.179 2.00e-02 2.50e+03 1.07e-01 2.59e+02 pdb=" C1D HEM F 801 " 0.023 2.00e-02 2.50e+03 pdb=" C2D HEM F 801 " -0.016 2.00e-02 2.50e+03 pdb=" C3D HEM F 801 " 0.033 2.00e-02 2.50e+03 pdb=" C4D HEM F 801 " -0.030 2.00e-02 2.50e+03 pdb=" CAD HEM F 801 " 0.116 2.00e-02 2.50e+03 pdb=" CHA HEM F 801 " 0.016 2.00e-02 2.50e+03 pdb=" CHD HEM F 801 " 0.184 2.00e-02 2.50e+03 pdb=" CMD HEM F 801 " -0.146 2.00e-02 2.50e+03 ... (remaining 1404 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 25 2.64 - 3.20: 6744 3.20 - 3.77: 12164 3.77 - 4.33: 18586 4.33 - 4.90: 30398 Nonbonded interactions: 67917 Sorted by model distance: nonbonded pdb=" CB THR F 308 " pdb="CA CA F 804 " model vdw 2.073 2.940 nonbonded pdb=" O ASP E 236 " pdb=" OD1 ASP E 236 " model vdw 2.209 3.040 nonbonded pdb=" OG SER F 314 " pdb="CA CA F 804 " model vdw 2.386 2.510 nonbonded pdb=" OD1 ASP F 312 " pdb="CA CA F 804 " model vdw 2.421 2.510 nonbonded pdb=" O ASP E 236 " pdb="CA CA F 804 " model vdw 2.421 2.510 ... (remaining 67912 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 3 or resid 5 through 84 or resid 86 through 92 o \ r resid 94 or resid 96 through 104 or resid 106)) selection = (chain 'D' and (resid 1 through 3 or resid 5 through 84 or resid 86 through 92 o \ r resid 94 or resid 96 through 104 or resid 106)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.890 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 0.216 8081 Z= 0.248 Angle : 0.613 16.789 10972 Z= 0.302 Chirality : 0.042 0.140 1179 Planarity : 0.011 0.274 1405 Dihedral : 16.922 88.851 3012 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.17 % Allowed : 23.68 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.08 (0.28), residues: 966 helix: -0.11 (0.36), residues: 220 sheet: 0.50 (0.33), residues: 239 loop : 0.05 (0.30), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 61 TYR 0.021 0.001 TYR C 80 PHE 0.013 0.001 PHE F 393 TRP 0.014 0.001 TRP A 50 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 ( 8068) covalent geometry : angle 0.60982 / 0.30 (10952) SS BOND : bond 0.00260 / 0.12 ( 7) SS BOND : angle 1.06938 / 0.61 ( 14) hydrogen bonds : bond 0.12460 / 8.03 ( 296) hydrogen bonds : angle 7.10224 / 4.78 ( 822) Misc. bond : bond 0.13222 / 6.28 ( 4) link_NAG-ASN : bond 0.00086 / 0.05 ( 2) link_NAG-ASN : angle 2.23408 / 1.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7730 (ttmm) cc_final: 0.7406 (tptt) REVERT: A 90 ASP cc_start: 0.8723 (m-30) cc_final: 0.8464 (m-30) REVERT: B 27 GLN cc_start: 0.8122 (tt0) cc_final: 0.7751 (tt0) REVERT: B 70 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7197 (m-30) REVERT: C 30 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7432 (p) REVERT: C 81 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8863 (ttm) REVERT: D 93 ASN cc_start: 0.8950 (t0) cc_final: 0.8664 (t0) REVERT: E 220 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.5986 (mm110) REVERT: F 269 LYS cc_start: 0.7564 (mtmm) cc_final: 0.6777 (mttp) REVERT: F 325 ARG cc_start: 0.7572 (mmt180) cc_final: 0.7217 (mtp180) REVERT: F 354 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: F 403 GLN cc_start: 0.7840 (mt0) cc_final: 0.7504 (mp10) REVERT: F 452 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: F 555 LEU cc_start: 0.7990 (mt) cc_final: 0.7563 (mp) REVERT: F 630 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8310 (mmm160) REVERT: F 666 GLN cc_start: 0.8345 (tt0) cc_final: 0.8096 (tt0) REVERT: F 717 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6740 (pt0) outliers start: 27 outliers final: 15 residues processed: 100 average time/residue: 0.6368 time to fit residues: 67.0713 Evaluate side-chains 101 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain E residue 220 GLN Chi-restraints excluded: chain F residue 308 THR Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 452 GLN Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 480 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.185297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.181429 restraints weight = 7295.691| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 0.15 r_work: 0.3895 rms_B_bonded: 0.60 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 1.44 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 8081 Z= 0.143 Angle : 0.558 11.717 10972 Z= 0.280 