Starting phenix.real_space_refine on Mon May 12 23:53:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l6c_62852/05_2025/9l6c_62852.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l6c_62852/05_2025/9l6c_62852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l6c_62852/05_2025/9l6c_62852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l6c_62852/05_2025/9l6c_62852.map" model { file = "/net/cci-nas-00/data/ceres_data/9l6c_62852/05_2025/9l6c_62852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l6c_62852/05_2025/9l6c_62852.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3402 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 4279 2.51 5 N 1137 2.21 5 O 1322 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6766 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 969 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "E" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1542 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 812 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 921 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 868 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "F" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 810 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.05, per 1000 atoms: 0.89 Number of scatterers: 6766 At special positions: 0 Unit cell: (68.64, 99.66, 122.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1322 8.00 N 1137 7.00 C 4279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.04 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=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN E 343 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 951.4 milliseconds 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 22 sheets defined 5.0% alpha, 41.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'E' and resid 364 through 368 removed outlier: 4.365A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 390 removed outlier: 3.869A pdb=" N LEU E 387 " --> pdb=" O PRO E 384 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP E 389 " --> pdb=" O LYS E 386 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 5.606A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.508A pdb=" N SER D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN D 32 " --> pdb=" O VAL D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.713A pdb=" N LYS D 64 " --> pdb=" O ASP D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.840A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 33 removed outlier: 3.610A pdb=" N TYR F 33 " --> pdb=" O SER F 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 30 through 33' Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.662A pdb=" N LEU A 81 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A 78 " --> pdb=" O ASP A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 5.961A pdb=" N GLY A 10 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET A 34 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 40 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 5.961A pdb=" N GLY A 10 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY A 33 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 97 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG A 98 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.029A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.574A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.824A pdb=" N LEU B 10 " --> pdb=" O GLU B 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 18 through 21 removed outlier: 3.833A pdb=" N ILE B 75 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 73 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.782A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR B 98 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.529A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.834A pdb=" N THR H 114 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR H 93 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.834A pdb=" N THR H 114 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR H 93 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N CYS H 95 " --> pdb=" O TRP H 110 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TRP H 110 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG H 97 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.588A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.891A pdb=" N LEU L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA