Starting phenix.real_space_refine on Fri Oct 23 02:56:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21rt_67951/10_2026/21rt_67951.cif Found real_map, /net/cci-nas-00/data/ceres_data/21rt_67951/10_2026/21rt_67951.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/21rt_67951/10_2026/21rt_67951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21rt_67951/10_2026/21rt_67951.map" model { file = "/net/cci-nas-00/data/ceres_data/21rt_67951/10_2026/21rt_67951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21rt_67951/10_2026/21rt_67951.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= 0.037 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 40 5.16 5 C 5029 2.51 5 N 1382 2.21 5 O 1464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 7917 Number of models: 1 Model: "" Number of chains: 8 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: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 831 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} 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: 3535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3535 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 406} Chain breaks: 2 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.57, per 1000 atoms: 0.20 Number of scatterers: 7917 At special positions: 0 Unit cell: (81.604, 98.457, 109.988, 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 40 16.00 O 1464 8.00 N 1382 7.00 C 5029 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=2.04 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=2.03 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 801 " - " ASN F 365 " " NAG F 802 " - " ASN F 329 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 284.1 milliseconds 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 29.1% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.679A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.713A pdb=" N SER A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.885A pdb=" N ILE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.774A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.728A pdb=" N SER C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.018A pdb=" N LEU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 208 Processing helix chain 'E' and resid 212 through 216 removed outlier: 3.650A pdb=" N GLN E 215 " --> pdb=" O PRO E 212 " (cutoff:3.500A) 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: 4.304A pdb=" N SER F 381 " --> pdb=" O MET F 378 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU F 382 " --> pdb=" O ARG F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 408 removed outlier: 3.952A pdb=" N THR F 387 " --> pdb=" O MET F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 442 removed outlier: 5.461A 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 479 removed outlier: 3.794A pdb=" N ILE F 479 " --> pdb=" O HIS F 476 " (cutoff:3.500A) 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 544 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 572 through 580 removed outlier: 3.511A 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 610 through 614 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 705 through 707 No H-bonds generated for 'chain 'F' and resid 705 through 707' Processing helix chain 'F' and resid 711 through 716 removed outlier: 4.281A pdb=" N SER F 714 " --> pdb=" O ASN F 711 " (cutoff:3.500A) 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: 6.397A pdb=" N ILE A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TRP A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.776A pdb=" N ILE B 33 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N HIS B 49 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.647A pdb=" N VAL C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AA8, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.247A pdb=" N MET D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 167 through 168 Processing sheet with id=AB2, first strand: chain 'E' and resid 218 through 223 removed outlier: 4.254A pdb=" N ALA F 529 " --> pdb=" O ASP E 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 328 through 329 removed outlier: 4.511A pdb=" N LEU F 336 " --> pdb=" O ASN F 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 482 through 484 Processing sheet with id=AB5, first strand: chain 'F' and resid 685 through 687 288 hydrogen bonds defined for protein. 