Chirality : 0.043 0.147 1179 Planarity : 0.005 0.038 1405 Dihedral : 8.444 86.221 1174 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.28 % Allowed : 22.51 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 966 helix: 0.19 (0.36), residues: 220 sheet: 0.64 (0.34), residues: 238 loop : 0.15 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 171 TYR 0.016 0.002 TYR C 80 PHE 0.015 0.001 PHE F 393 TRP 0.011 0.001 TRP A 50 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 8068) covalent geometry : angle 0.55556 / 0.28 (10952) SS BOND : bond 0.00271 / 0.13 ( 7) SS BOND : angle 1.09806 / 0.62 ( 14) hydrogen bonds : bond 0.03689 / 2.36 ( 296) hydrogen bonds : angle 5.65712 / 3.79 ( 822) Misc. bond : bond 0.05248 / 2.62 ( 4) link_NAG-ASN : bond 0.00140 / 0.07 ( 2) link_NAG-ASN : angle 1.50367 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.299 Fit side-chains REVERT: A 19 LYS cc_start: 0.7857 (ttmm) cc_final: 0.7514 (tptt) REVERT: C 30 THR cc_start: 0.7837 (m) cc_final: 0.7327 (p) REVERT: C 63 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7818 (ttmm) REVERT: D 93 ASN cc_start: 0.8850 (t0) cc_final: 0.8602 (t0) REVERT: F 269 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7304 (mttp) REVERT: F 452 GLN cc_start: 0.8633 (tt0) cc_final: 0.8387 (tm-30) REVERT: F 544 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6786 (mm-30) REVERT: F 555 LEU cc_start: 0.8317 (mt) cc_final: 0.7892 (mp) REVERT: F 630 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8415 (mmm160) REVERT: F 666 GLN cc_start: 0.8334 (tt0) cc_final: 0.8018 (tt0) outliers start: 28 outliers final: 12 residues processed: 107 average time/residue: 0.5923 time to fit residues: 67.0137 Evaluate side-chains 94 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [16, 57, 25, 63, 79, 13, 46, 54, 69, 22, 0] chunk 16 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 22 optimal weight: 0.0270 chunk 0 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 480 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.186113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.182689 restraints weight = 7172.612| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 0.14 r_work: 0.3931 rms_B_bonded: 0.52 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 1.37 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.0668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8081 Z= 0.142 Angle : 0.552 11.674 10972 Z= 0.277 Chirality : 0.043 0.139 1179 Planarity : 0.005 0.038 1405 Dihedral : 6.931 86.564 1147 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.69 % Allowed : 21.22 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.43 (0.28), residues: 966 helix: 0.38 (0.36), residues: 220 sheet: 0.69 (0.34), residues: 238 loop : 0.17 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 454 TYR 0.012 0.001 TYR A 104 PHE 0.015 0.001 PHE F 393 TRP 0.011 0.001 TRP E 229 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 8068) covalent geometry : angle 0.54967 / 0.28 (10952) SS BOND : bond 0.00307 / 0.14 ( 7) SS BOND : angle 1.15739 / 0.66 ( 14) hydrogen bonds : bond 0.03596 / 2.30 ( 296) hydrogen bonds : angle 5.44010 / 3.63 ( 822) Misc. bond : bond 0.05108 / 2.55 ( 4) link_NAG-ASN : bond 0.00152 / 0.07 ( 2) link_NAG-ASN : angle 1.52960 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 80 time to evaluate : 0.243 Fit side-chains REVERT: A 19 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7492 (tptt) REVERT: B 70 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: C 30 THR cc_start: 0.7800 (m) cc_final: 0.7315 (p) REVERT: C 63 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7844 (ttmm) REVERT: D 93 ASN cc_start: 0.8850 (t0) cc_final: 0.8588 (t0) REVERT: F 269 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7321 (mttp) REVERT: F 382 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6306 (mm-30) REVERT: F 452 GLN cc_start: 0.8552 (tt0) cc_final: 0.8344 (tm-30) REVERT: F 544 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: F 555 LEU cc_start: 0.8295 (mt) cc_final: 0.7856 (mp) REVERT: F 630 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8369 (mmm160) REVERT: F 666 GLN cc_start: 0.8327 (tt0) cc_final: 0.8046 (tt0) REVERT: F 717 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6849 (pt0) outliers start: 40 outliers final: 19 