L 13 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.552A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.819A pdb=" N TYR D 33 " --> pdb=" O ASP D 98 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET D 34 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.458A pdb=" N VAL D 106 " --> pdb=" O ARG D 97 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.552A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER F 54 " --> pdb=" O TYR F 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.552A pdb=" N LEU F 11 " --> pdb=" O LYS F 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 21 through 22 removed outlier: 4.226A pdb=" N ASP F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 68 " --> pdb=" O ASP F 71 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2166 1.34 - 1.46: 1872 1.46 - 1.58: 2854 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 6928 Sorted by residual: bond pdb=" C LYS B 39 " pdb=" N PRO B 40 " ideal model delta sigma weight residual 1.331 1.360 -0.029 1.20e-02 6.94e+03 5.87e+00 bond pdb=" C LYS F 40 " pdb=" N PRO F 41 " ideal model delta sigma weight residual 1.331 1.360 -0.028 1.27e-02 6.20e+03 5.03e+00 bond pdb=" C ALA D 40 " pdb=" N PRO D 41 " ideal model delta sigma weight residual 1.332 1.359 -0.027 1.32e-02 5.74e+03 4.32e+00 bond pdb=" C TYR H 59 " pdb=" N PRO H 60 " ideal model delta sigma weight residual 1.330 1.355 -0.025 1.25e-02 6.40e+03 3.91e+00 bond pdb=" N PRO H 60 " pdb=" CD PRO H 60 " ideal model delta sigma weight residual 1.473 1.449 0.024 1.40e-02 5.10e+03 2.99e+00 ... (remaining 6923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 9184 1.63 - 3.27: 190 3.27 - 4.90: 23 4.90 - 6.53: 6 6.53 - 8.17: 1 Bond angle restraints: 9404 Sorted by residual: angle pdb=" CA GLU A 89 " pdb=" CB GLU A 89 " pdb=" CG GLU A 89 " ideal model delta sigma weight residual 114.10 122.27 -8.17 2.00e+00 2.50e-01 1.67e+01 angle pdb=" O TYR H 59 " pdb=" C TYR H 59 " pdb=" N PRO H 60 " ideal model delta sigma weight residual 121.80 119.29 2.51 8.60e-01 1.35e+00 8.54e+00 angle pdb=" C SER A 56 " pdb=" N ASN A 57 " pdb=" CA ASN A 57 " ideal model delta sigma weight residual 121.54 126.68 -5.14 1.91e+00 2.74e-01 7.25e+00 angle pdb=" C GLY A 108 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " ideal model delta sigma weight residual 121.54 126.39 -4.85 1.91e+00 2.74e-01 6.44e+00 angle pdb=" N LEU A 109 " pdb=" CA LEU A 109 " pdb=" C LEU A 109 " ideal model delta sigma weight residual 110.80 116.08 -5.28 2.13e+00 2.20e-01 6.14e+00 ... (remaining 9399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3577 17.43 - 34.86: 387 34.86 - 52.28: 96 52.28 - 69.71: 15 69.71 - 87.14: 9 Dihedral angle restraints: 4084 sinusoidal: 1592 harmonic: 2492 Sorted by residual: dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual -86.00 -41.64 -44.36 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CA ASN E 440 " pdb=" C ASN E 440 " pdb=" N LEU E 441 " pdb=" CA LEU E 441 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" N LEU A 109 " pdb=" CA LEU A 109 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 4081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 664 0.033 - 0.066: 243 0.066 - 0.099: 64 0.099 - 0.131: 42 0.131 - 0.164: 3 Chirality restraints: 1016 Sorted by residual: chirality pdb=" CA PRO B 40 " pdb=" N PRO B 40 " pdb=" C PRO B 40 " pdb=" CB PRO B 40 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA ILE F 49 " pdb=" N ILE F 49 " pdb=" C ILE F 49 " pdb=" CB ILE F 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1013 not shown) Planarity restraints: 1210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS E 336 " -0.057 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO E 337 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 94 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.85e+00 pdb=" N PRO B 95 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 80 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO F 81 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 81 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 81 " -0.028 5.00e-02 4.00e+02 ... (remaining 1207 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1468 2.78 - 3.31: 5588 3.31 - 3.84: 10559 3.84 - 4.37: 11980 4.37 - 4.90: 21898 Nonbonded interactions: 51493 Sorted by model distance: nonbonded pdb=" O SER L 7 " pdb=" OG1 THR L 22 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR B 36 " pdb=" OE1 GLN B 89 " model vdw 2.259 3.040 nonbonded pdb=" O SER H 119 " pdb=" OG SER H 119 " model vdw 2.287 3.040 nonbonded pdb=" OD1 ASN E 501 " pdb=" N GLY E 502 " model vdw 2.301 3.120 nonbonded pdb=" N GLY E 476 " pdb=" OD1 ASN E 487 " model vdw 2.305 3.120 ... (remaining 51488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 1 through 95 or resid 98 through 100 or resid 102 through \ 104 or resid 106 through 108)) selection = (chain 'F' and (resid 2 through 99 or resid 101 through 103 or resid 105 through \ 107)) } 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: 10.