744 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: 1.15 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 2878 1.38 - 1.53: 4821 1.53 - 1.69: 358 1.69 - 1.84: 62 1.84 - 2.00: 4 Bond restraints: 8123 Sorted by residual: bond pdb=" C3B HEM E 301 " pdb=" CAB HEM E 301 " ideal model delta sigma weight residual 1.544 1.461 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C3C HEM E 301 " pdb=" CAC HEM E 301 " ideal model delta sigma weight residual 1.544 1.466 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" CAB HEM E 301 " pdb=" CBB HEM E 301 " ideal model delta sigma weight residual 1.337 1.281 0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" C2C HEM E 301 " pdb=" CMC HEM E 301 " ideal model delta sigma weight residual 1.544 1.495 0.049 2.00e-02 2.50e+03 6.07e+00 bond pdb=" C2C HEM E 301 " pdb=" C3C HEM E 301 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.00e-02 2.50e+03 5.57e+00 ... (remaining 8118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 10962 2.84 - 5.67: 69 5.67 - 8.51: 5 8.51 - 11.35: 1 11.35 - 14.18: 1 Bond angle restraints: 11038 Sorted by residual: angle pdb=" C3C HEM E 301 " pdb=" CAC HEM E 301 " pdb=" CBC HEM E 301 " ideal model delta sigma weight residual 120.00 130.48 -10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C THR F 308 " pdb=" CA THR F 308 " pdb=" CB THR F 308 " ideal model delta sigma weight residual 110.29 105.00 5.29 1.64e+00 3.72e-01 1.04e+01 angle pdb=" C TYR B 50 " pdb=" N THR B 51 " pdb=" CA THR B 51 " ideal model delta sigma weight residual 121.54 127.61 -6.07 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N SER F 309 " pdb=" CA SER F 309 " pdb=" C SER F 309 " ideal model delta sigma weight residual 113.20 109.37 3.83 1.36e+00 5.41e-01 7.91e+00 angle pdb=" C2C HEM E 301 " pdb=" C3C HEM E 301 " pdb=" CAC HEM E 301 " ideal model delta sigma weight residual 126.00 134.18 -8.18 3.00e+00 1.11e-01 7.43e+00 ... (remaining 11033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4173 17.70 - 35.40: 504 35.40 - 53.10: 152 53.10 - 70.80: 29 70.80 - 88.50: 11 Dihedral angle restraints: 4869 sinusoidal: 2012 harmonic: 2857 Sorted by residual: dihedral pdb=" C2C HEM E 301 " pdb=" C3C HEM E 301 " pdb=" CAC HEM E 301 " pdb=" CBC HEM E 301 " ideal model delta sinusoidal sigma weight residual 0.00 51.50 -51.50 2 1.00e+01 1.00e-02 2.94e+01 dihedral pdb=" CA TYR C 104 " pdb=" C TYR C 104 " pdb=" N PHE C 105 " pdb=" CA PHE C 105 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA ASP B 28 " pdb=" C ASP B 28 " pdb=" N ILE B 29 " pdb=" CA ILE B 29 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 688 0.031 - 0.062: 330 0.062 - 0.092: 89 0.092 - 0.123: 72 0.123 - 0.154: 7 Chirality restraints: 1186 Sorted by residual: chirality pdb=" CA ILE D 48 " pdb=" N ILE D 48 " pdb=" C ILE D 48 " pdb=" CB ILE D 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA TYR D 49 " pdb=" N TYR D 49 " pdb=" C TYR D 49 " pdb=" CB TYR D 49 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA TYR C 104 " pdb=" N TYR C 104 " pdb=" C TYR C 104 " pdb=" CB TYR C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 1183 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB HEM E 301 " -0.179 2.00e-02 2.50e+03 1.28e-01 3.66e+02 pdb=" C1B HEM E 301 " 0.010 2.00e-02 2.50e+03 pdb=" C2B HEM E 301 " -0.057 2.00e-02 2.50e+03 pdb=" C3B HEM E 301 " 0.027 2.00e-02 2.50e+03 pdb=" C4B HEM E 301 " -0.041 2.00e-02 2.50e+03 pdb=" CAB HEM E 301 " 0.170 2.00e-02 2.50e+03 pdb=" CHB HEM E 301 " 0.230 2.00e-02 2.50e+03 pdb=" CHC HEM E 301 " 0.003 2.00e-02 2.50e+03 pdb=" CMB HEM E 301 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM E 301 " -0.161 2.00e-02 2.50e+03 7.87e-02 1.39e+02 pdb=" C1D HEM E 301 " -0.022 2.00e-02 2.50e+03 pdb=" C2D HEM E 301 " -0.014 2.00e-02 2.50e+03 pdb=" C3D HEM E 301 " -0.024 2.00e-02 2.50e+03 pdb=" C4D HEM E 301 " -0.010 2.00e-02 2.50e+03 pdb=" CAD HEM E 301 " -0.032 2.00e-02 2.50e+03 pdb=" CHA HEM E 301 " 0.133 2.00e-02 2.50e+03 pdb=" CHD HEM E 301 " 0.090 2.00e-02 2.50e+03 pdb=" CMD HEM E 301 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A HEM E 301 " 0.000 2.00e-02 2.50e+03 7.83e-02 1.38e+02 pdb=" C2A HEM E 301 " 0.047 2.00e-02 2.50e+03 pdb=" C3A HEM E 301 " -0.008 2.00e-02 2.50e+03 pdb=" C4A HEM E 301 " 0.033 2.00e-02 2.50e+03 pdb=" CAA HEM E 301 " 0.101 2.00e-02 2.50e+03 pdb=" CHA HEM E 301 " -0.142 2.00e-02 2.50e+03 pdb=" CHB HEM E 301 " 0.004 2.00e-02 2.50e+03 pdb=" CMA HEM E 301 " -0.120 2.00e-02 2.50e+03 pdb=" NA HEM E 301 " 0.083 2.00e-02 2.50e+03 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 14 2.59 - 3.17: 6235 3.17 - 3.75: 12351 3.75 - 4.32: 18847 4.32 - 4.90: 31260 Nonbonded interactions: 68707 Sorted by model distance: nonbonded pdb=" CB THR F 308 " pdb="CA CA F 803 " model vdw 2.015 2.940 nonbonded pdb=" O ASP E 236 " pdb=" OD1 ASP E 236 " model vdw 2.156 3.040 nonbonded pdb=" OG SER F 314 " pdb="CA CA F 803 " model vdw 2.387 2.510 nonbonded pdb=" OD1 ASP F 312 " pdb="CA CA F 803 " model vdw 2.434 2.510 nonbonded pdb=" O ASP E 236 " pdb="CA CA F 803 " model vdw 2.442 2.510 ... (remaining 68702 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.830 