residues processed: 113 average time/residue: 0.6220 time to fit residues: 74.1667 Evaluate side-chains 103 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [44, 49, 41, 34, 28, 90, 94, 62, 38, 73, 40] chunk 44 optimal weight: 0.0980 chunk 49 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 480 GLN F 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.189839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.186969 restraints weight = 7207.441| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 0.11 r_work: 0.3922 rms_B_bonded: 0.46 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 1.12 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 8081 Z= 0.144 Angle : 0.552 11.291 10972 Z= 0.277 Chirality : 0.043 0.139 1179 Planarity : 0.005 0.037 1405 Dihedral : 6.723 82.398 1146 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.81 % Allowed : 21.22 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.43 (0.28), residues: 966 helix: 0.43 (0.36), residues: 220 sheet: 0.65 (0.34), residues: 239 loop : 0.17 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 171 TYR 0.013 0.002 TYR C 80 PHE 0.015 0.001 PHE F 393 TRP 0.011 0.001 TRP E 229 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 8068) covalent geometry : angle 0.54937 / 0.28 (10952) SS BOND : bond 0.00306 / 0.14 ( 7) SS BOND : angle 1.15505 / 0.65 ( 14) hydrogen bonds : bond 0.03565 / 2.30 ( 296) hydrogen bonds : angle 5.34796 / 3.57 ( 822) Misc. bond : bond 0.04640 / 2.32 ( 4) link_NAG-ASN : bond 0.00126 / 0.06 ( 2) link_NAG-ASN : angle 1.56765 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.296 Fit side-chains REVERT: A 19 LYS cc_start: 0.7834 (ttmm) cc_final: 0.7507 (tptt) REVERT: C 30 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7285 (p) REVERT: C 63 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7802 (ttmm) REVERT: D 93 ASN cc_start: 0.8813 (t0) cc_final: 0.8558 (t0) REVERT: F 269 LYS cc_start: 0.7720 (mtmm) cc_final: 0.7314 (mttp) REVERT: F 354 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: F 382 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6298 (mm-30) REVERT: F 452 GLN cc_start: 0.8548 (tt0) cc_final: 0.8328 (tm-30) REVERT: F 555 LEU cc_start: 0.8263 (mt) cc_final: 0.7855 (mp) REVERT: F 630 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8378 (mmm160) REVERT: F 666 GLN cc_start: 0.8318 (tt0) cc_final: 0.8039 (tt0) REVERT: F 717 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6861 (pt0) outliers start: 41 outliers final: 22 residues processed: 111 average time/residue: 0.5730 time to fit residues: 67.3045 Evaluate side-chains 103 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [77, 57, 38, 69, 89, 29, 73, 36, 72, 8, 87] chunk 77 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 0.0040 chunk 89 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 480 GLN F 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.185905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.167286 restraints weight = 7290.407| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 1.11 r_work: 0.3491 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 8081 Z= 0.144 Angle : 0.552 11.025 10972 Z= 0.277 Chirality : 0.043 0.139 1179 Planarity : 0.004 0.037 1405 Dihedral : 6.648 79.468 1146 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.51 % Allowed : 20.87 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.44 (0.28), residues: 966 helix: 0.47 (0.37), residues: 220 sheet: 0.65 (0.34), residues: 239 loop : 0.17 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 171 TYR 0.012 0.001 TYR A 104 PHE 0.014 0.001 PHE F 393 TRP 0.011 0.001 TRP E 229 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 8068) covalent geometry : angle 0.54937 / 0.28 (10952) SS BOND : bond 0.00306 / 0.14 ( 7) SS BOND : angle 1.22735 / 0.69 ( 14) hydrogen bonds : bond 0.03536 / 2.29 ( 296) hydrogen bonds : angle 5.30187 / 3.54 ( 822) Misc. bond : bond 0.04402 / 2.20 ( 4) link_NAG-ASN : bond 0.00122 / 0.06 ( 2) link_NAG-ASN : angle 1.57706 / 0.84 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 77 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7365 (tptt) REVERT: B 45 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8289 (ttt180) REVERT: C 30 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7356 (p) REVERT: C 63 