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.550 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 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 : 0.002 0.029 6940 Z= 0.131 Angle : 0.575 8.165 9430 Z= 0.309 Chirality : 0.041 0.164 1016 Planarity : 0.005 0.087 1209 Dihedral : 15.305 87.139 2488 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.47 % Favored : 94.19 % Rotamer: Outliers : 0.27 % Allowed : 20.60 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.29), residues: 860 helix: -5.52 (0.31), residues: 6 sheet: -0.49 (0.31), residues: 333 loop : -0.68 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 35 PHE 0.009 0.001 PHE A 107 TYR 0.013 0.001 TYR D 59 ARG 0.005 0.000 ARG A 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 1) link_NAG-ASN : angle 1.52723 ( 3) link_BETA1-4 : bond 0.00552 ( 1) link_BETA1-4 : angle 0.88947 ( 3) hydrogen bonds : bond 0.28428 ( 199) hydrogen bonds : angle 10.32523 ( 567) SS BOND : bond 0.00305 ( 10) SS BOND : angle 0.97029 ( 20) covalent geometry : bond 0.00240 ( 6928) covalent geometry : angle 0.57347 ( 9404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 97 TYR cc_start: 0.8271 (m-80) cc_final: 0.8047 (m-80) outliers start: 2 outliers final: 2 residues processed: 134 average time/residue: 0.1764 time to fit residues: 32.0824 Evaluate side-chains 134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain F residue 90 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.121007 restraints weight = 9698.858| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.58 r_work: 0.3510 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6940 Z= 0.170 Angle : 0.584 5.618 9430 Z= 0.312 Chirality : 0.042 0.144 1016 Planarity : 0.005 0.075 1209 Dihedral : 5.764 73.910 1017 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.63 % Favored : 93.02 % Rotamer: Outliers : 2.75 % Allowed : 18.13 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.29), residues: 860 helix: -4.90 (0.34), residues: 13 sheet: -0.29 (0.31), residues: 308 loop : -0.74 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 107 HIS 0.005 0.001 HIS D 94 PHE 0.016 0.002 PHE E 400 TYR 0.015 0.002 TYR D 93 ARG 0.004 0.000 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 1) link_NAG-ASN : angle 0.87600 ( 3) link_BETA1-4 : bond 0.00663 ( 1) link_BETA1-4 : angle 0.59538 ( 3) hydrogen bonds : bond 0.04460 ( 199) hydrogen bonds : angle 6.70687 ( 567) SS BOND : bond 0.00504 ( 10) SS BOND : angle 1.26261 ( 20) covalent geometry : bond 0.00382 ( 6928) covalent geometry : angle 0.58119 ( 9404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8193 (t0) cc_final: 0.7955 (t0) REVERT: D 81 GLN cc_start: 0.7550 (tp40) cc_final: 0.7072 (tt0) outliers start: 20 outliers final: 16 residues processed: 141 average time/residue: 0.1821 time to fit residues: 34.8312 Evaluate side-chains 147 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 58 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 9 optimal weight: 0.5980 chunk 81 optimal weight: 0.0570 chunk 82 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122493 restraints weight = 9802.136| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.61 r_work: 0.3530 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6940 Z= 0.113 Angle : 0.523 5.380 9430 Z= 0.277 Chirality : 0.040 0.142 1016 Planarity : 0.005 0.069 1209 Dihedral : 4.629 27.129 1013 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.58 % Favored : 94.07 % Rotamer: Outliers : 2.47 % Allowed : 19.09 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.29), residues: 860 helix: -5.49 (0.33), residues: 6 sheet: -0.27 (0.31), residues: 306 loop : -0.71 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 107 HIS 0.003 0.001 HIS D 94 PHE 0.011 0.001 PHE A 107 TYR 0.009 0.001 TYR D 93 ARG 0.003 0.000 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00497 ( 1) link_NAG-ASN : angle 0.65582 ( 3) link_BETA1-4 : bond 