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 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 0.225 8136 Z= 0.216 Angle : 0.609 14.185 11058 Z= 0.303 Chirality : 0.044 0.154 1186 Planarity : 0.006 0.128 1416 Dihedral : 17.044 88.503 3018 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.09 % Allowed : 21.98 % Favored : 75.93 % 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: 0.71 (0.29), residues: 974 helix: 0.48 (0.36), residues: 211 sheet: 0.24 (0.34), residues: 250 loop : 0.81 (0.31), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.027 0.001 TYR D 49 PHE 0.014 0.001 PHE F 310 TRP 0.011 0.001 TRP A 50 HIS 0.007 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 ( 8123) covalent geometry : angle 0.60673 / 0.30 (11038) SS BOND : bond 0.00335 / 0.16 ( 7) SS BOND : angle 1.39066 / 0.73 ( 14) hydrogen bonds : bond 0.10619 / 6.43 ( 288) hydrogen bonds : angle 6.59794 / 4.48 ( 744) Misc. bond : bond 0.12297 / 6.13 ( 4) link_NAG-ASN : bond 0.00106 / 0.05 ( 2) link_NAG-ASN : angle 1.49013 / 0.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 46 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7847 (mt-10) REVERT: B 89 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8515 (tp) REVERT: C 40 SER cc_start: 0.7688 (p) cc_final: 0.7163 (t) REVERT: C 82 GLU cc_start: 0.8311 (tt0) cc_final: 0.8060 (tt0) REVERT: F 280 GLN cc_start: 0.7568 (tp40) cc_final: 0.7318 (tp40) REVERT: F 366 ARG cc_start: 0.7640 (mtp-110) cc_final: 0.7232 (mtt90) REVERT: F 367 SER cc_start: 0.6896 (OUTLIER) cc_final: 0.6593 (t) REVERT: F 410 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7639 (mmp80) REVERT: F 447 LYS cc_start: 0.8398 (tttt) cc_final: 0.7921 (pttm) outliers start: 18 outliers final: 15 residues processed: 132 average time/residue: 0.6185 time to fit residues: 86.0067 Evaluate side-chains 133 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 367 SER Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 714 SER Chi-restraints excluded: chain F residue 717 GLU 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: 2.9990 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 194 ASN F 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.124863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.105886 restraints weight = 8330.029| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.31 r_work: 0.2940 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.0391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 8136 Z= 0.146 Angle : 0.559 12.443 11058 Z= 0.282 Chirality : 0.044 0.174 1186 Planarity : 0.004 0.034 1416 Dihedral : 7.298 88.150 1166 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.65 % Allowed : 18.72 % Favored : 76.63 % 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: 0.81 (0.29), residues: 974 helix: 0.75 (0.37), residues: 212 sheet: 0.32 (0.34), residues: 250 loop : 0.76 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 61 TYR 0.024 0.001 TYR D 49 PHE 0.013 0.001 PHE F 393 TRP 0.011 0.001 TRP E 229 HIS 0.007 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 8123) covalent geometry : angle 0.55632 / 0.28 (11038) SS BOND : bond 0.00330 / 0.16 ( 7) SS BOND : angle 1.35742 / 0.71 ( 14) hydrogen bonds : bond 0.03614 / 2.22 ( 288) hydrogen bonds : angle 5.54611 / 3.72 ( 744) Misc. bond : bond 0.05891 / 2.95 ( 4) link_NAG-ASN : bond 0.00065 / 0.03 ( 2) link_NAG-ASN : angle 1.54297 / 0.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 82 GLU cc_start: 0.8276 (tt0) cc_final: 0.7896 (tt0) REVERT: D 24 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7442 (tmtt) REVERT: D 28 ASP cc_start: 0.7624 (t0) cc_final: 0.7361 (t0) REVERT: D 49 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.6523 (p90) REVERT: E 221 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: E 227 MET cc_start: 0.8544 (tmm) cc_final: 0.8288 (tmm) REVERT: F 366 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7251 (mtt90) REVERT: F 367 SER cc_start: 0.6824 (m) cc_final: 0.6589 (t) REVERT: F 410 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7530 (mmp80) REVERT: F 447 LYS cc_start: 0.8348 (tttt) cc_final: 0.7933 (pttm) REVERT: F 544 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8139 (mt-10) outliers start: 40 outliers final: 16 residues processed: 146 average time/residue: 0.5938 time to fit residues: 91.5287 Evaluate side-chains 137 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 366 ARG Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 450 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 714 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [41, 62, 9, 71, 78, 51, 39, 73, 68, 22, 28] chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 GLN E 194 ASN F 457 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.126638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110815 