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7983 (ttmm) REVERT: D 42 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7654 (mtmm) REVERT: D 93 ASN cc_start: 0.8838 (t0) cc_final: 0.8555 (t0) REVERT: F 269 LYS cc_start: 0.7630 (mtmm) cc_final: 0.6905 (mttp) REVERT: F 354 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: F 382 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6072 (mm-30) REVERT: F 452 GLN cc_start: 0.8742 (tt0) cc_final: 0.8381 (tm-30) REVERT: F 555 LEU cc_start: 0.8131 (mt) cc_final: 0.7673 (mp) REVERT: F 630 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8527 (mmm160) REVERT: F 666 GLN cc_start: 0.8463 (tt0) cc_final: 0.8246 (tt0) REVERT: F 717 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6846 (pt0) outliers start: 47 outliers final: 22 residues processed: 115 average time/residue: 0.5875 time to fit residues: 71.5044 Evaluate side-chains 105 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [68, 89, 58, 2, 24, 21, 11, 70, 44, 38, 22] chunk 68 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 58 optimal weight: 0.0030 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 480 GLN F 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.185608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.181719 restraints weight = 7248.803| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 0.17 r_work: 0.3874 rms_B_bonded: 0.75 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 8081 Z= 0.151 Angle : 0.559 11.327 10972 Z= 0.280 Chirality : 0.043 0.137 1179 Planarity : 0.005 0.037 1405 Dihedral : 6.701 77.898 1146 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.28 % Allowed : 21.10 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.43 (0.28), residues: 966 helix: 0.43 (0.36), residues: 221 sheet: 0.65 (0.34), residues: 238 loop : 0.18 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 171 TYR 0.013 0.002 TYR C 80 PHE 0.015 0.001 PHE F 393 TRP 0.011 0.002 TRP E 229 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 ( 8068) covalent geometry : angle 0.55654 / 0.28 (10952) SS BOND : bond 0.00318 / 0.15 ( 7) SS BOND : angle 1.25474 / 0.71 ( 14) hydrogen bonds : bond 0.03599 / 2.33 ( 296) hydrogen bonds : angle 5.32535 / 3.56 ( 822) Misc. bond : bond 0.04748 / 2.37 ( 4) link_NAG-ASN : bond 0.00121 / 0.06 ( 2) link_NAG-ASN : angle 1.61140 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 0.325 Fit side-chains REVERT: A 19 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7541 (tptt) REVERT: B 45 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7938 (ttt180) REVERT: C 30 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7368 (p) REVERT: C 63 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7842 (ttmm) REVERT: D 42 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.7616 (mtmm) REVERT: D 93 ASN cc_start: 0.8867 (t0) cc_final: 0.8591 (t0) REVERT: F 269 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7331 (mttp) REVERT: F 354 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: F 382 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6291 (mm-30) REVERT: F 452 GLN cc_start: 0.8604 (tt0) cc_final: 0.8300 (tm-30) REVERT: F 555 LEU cc_start: 0.8404 (mt) cc_final: 0.7968 (mp) REVERT: F 630 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8459 (mmm160) REVERT: F 666 GLN cc_start: 0.8388 (tt0) cc_final: 0.8131 (tt0) REVERT: F 717 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6942 (pt0) outliers start: 45 outliers final: 25 residues processed: 114 average time/residue: 0.5784 time to fit residues: 69.8844 Evaluate side-chains 109 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 76 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 557 LEU Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [67, 76, 13, 35, 16, 12, 42, 11, 64, 33, 62] chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 0.0070 chunk 64 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 0.0870 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 228 GLN F 480 GLN F 563 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.185437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.180846 restraints weight = 7294.806| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 0.20 r_work: 0.3861 rms_B_bonded: 0.84 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 1.70 