0.00503 ( 1) link_BETA1-4 : angle 0.65265 ( 3) hydrogen bonds : bond 0.03623 ( 199) hydrogen bonds : angle 6.01244 ( 567) SS BOND : bond 0.00439 ( 10) SS BOND : angle 0.82553 ( 20) covalent geometry : bond 0.00252 ( 6928) covalent geometry : angle 0.52161 ( 9404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8105 (t0) cc_final: 0.7847 (t0) REVERT: H 82 MET cc_start: 0.7529 (mtm) cc_final: 0.7277 (mtp) REVERT: L 97 TYR cc_start: 0.8390 (m-80) cc_final: 0.8171 (m-80) REVERT: D 79 TYR cc_start: 0.7529 (m-10) cc_final: 0.7125 (m-10) REVERT: D 81 GLN cc_start: 0.7529 (tp40) cc_final: 0.7103 (tt0) outliers start: 18 outliers final: 17 residues processed: 145 average time/residue: 0.1774 time to fit residues: 35.1877 Evaluate side-chains 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 90 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 42 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 67 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 5 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.137482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.121481 restraints weight = 9834.470| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.59 r_work: 0.3481 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6940 Z= 0.210 Angle : 0.577 6.132 9430 Z= 0.310 Chirality : 0.042 0.145 1016 Planarity : 0.005 0.064 1209 Dihedral : 5.019 29.913 1013 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 3.85 % Allowed : 19.78 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.28), residues: 860 helix: -5.54 (0.32), residues: 6 sheet: -0.43 (0.31), residues: 307 loop : -0.84 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 36 HIS 0.006 0.002 HIS D 94 PHE 0.019 0.002 PHE A 107 TYR 0.015 0.002 TYR D 93 ARG 0.006 0.001 ARG A 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00483 ( 1) link_NAG-ASN : angle 1.40191 ( 3) link_BETA1-4 : bond 0.00379 ( 1) link_BETA1-4 : angle 0.79486 ( 3) hydrogen bonds : bond 0.03897 ( 199) hydrogen bonds : angle 6.03867 ( 567) SS BOND : bond 0.00620 ( 10) SS BOND : angle 1.26891 ( 20) covalent geometry : bond 0.00476 ( 6928) covalent geometry : angle 0.57419 ( 9404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8111 (t0) cc_final: 0.7834 (t0) REVERT: L 4 MET cc_start: 0.6854 (tpp) cc_final: 0.6521 (mmm) REVERT: L 97 TYR cc_start: 0.8420 (m-80) cc_final: 0.8145 (m-80) REVERT: D 81 GLN cc_start: 0.7573 (tp40) cc_final: 0.7118 (tt0) outliers start: 28 outliers final: 24 residues processed: 143 average time/residue: 0.1672 time to fit residues: 33.2357 Evaluate side-chains 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 90 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.0670 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.122212 restraints weight = 9760.769| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.61 r_work: 0.3522 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6940 Z= 0.108 Angle : 0.510 5.370 9430 Z= 0.272 Chirality : 0.041 0.144 1016 Planarity : 0.005 0.060 1209 Dihedral : 4.554 27.221 1013 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.16 % Favored : 93.60 % Rotamer: Outliers : 4.12 % Allowed : 19.92 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.29), residues: 860 helix: -5.45 (0.34), residues: 6 sheet: -0.34 (0.30), residues: 306 loop : -0.71 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 HIS 0.003 0.001 HIS D 94 PHE 0.011 0.001 PHE A 107 TYR 0.011 0.001 TYR H 105 ARG 0.006 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 1) link_NAG-ASN : angle 0.73524 ( 3) link_BETA1-4 : bond 0.00358 ( 1) link_BETA1-4 : angle 0.72411 ( 3) hydrogen bonds : bond 0.03063 ( 199) hydrogen bonds : angle 5.59681 ( 567) SS BOND : bond 0.00348 ( 10) SS BOND : angle 0.82124 ( 20) covalent geometry : bond 0.00246 ( 6928) covalent geometry : angle 0.50943 ( 9404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8073 (t0) cc_final: 0.7809 (t0) REVERT: H 82 MET cc_start: 0.7513 (mtm) cc_final: 0.7275 (mtp) REVERT: L 4 MET cc_start: 0.6742 (tpp) cc_final: 0.6403 (mmm) REVERT: D 79 TYR cc_start: 0.7523 (m-10) cc_final: 0.7123 (m-10) REVERT: D 81 GLN cc_start: 0.7539 (tp40) cc_final: 0.7087 (tt0) outliers start: 30 outliers final: 25 residues processed: 145 average time/residue: 0.1802 time to fit residues: 35.3440 Evaluate side-chains 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 66 SER Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.120586 restraints weight = 