restraints weight = 8303.638| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.04 r_work: 0.3001 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.0531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8136 Z= 0.179 Angle : 0.593 13.006 11058 Z= 0.300 Chirality : 0.045 0.177 1186 Planarity : 0.004 0.036 1416 Dihedral : 6.632 81.601 1146 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.58 % Allowed : 18.84 % Favored : 75.58 % 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: 0.64 (0.28), residues: 974 helix: 0.70 (0.37), residues: 212 sheet: 0.19 (0.33), residues: 260 loop : 0.64 (0.31), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.027 0.002 TYR D 49 PHE 0.015 0.001 PHE F 393 TRP 0.013 0.002 TRP E 229 HIS 0.009 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 8123) covalent geometry : angle 0.58961 / 0.30 (11038) SS BOND : bond 0.00390 / 0.18 ( 7) SS BOND : angle 1.69220 / 0.84 ( 14) hydrogen bonds : bond 0.03813 / 2.35 ( 288) hydrogen bonds : angle 5.54719 / 3.73 ( 744) Misc. bond : bond 0.05080 / 2.54 ( 4) link_NAG-ASN : bond 0.00210 / 0.10 ( 2) link_NAG-ASN : angle 1.67315 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 115 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: C 67 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8027 (ttmm) REVERT: C 74 LYS cc_start: 0.7411 (mtmt) cc_final: 0.6997 (mtmm) REVERT: C 82 GLU cc_start: 0.8315 (tt0) cc_final: 0.8060 (tt0) REVERT: D 24 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7474 (tptm) REVERT: D 49 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.6614 (p90) REVERT: E 221 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8248 (mt-10) REVERT: E 227 MET cc_start: 0.8632 (tmm) cc_final: 0.8404 (tmm) REVERT: F 366 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7282 (mtt90) REVERT: F 367 SER cc_start: 0.6869 (m) cc_final: 0.6647 (t) REVERT: F 410 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7653 (mmp80) REVERT: F 447 LYS cc_start: 0.8396 (tttt) cc_final: 0.8091 (pttm) REVERT: F 544 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8131 (mt-10) outliers start: 48 outliers final: 22 residues processed: 147 average time/residue: 0.5709 time to fit residues: 88.8455 Evaluate side-chains 143 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 366 ARG Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 714 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [79, 74, 26, 37, 69, 32, 24, 61, 45, 44, 88] chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 61 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 194 ASN F 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.127054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.110998 restraints weight = 8439.068| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.07 r_work: 0.3002 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 8136 Z= 0.176 Angle : 0.604 14.411 11058 Z= 0.301 Chirality : 0.045 0.177 1186 Planarity : 0.004 0.036 1416 Dihedral : 6.612 85.941 1146 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.70 % Allowed : 19.07 % Favored : 75.23 % 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: 0.67 (0.28), residues: 974 helix: 0.70 (0.36), residues: 212 sheet: 0.25 (0.34), residues: 250 loop : 0.62 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 63 TYR 0.027 0.002 TYR D 49 PHE 0.014 0.001 PHE F 393 TRP 0.012 0.002 TRP E 229 HIS 0.008 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 8123) covalent geometry : angle 0.60064 / 0.30 (11038) SS BOND : bond 0.00382 / 0.18 ( 7) SS BOND : angle 1.72053 / 0.88 ( 14) hydrogen bonds : bond 0.03741 / 2.31 ( 288) hydrogen bonds : angle 5.49919 / 3.69 ( 744) Misc. bond : bond 0.06706 / 3.35 ( 4) link_NAG-ASN : bond 0.00170 / 0.08 ( 2) link_NAG-ASN : angle 1.63831 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7841 (mmmt) REVERT: C 46 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: C 67 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8037 (ttmm) REVERT: C 74 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7071 (mtmm) REVERT: C 82 GLU cc_start: 0.8310 (tt0) cc_final: 0.8051 (tt0) REVERT: D 24 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7502 (tptm) REVERT: D 28 ASP cc_start: 0.7643 (t0) cc_final: 0.7432 (t0) REVERT: D 49 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6623 (p90) REVERT: E 227 MET cc_start: 0.8661 (tmm) cc_final: 0.8433 (tmm) REVERT: F 366 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7303 (mtt90) REVERT: F 367 SER cc_start: 0.6878 (m) cc_final: 0.6656 (t) REVERT: F 410 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7657 (mmp80) REVERT: F 447 LYS cc_start: 0.8398 (tttt) cc_final: 0.8096 (pttm) REVERT: F 544 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8139 (mt-10) outliers start: 49 outliers final: 24 residues processed: 152 average time/residue: 0.5753 time to fit residues: 92.4847 Evaluate side-chains 144 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 366 ARG Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 714 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [42, 47, 84, 10, 66, 54, 4, 14, 77, 85, 50] chunk 42 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 194 ASN F 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.126768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.110971 restraints weight = 8355.225| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.04 r_work: 0.3007 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.0605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 8136 Z= 0.180 Angle : 0.607 14.159 11058 Z= 0.302 Chirality : 0.045 0.177 1186 Planarity : 0.004 0.036 1416 Dihedral : 6.478 88.545 1144 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.70 % Allowed : 19.19 % Favored : 75.12 % 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: 0.64 (0.28), residues: 974 helix: 0.69 (0.36), residues: 212 sheet: 0.23 (0.34), residues: 250 loop : 0.60 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.027 0.002 TYR D 49 PHE 0.015 0.001 PHE F 393 TRP 0.012 0.002 TRP E 229 HIS 0.009 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 8123) covalent geometry : angle 0.60339 / 0.30 (11038) SS BOND : bond 0.00388 / 0.18 ( 7) SS BOND : angle 1.78101 / 0.92 ( 14) hydrogen bonds : bond 0.03765 / 2.33 ( 288) hydrogen bonds : angle 5.48971 / 3.69 ( 744) Misc. bond : bond 0.05549 / 2.77 ( 4) link_NAG-ASN : bond 0.00196 / 0.09 ( 2) link_NAG-ASN : angle 1.64655 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 113 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7830 (mmmt) REVERT: C 40 SER cc_start: 0.7283 (OUTLIER) cc_final: 0.6732 (t) REVERT: C 46 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: C 67 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8031 (ttmm) REVERT: C 74 LYS cc_start: 0.7474 (mtmt) cc_final: 0.7061 (mtmm) REVERT: C 82 GLU cc_start: 0.8300 (tt0) cc_final: 0.8046 (tt0) REVERT: D 24 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7500 (tptm) REVERT: D 49 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.6609 (p90) REVERT: E 227 MET cc_start: 0.8650 (tmm) cc_final: 0.8410 (tmm) REVERT: F 366 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7284 (mtt90) REVERT: F 367 SER cc_start: 0.6884 (m) cc_final: 0.6638 (t) REVERT: F 410 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7659 (mmp80) REVERT: F 447 LYS cc_start: 0.8380 (tttt) cc_final: 0.8089 (pttm) REVERT: F 525 MET cc_start: 0.9014 (mtp) cc_final: 0.8770 (mtm) REVERT: F 543 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8274 (ttp-170) REVERT: F 544 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8126 (mt-10) outliers start: 49 outliers final: 26 residues processed: 149 average time/residue: 0.5726 time to fit residues: 90.1942 Evaluate side-chains 148 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 366 ARG Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 543 ARG Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 714 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [30, 80, 65, 0, 91, 9, 48, 45, 47, 50, 87] chunk 30 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 194 ASN F 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.127676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.111785 restraints weight = 8340.027| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.04 r_work: 0.3016 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 8136 Z= 0.154 Angle : 0.582 13.647 11058 Z= 0.289 Chirality : 0.044 0.176 1186 Planarity : 0.004 0.035 1416 Dihedral : 6.299 86.646 1144 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.70 % Allowed : 19.30 % Favored : 75.00 % 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: 0.73 (0.28), residues: 974 helix: 0.77 (0.36), residues: 212 sheet: 0.29 (0.34), residues: 250 loop : 0.66 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.025 0.001 TYR D 49 PHE 0.013 0.001 PHE F 393 TRP 0.012 0.001 TRP E 229 HIS 0.008 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 8123) covalent geometry : angle 0.57848 / 0.29 (11038) SS BOND : bond 0.00342 / 0.16 ( 7) SS BOND : angle 1.57810 / 0.83 ( 14) hydrogen bonds : bond 0.03537 / 2.20 ( 288) hydrogen bonds : angle 5.37971 / 3.60 ( 744) Misc. bond : bond 0.05797 / 2.90 ( 4) link_NAG-ASN : bond 0.00102 / 0.05 ( 2) link_NAG-ASN : angle 1.54955 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 SER cc_start: 0.7334 (OUTLIER) cc_final: 0.6788 (t) REVERT: C 46 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: C 67 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8047 (ttmm) REVERT: C 74 LYS cc_start: 0.7482 (mtmt) cc_final: 0.7076 (mtmm) REVERT: C 82 GLU cc_start: 0.8314 (tt0) cc_final: 0.8068 (tt0) REVERT: D 24 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7490 (tptm) REVERT: D 28 ASP cc_start: 0.7625 (t0) cc_final: 0.7403 (t0) REVERT: D 49 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6588 (p90) REVERT: E 197 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7277 (tttp) REVERT: E 221 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8244 (mt-10) REVERT: E 227 MET cc_start: 0.8659 (tmm) cc_final: 0.8418 (tmm) REVERT: F 366 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7303 (mtt90) REVERT: F 367 SER cc_start: 0.6908 (m) cc_final: 0.6664 (t) REVERT: F 410 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7683 (mmp80) REVERT: F 447 LYS cc_start: 0.8399 (tttt) cc_final: 0.8120 (pttm) REVERT: F 544 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8153 (mt-10) outliers start: 49 outliers final: 27 residues processed: 150 average time/residue: 0.6147 time to fit residues: 97.4321 Evaluate side-chains 151 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 366 ARG Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 714 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [19, 29, 92, 1, 43, 54, 47, 61, 34, 58, 46] chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 194 ASN F 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.127101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.111200 restraints weight = 8361.149| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.05 r_work: 0.3007 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.0626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 8136 Z= 0.171 Angle : 0.597 13.890 11058 Z= 0.297 Chirality : 0.045 0.179 1186 Planarity : 0.004 0.036 1416 Dihedral : 6.366 86.610 1144 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 5.35 % Allowed : 20.00 % Favored : 74.65 % 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: 0.68 (0.28), residues: 974 helix: 0.70 (0.36), residues: 212 sheet: 0.27 (0.34), residues: 250 loop : 0.62 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.026 0.002 TYR D 49 PHE 0.014 0.001 PHE F 393 TRP 0.012 0.002 TRP E 229 HIS 0.008 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 ( 8123) covalent geometry : angle 0.59364 / 0.30 (11038) SS BOND : bond 0.00371 / 0.18 ( 7) SS BOND : angle 1.69677 / 0.89 ( 14) hydrogen bonds : bond 0.03667 / 2.28 ( 288) hydrogen bonds : angle 5.42142 / 3.64 ( 744) Misc. bond : bond 0.05683 / 2.84 ( 4) link_NAG-ASN : bond 0.00155 / 0.07 ( 2) link_NAG-ASN : angle 1.59994 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 111 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7816 (mmmt) REVERT: A 46 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7737 (mp0) REVERT: C 40 SER cc_start: 0.7256 (OUTLIER) cc_final: 0.6699 (t) REVERT: C 46 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: C 67 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8031 (ttmm) REVERT: C 74 LYS cc_start: 0.7479 (mtmt) cc_final: 0.7061 (mtmm) REVERT: C 82 GLU cc_start: 0.8304 (tt0) cc_final: 0.8056 (tt0) REVERT: D 24 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.7531 (tptm) REVERT: D 28 ASP cc_start: 0.7686 (t0) cc_final: 0.7478 (t0) REVERT: D 49 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.6613 (p90) REVERT: E 197 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7260 (tttp) REVERT: E 221 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: E 227 MET cc_start: 0.8650 (tmm) cc_final: 0.8437 (tmm) REVERT: F 366 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7300 (mtt90) REVERT: F 367 SER cc_start: 0.6908 (m) cc_final: 0.6658 (t) REVERT: F 410 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7666 (mmp80) REVERT: F 447 LYS cc_start: 0.8420 (tttt) cc_final: 0.8107 (pttm) REVERT: F 544 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8108 (mt-10) outliers start: 46 outliers final: 28 residues processed: 143 average time/residue: 0.5879 time to fit residues: 89.0001 Evaluate side-chains 150 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 366 ARG Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 553 ILE Chi-restraints excluded: chain F residue 586 SER Chi-restraints excluded: chain F residue 714 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [49, 45, 18, 24, 94, 12, 22, 2, 75, 47, 81] chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 81 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 194 ASN F 457 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.128331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.112462 restraints weight = 8331.521| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.05 r_work: 0.3023 