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8081 Z= 0.141 Angle : 0.549 10.613 10972 Z= 0.276 Chirality : 0.043 0.137 1179 Planarity : 0.004 0.037 1405 Dihedral : 6.572 77.474 1146 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.16 % Allowed : 21.45 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.49 (0.28), residues: 966 helix: 0.46 (0.36), residues: 220 sheet: 0.70 (0.34), residues: 238 loop : 0.21 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 454 TYR 0.012 0.001 TYR A 104 PHE 0.014 0.001 PHE F 393 TRP 0.010 0.001 TRP A 50 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 8068) covalent geometry : angle 0.54664 / 0.28 (10952) SS BOND : bond 0.00305 / 0.14 ( 7) SS BOND : angle 1.17048 / 0.67 ( 14) hydrogen bonds : bond 0.03520 / 2.28 ( 296) hydrogen bonds : angle 5.26950 / 3.52 ( 822) Misc. bond : bond 0.03907 / 1.95 ( 4) link_NAG-ASN : bond 0.00107 / 0.05 ( 2) link_NAG-ASN : angle 1.54630 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7556 (tptt) REVERT: B 45 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7927 (ttt90) REVERT: B 70 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7389 (m-30) REVERT: C 30 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7360 (p) REVERT: C 63 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7829 (ttmm) REVERT: D 42 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.7614 (mtmm) REVERT: D 78 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7695 (mp) REVERT: D 93 ASN cc_start: 0.8837 (t0) cc_final: 0.8578 (t0) REVERT: E 216 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7332 (tm) REVERT: F 269 LYS cc_start: 0.7770 (mtmm) cc_final: 0.7319 (mttp) REVERT: F 382 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6303 (mm-30) REVERT: F 452 GLN cc_start: 0.8583 (tt0) cc_final: 0.8294 (tm-30) REVERT: F 555 LEU cc_start: 0.8379 (mt) cc_final: 0.7930 (mp) REVERT: F 630 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8427 (mmm160) REVERT: F 666 GLN cc_start: 0.8360 (tt0) cc_final: 0.8112 (tt0) REVERT: F 717 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6925 (pt0) outliers start: 44 outliers final: 24 residues processed: 112 average time/residue: 0.5883 time to fit residues: 69.8743 Evaluate side-chains 110 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 76 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 542 ILE Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [0, 23, 5, 69, 45, 33, 41, 86, 56, 49, 54] chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.0770 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 86 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 228 GLN F 480 GLN F 563 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.186831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.182954 restraints weight = 7244.686| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 0.17 r_work: 0.3861 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 1.57 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 8081 Z= 0.120 Angle : 0.528 10.379 10972 Z= 0.265 Chirality : 0.042 0.136 1179 Planarity : 0.004 0.037 1405 Dihedral : 6.321 73.998 1146 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.81 % Allowed : 21.81 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.58 (0.28), residues: 966 helix: 0.55 (0.37), residues: 220 sheet: 0.76 (0.34), residues: 238 loop : 0.26 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 564 TYR 0.014 0.001 TYR A 104 PHE 0.013 0.001 PHE F 393 TRP 0.011 0.001 TRP A 50 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 8068) covalent geometry : angle 0.52661 / 0.26 (10952) SS BOND : bond 0.00288 / 0.13 ( 7) SS BOND : angle 1.01560 / 0.57 ( 14) hydrogen bonds : bond 0.03310 / 2.14 ( 296) hydrogen bonds : angle 5.12773 / 3.43 ( 822) Misc. bond : bond 0.03990 / 1.99 ( 4) link_NAG-ASN : bond 0.00125 / 0.06 ( 2) link_NAG-ASN : angle 1.43582 / 0.