9750.782| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.61 r_work: 0.3502 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6940 Z= 0.164 Angle : 0.549 8.011 9430 Z= 0.291 Chirality : 0.041 0.139 1016 Planarity : 0.005 0.057 1209 Dihedral : 4.689 28.657 1013 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.09 % Favored : 92.67 % Rotamer: Outliers : 3.57 % Allowed : 20.33 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.28), residues: 860 helix: -5.45 (0.34), residues: 6 sheet: -0.35 (0.30), residues: 306 loop : -0.77 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 36 HIS 0.004 0.001 HIS D 94 PHE 0.016 0.002 PHE A 107 TYR 0.019 0.002 TYR H 105 ARG 0.006 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00457 ( 1) link_NAG-ASN : angle 1.18521 ( 3) link_BETA1-4 : bond 0.00352 ( 1) link_BETA1-4 : angle 0.81788 ( 3) hydrogen bonds : bond 0.03350 ( 199) hydrogen bonds : angle 5.66219 ( 567) SS BOND : bond 0.00515 ( 10) SS BOND : angle 1.13379 ( 20) covalent geometry : bond 0.00373 ( 6928) covalent geometry : angle 0.54706 ( 9404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7536 (p) REVERT: E 501 ASN cc_start: 0.8060 (t0) cc_final: 0.7799 (t0) REVERT: L 4 MET cc_start: 0.6817 (tpp) cc_final: 0.6425 (mmm) REVERT: D 81 GLN cc_start: 0.7555 (tp40) cc_final: 0.7103 (tt0) outliers start: 26 outliers final: 24 residues processed: 142 average time/residue: 0.1680 time to fit residues: 32.3697 Evaluate side-chains 152 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.134940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118962 restraints weight = 9803.717| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.60 r_work: 0.3477 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6940 Z= 0.211 Angle : 0.582 6.975 9430 Z= 0.310 Chirality : 0.042 0.158 1016 Planarity : 0.005 0.055 1209 Dihedral : 4.974 30.400 1013 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.09 % Favored : 92.67 % Rotamer: Outliers : 4.26 % Allowed : 19.64 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.28), residues: 860 helix: -4.44 (1.01), residues: 8 sheet: -0.40 (0.31), residues: 306 loop : -0.85 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 36 HIS 0.005 0.002 HIS D 94 PHE 0.019 0.002 PHE A 107 TYR 0.020 0.002 TYR H 105 ARG 0.008 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 1) link_NAG-ASN : angle 1.35427 ( 3) link_BETA1-4 : bond 0.00371 ( 1) link_BETA1-4 : angle 0.87255 ( 3) hydrogen bonds : bond 0.03629 ( 199) hydrogen bonds : angle 5.85155 ( 567) SS BOND : bond 0.00633 ( 10) SS BOND : angle 1.28015 ( 20) covalent geometry : bond 0.00479 ( 6928) covalent geometry : angle 0.57899 ( 9404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7583 (p) REVERT: E 423 TYR cc_start: 0.7457 (t80) cc_final: 0.7118 (t80) REVERT: E 501 ASN cc_start: 0.8089 (t0) cc_final: 0.7846 (t0) REVERT: H 112 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7561 (mm110) REVERT: D 81 GLN cc_start: 0.7569 (tp40) cc_final: 0.7114 (tt0) outliers start: 31 outliers final: 27 residues processed: 152 average time/residue: 0.1598 time to fit residues: 33.6361 Evaluate side-chains 161 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 36 optimal weight: 0.1980 chunk 58 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 76 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.137381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121212 restraints weight = 9836.383| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.66 r_work: 0.3506 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6940 Z= 0.123 Angle : 0.542 7.193 9430 Z= 0.286 Chirality : 0.041 0.153 1016 Planarity : 0.005 0.055 1209 Dihedral : 4.642 28.447 1013 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.74 % Favored : 93.02 % Rotamer: Outliers : 3.71 % Allowed : 20.60 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.28), residues: 860 helix: -4.75 (0.70), residues: 8 sheet: -0.34 (0.30), residues: 313 loop : -0.80 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 HIS 0.003 0.001 HIS D 94 PHE 0.012 0.001 PHE A 107 TYR 0.013 0.001 TYR H 105 ARG 0.009 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00439 ( 1) link_NAG-ASN : angle 0.88459 ( 3) link_BETA1-4 : bond 0.00406 ( 1) link_BETA1-4 : angle 0.82853 ( 3) hydrogen bonds : bond 0.03024 ( 199) hydrogen bonds : angle 5.59774 ( 567) SS BOND : bond 0.00408 ( 10) SS BOND : angle 1.05123 ( 20) covalent geometry : bond 0.00281 ( 6928) covalent geometry : angle 0.54021 ( 