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 8136 Z= 0.144 Angle : 0.573 13.256 11058 Z= 0.284 Chirality : 0.044 0.174 1186 Planarity : 0.004 0.035 1416 Dihedral : 6.189 84.668 1144 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.88 % Allowed : 20.47 % Favored : 74.65 % 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: 0.79 (0.28), residues: 974 helix: 0.82 (0.36), residues: 212 sheet: 0.33 (0.34), residues: 250 loop : 0.69 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.024 0.001 TYR D 49 PHE 0.013 0.001 PHE F 393 TRP 0.012 0.001 TRP E 229 HIS 0.007 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 8123) covalent geometry : angle 0.56988 / 0.28 (11038) SS BOND : bond 0.00326 / 0.15 ( 7) SS BOND : angle 1.49757 / 0.79 ( 14) hydrogen bonds : bond 0.03416 / 2.12 ( 288) hydrogen bonds : angle 5.30636 / 3.55 ( 744) Misc. bond : bond 0.05570 / 2.78 ( 4) link_NAG-ASN : bond 0.00078 / 0.04 ( 2) link_NAG-ASN : angle 1.50812 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 SER cc_start: 0.7302 (OUTLIER) cc_final: 0.6745 (t) REVERT: C 67 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8025 (ttmm) REVERT: C 74 LYS cc_start: 0.7453 (mtmt) cc_final: 0.7045 (mtmm) REVERT: C 82 GLU cc_start: 0.8299 (tt0) cc_final: 0.8053 (tt0) REVERT: D 24 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7482 (tptm) REVERT: D 49 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.6568 (p90) REVERT: E 197 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7229 (tttp) REVERT: E 221 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: E 227 MET cc_start: 0.8631 (tmm) cc_final: 0.8419 (tmm) REVERT: F 366 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7307 (mtt90) REVERT: F 367 SER cc_start: 0.6909 (m) cc_final: 0.6652 (t) REVERT: F 410 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7664 (mmp80) REVERT: F 447 LYS cc_start: 0.8401 (tttt) cc_final: 0.8103 (pttm) REVERT: F 544 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8142 (mt-10) outliers start: 42 outliers final: 28 residues processed: 140 average time/residue: 0.5959 time to fit residues: 88.1521 Evaluate side-chains 150 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 67 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 202 ARG Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 366 ARG Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 544 GLU Chi-restraints excluded: chain F residue 586 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [76, 88, 81, 46, 6, 61, 95, 71, 2, 52, 69] chunk 76 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 0.0270 chunk 61 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 71 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 194 ASN F 457 ASN F 666 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.129435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.113648 restraints weight = 8317.424| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.04 r_work: 0.3042 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 8136 Z= 0.127 Angle : 0.555 12.813 11058 Z= 0.275 Chirality : 0.043 0.173 1186 Planarity : 0.004 0.035 1416 Dihedral : 5.967 81.594 1143 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.53 % Allowed : 20.81 % Favored : 74.65 % 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: 0.89 (0.29), residues: 974 helix: 0.88 (0.36), residues: 214 sheet: 0.43 (0.34), residues: 248 loop : 0.73 (0.30), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.023 0.001 TYR D 49 PHE 0.012 0.001 PHE F 393 TRP 0.011 0.001 TRP A 50 HIS 0.007 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 8123) covalent geometry : angle 0.55196 / 0.27 (11038) SS BOND : bond 0.00309 / 0.15 ( 7) SS BOND : angle 1.34412 / 0.71 ( 14) hydrogen bonds : bond 0.03241 / 2.02 ( 288) hydrogen bonds : angle 5.20486 / 3.48 ( 744) Misc. bond : bond 0.05528 / 2.76 ( 4) link_NAG-ASN : bond 0.00042 / 0.02 ( 2) link_NAG-ASN : angle 1.44423 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7850 (mmmt) REVERT: A 46 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7716 (mp0) REVERT: C 40 SER cc_start: 0.7334 (OUTLIER) cc_final: 0.6764 (t) REVERT: C 74 LYS cc_start: 0.7430 (mtmt) cc_final: 0.7020 (mtmm) REVERT: C 82 GLU cc_start: 0.8291 (tt0) cc_final: 0.8045 (tt0) REVERT: D 24 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7409 (tmtt) REVERT: D 49 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.6543 (p90) REVERT: E 221 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: F 366 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7301 (mtt90) REVERT: F 367 SER cc_start: 0.6929 (m) cc_final: 0.6663 (t) REVERT: F 410 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7659 (mmp80) REVERT: F 447 LYS cc_start: 0.8414 (tttt) cc_final: 0.8109 (pttm) outliers start: 39 outliers