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 79 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7517 (tptt) REVERT: B 45 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7912 (ttt90) REVERT: B 70 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: C 30 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7303 (p) REVERT: C 63 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7816 (ttmm) REVERT: D 42 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.7625 (mtmm) REVERT: D 78 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7745 (mp) REVERT: D 93 ASN cc_start: 0.8806 (t0) cc_final: 0.8571 (t0) REVERT: E 216 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7296 (tm) REVERT: F 269 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7298 (mttp) REVERT: F 382 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6275 (mm-30) REVERT: F 452 GLN cc_start: 0.8529 (tt0) cc_final: 0.8297 (tm-30) REVERT: F 513 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7513 (mt) REVERT: F 555 LEU cc_start: 0.8344 (mt) cc_final: 0.7895 (mp) REVERT: F 630 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8440 (mmm160) REVERT: F 666 GLN cc_start: 0.8338 (tt0) cc_final: 0.8121 (tt0) REVERT: F 717 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6923 (pt0) outliers start: 41 outliers final: 22 residues processed: 110 average time/residue: 0.6245 time to fit residues: 72.4361 Evaluate side-chains 107 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 70 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 228 GLN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [63, 32, 69, 13, 28, 84, 24, 91, 9, 66, 6] chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 69 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 228 GLN F 480 GLN F 563 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.184605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.180821 restraints weight = 7284.942| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 0.15 r_work: 0.3885 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 1.39 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 8081 Z= 0.184 Angle : 0.600 11.420 10972 Z= 0.300 Chirality : 0.044 0.140 1179 Planarity : 0.005 0.038 1405 Dihedral : 6.774 77.092 1146 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.04 % Allowed : 21.92 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.41 (0.28), residues: 966 helix: 0.33 (0.36), residues: 221 sheet: 0.71 (0.34), residues: 238 loop : 0.17 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 454 TYR 0.012 0.002 TYR D 86 PHE 0.016 0.001 PHE F 393 TRP 0.011 0.002 TRP E 229 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 ( 8068) covalent geometry : angle 0.59642 / 0.30 (10952) SS BOND : bond 0.00346 / 0.16 ( 7) SS BOND : angle 1.47406 / 0.82 ( 14) hydrogen bonds : bond 0.03859 / 2.51 ( 296) hydrogen bonds : angle 5.37955 / 3.59 ( 822) Misc. bond : bond 0.04632 / 2.31 ( 4) link_NAG-ASN : bond 0.00154 / 0.08 ( 2) link_NAG-ASN : angle 1.69830 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 78 time to evaluate : 0.208 Fit side-chains REVERT: A 19 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7518 (tptt) REVERT: B 45 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7909 (ttt180) REVERT: C 30 THR cc_start: 0.7797 (OUTLIER) cc_final: 0.7321 (p) REVERT: C 63 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7857 (ttmm) REVERT: D 42 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7574 (mtmm) REVERT: D 78 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7733 (mp) REVERT: D 93 ASN cc_start: 0.8847 (t0) cc_final: 0.8575 (t0) REVERT: E 216 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7310 (tm) REVERT: F 269 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7376 (mttp) REVERT: F 382 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6345 (mm-30) REVERT: F 452 GLN cc_start: 0.8584 (tt0) cc_final: 0.8280 (tm-30) REVERT: F 513 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7551 (mt) REVERT: F 555 LEU cc_start: 0.8351 (mt) cc_final: 0.7916 (mp) REVERT: F 630 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8435 (mmm160) REVERT: F 666 GLN cc_start: 0.8364 (tt0) cc_final: 0.8096 (tt0) outliers start: 43 outliers final: 24 residues processed: 108 average time/residue: 0.6278 time to fit residues: 71.6413 Evaluate side-chains 111 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 228 GLN Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [66, 58, 62, 11, 35, 76, 37, 34, 80, 55, 88] chunk 66 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 480 GLN F 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.185742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.182031 restraints weight = 