final: 24 residues processed: 139 average time/residue: 0.5668 time to fit residues: 83.5576 Evaluate side-chains 143 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 218 LYS Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 366 ARG Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 586 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [8, 43, 23, 55, 69, 77, 62, 0, 51, 68, 61] chunk 8 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 chunk 61 optimal weight: 0.0070 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 194 ASN F 457 ASN F 666 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.130796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.115050 restraints weight = 8279.825| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.05 r_work: 0.3064 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 8136 Z= 0.111 Angle : 0.538 12.429 11058 Z= 0.266 Chirality : 0.042 0.175 1186 Planarity : 0.004 0.034 1416 Dihedral : 5.749 77.605 1143 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.37 % Allowed : 21.51 % Favored : 75.12 % 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: 0.99 (0.29), residues: 974 helix: 1.00 (0.37), residues: 214 sheet: 0.50 (0.35), residues: 248 loop : 0.78 (0.31), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.021 0.001 TYR D 49 PHE 0.010 0.001 PHE F 393 TRP 0.012 0.001 TRP A 50 HIS 0.007 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 8123) covalent geometry : angle 0.53622 / 0.27 (11038) SS BOND : bond 0.00273 / 0.13 ( 7) SS BOND : angle 1.19689 / 0.64 ( 14) hydrogen bonds : bond 0.03052 / 1.90 ( 288) hydrogen bonds : angle 5.07040 / 3.38 ( 744) Misc. bond : bond 0.05738 / 2.87 ( 4) link_NAG-ASN : bond 0.00062 / 0.03 ( 2) link_NAG-ASN : angle 1.35495 / 0.76 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1948 Ramachandran restraints generated. 974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7849 (mmmt) REVERT: A 46 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7713 (mp0) REVERT: C 40 SER cc_start: 0.7303 (OUTLIER) cc_final: 0.6761 (t) REVERT: C 74 LYS cc_start: 0.7417 (mtmt) cc_final: 0.7006 (mtmm) REVERT: C 82 GLU cc_start: 0.8264 (tt0) cc_final: 0.8018 (tt0) REVERT: D 24 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7371 (tmtt) REVERT: D 49 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6559 (p90) REVERT: E 221 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: F 366 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7359 (mtt90) REVERT: F 367 SER cc_start: 0.6968 (m) cc_final: 0.6699 (t) REVERT: F 410 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7658 (mmp80) REVERT: F 447 LYS cc_start: 0.8410 (tttt) cc_final: 0.8116 (pttm) outliers start: 29 outliers final: 18 residues processed: 130 average time/residue: 0.6082 time to fit residues: 83.3941 Evaluate side-chains 137 residues out of total 860 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain C residue 31 HIS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain F residue 282 ASP Chi-restraints excluded: chain F residue 366 ARG Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 410 ARG Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 586 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [46, 49, 11, 43, 62, 70, 29, 89, 19, 51, 76] chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.0570 chunk 62 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 194 ASN F 457 ASN F 666 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.124705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.106000 restraints weight = 8297.440| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.28 r_work: 0.2938 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 8136 Z= 0.165 Angle : 0.594 13.861 11058 Z= 0.294 Chirality : 0.044 0.180 1186 Planarity : 0.004 0.035 1416 Dihedral : 6.095 81.468 1143 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.49 % Allowed : 21.63 % Favored : 74.88 % 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: 0.81 (0.28), residues: 974 helix: 0.82 (0.36), residues: 213 sheet: 0.36 (0.34), residues: 250 loop : 0.70 (0.30), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 63 TYR 0.026 0.002 TYR D 49 PHE 0.014 0.001 PHE F 393 TRP 0.011 0.001 TRP E 229 HIS 0.007 0.001 HIS D 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 ( 8123) covalent geometry : angle 0.59025 / 0.29 (11038) SS BOND : bond 0.00360 / 0.17 ( 7) SS BOND : angle 1.68489 / 0.89 ( 14) hydrogen bonds : bond 0.03558 / 2.21 ( 288) hydrogen bonds : angle 5.27003 / 3.53 ( 744) Misc. bond : bond 0.05710 / 2.85 ( 4) link_NAG-ASN : bond 0.00124 / 0.06 ( 2) link_NAG-ASN : angle 1.51991 / 0.85 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2917.46 seconds wall clock time: 50 minutes 26.51 seconds (3026.51 seconds total)