7240.626| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 0.15 r_work: 0.3896 rms_B_bonded: 0.65 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 1.52 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 8081 Z= 0.150 Angle : 0.581 11.565 10972 Z= 0.289 Chirality : 0.043 0.156 1179 Planarity : 0.005 0.038 1405 Dihedral : 6.607 73.900 1146 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.57 % Allowed : 22.27 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.48 (0.28), residues: 966 helix: 0.45 (0.36), residues: 220 sheet: 0.70 (0.34), residues: 238 loop : 0.21 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.013 0.002 TYR C 80 PHE 0.014 0.001 PHE F 393 TRP 0.013 0.002 TRP E 229 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 8068) covalent geometry : angle 0.57890 / 0.29 (10952) SS BOND : bond 0.00300 / 0.14 ( 7) SS BOND : angle 1.25655 / 0.71 ( 14) hydrogen bonds : bond 0.03606 / 2.34 ( 296) hydrogen bonds : angle 5.29564 / 3.54 ( 822) Misc. bond : bond 0.04862 / 2.43 ( 4) link_NAG-ASN : bond 0.00107 / 0.05 ( 2) link_NAG-ASN : angle 1.56212 / 0.83 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 74 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 19 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7497 (tptt) REVERT: B 45 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7898 (ttt90) REVERT: C 30 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7332 (p) REVERT: C 63 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7846 (ttmm) REVERT: D 42 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.7569 (mtmm) REVERT: D 78 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7637 (mp) REVERT: D 93 ASN cc_start: 0.8843 (t0) cc_final: 0.8582 (t0) REVERT: E 216 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7290 (tm) REVERT: F 269 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7377 (mttp) REVERT: F 382 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6310 (mm-30) REVERT: F 452 GLN cc_start: 0.8577 (tt0) cc_final: 0.8293 (tm-30) REVERT: F 513 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7544 (mt) REVERT: F 555 LEU cc_start: 0.8363 (mt) cc_final: 0.7919 (mp) REVERT: F 630 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8430 (mmm160) REVERT: F 666 GLN cc_start: 0.8356 (tt0) cc_final: 0.8099 (tt0) outliers start: 39 outliers final: 23 residues processed: 104 average time/residue: 0.5929 time to fit residues: 65.4142 Evaluate side-chains 107 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 74 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LYS Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 22 THR Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 504 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 588 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 630 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [43, 39, 89, 20, 55, 62, 47, 50, 1, 90, 33] chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 90 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 480 GLN F 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.179569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.160675 restraints weight = 7348.838| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.43 r_work: 0.3407 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 8081 Z= 0.178 Angle : 0.613 11.905 10972 Z= 0.305 Chirality : 0.044 0.162 1179 Planarity : 0.005 0.038 1405 Dihedral : 6.809 72.747 1146 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.45 % Allowed : 22.27 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.37 (0.28), residues: 966 helix: 0.32 (0.36), residues: 221 sheet: 0.64 (0.34), residues: 238 loop : 0.15 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 171 TYR 0.011 0.002 TYR D 86 PHE 0.016 0.001 PHE F 393 TRP 0.013 0.002 TRP E 229 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 8068) covalent geometry : angle 0.61038 / 0.30 (10952) SS BOND : bond 0.00322 / 0.15 ( 7) SS BOND : angle 1.43198 / 0.80 ( 14) hydrogen bonds : bond 0.03859 / 2.51 ( 296) hydrogen bonds : angle 5.43283 / 3.64 ( 822) Misc. bond : bond 0.04633 / 2.31 ( 4) link_NAG-ASN : bond 0.00146 / 0.08 ( 2) link_NAG-ASN : angle 1.70122 / 0.90 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2505.46 seconds wall clock time: 43 minutes 36.07 seconds (2616.07 seconds total)