9404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7543 (p) REVERT: E 501 ASN cc_start: 0.8062 (t0) cc_final: 0.7823 (t0) REVERT: L 4 MET cc_start: 0.6912 (mmm) cc_final: 0.6595 (mmm) REVERT: D 81 GLN cc_start: 0.7540 (tp40) cc_final: 0.7095 (tt0) outliers start: 27 outliers final: 22 residues processed: 153 average time/residue: 0.1726 time to fit residues: 35.5209 Evaluate side-chains 159 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 19 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 4 optimal weight: 0.0670 chunk 42 optimal weight: 0.2980 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.137881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.121713 restraints weight = 9817.210| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.65 r_work: 0.3515 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6940 Z= 0.122 Angle : 0.532 6.922 9430 Z= 0.280 Chirality : 0.041 0.149 1016 Planarity : 0.005 0.056 1209 Dihedral : 4.493 27.846 1013 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.40 % Favored : 93.37 % Rotamer: Outliers : 3.30 % Allowed : 20.60 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.29), residues: 860 helix: -4.68 (0.76), residues: 8 sheet: -0.33 (0.30), residues: 313 loop : -0.76 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 107 HIS 0.004 0.001 HIS D 94 PHE 0.012 0.001 PHE A 107 TYR 0.014 0.001 TYR H 105 ARG 0.008 0.000 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00414 ( 1) link_NAG-ASN : angle 0.90750 ( 3) link_BETA1-4 : bond 0.00349 ( 1) link_BETA1-4 : angle 0.83375 ( 3) hydrogen bonds : bond 0.02935 ( 199) hydrogen bonds : angle 5.48295 ( 567) SS BOND : bond 0.00412 ( 10) SS BOND : angle 1.03422 ( 20) covalent geometry : bond 0.00281 ( 6928) covalent geometry : angle 0.53027 ( 9404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7534 (p) REVERT: E 501 ASN cc_start: 0.8072 (t0) cc_final: 0.7831 (t0) REVERT: D 79 TYR cc_start: 0.7541 (m-10) cc_final: 0.7156 (m-10) REVERT: D 81 GLN cc_start: 0.7540 (tp40) cc_final: 0.7089 (tt0) outliers start: 24 outliers final: 23 residues processed: 144 average time/residue: 0.1696 time to fit residues: 33.3796 Evaluate side-chains 154 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 62 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.136158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119916 restraints weight = 9933.999| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.65 r_work: 0.3488 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6940 Z= 0.186 Angle : 0.570 6.621 9430 Z= 0.302 Chirality : 0.041 0.149 1016 Planarity : 0.005 0.057 1209 Dihedral : 4.760 29.436 1013 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.56 % Favored : 92.21 % Rotamer: Outliers : 3.16 % Allowed : 20.47 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.28), residues: 860 helix: -4.48 (0.96), residues: 8 sheet: -0.40 (0.30), residues: 313 loop : -0.88 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 36 HIS 0.005 0.001 HIS D 94 PHE 0.017 0.002 PHE A 107 TYR 0.019 0.002 TYR H 105 ARG 0.009 0.001 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 1) link_NAG-ASN : angle 1.21322 ( 3) link_BETA1-4 : bond 0.00207 ( 1) link_BETA1-4 : angle 0.84627 ( 3) hydrogen bonds : bond 0.03367 ( 199) hydrogen bonds : angle 5.70964 ( 567) SS BOND : bond 0.00627 ( 10) SS BOND : angle 1.31952 ( 20) covalent geometry : bond 0.00425 ( 6928) covalent geometry : angle 0.56733 ( 9404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1720 Ramachandran restraints generated. 860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8097 (t0) cc_final: 0.7863 (t0) REVERT: D 32 ASN cc_start: 0.8448 (OUTLIER) cc_final: 0.8228 (m110) REVERT: D 81 GLN cc_start: 0.7567 (tp40) cc_final: 0.7105 (tt0) outliers start: 23 outliers final: 21 residues processed: 148 average time/residue: 0.1740 time to fit residues: 35.4681 Evaluate side-chains 158 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 53 PHE Chi-restraints excluded: chain A residue 104 GLU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 400 PHE Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain F residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119887 restraints weight = 9886.655| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.63 r_work: 0.3489 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.180 6940 Z= 0.283 Angle : 1.027 59.196 9430 Z= 0.610 Chirality : 0.047 0.719 1016 Planarity : 0.005 0.057 1209 Dihedral : 4.797 29.427 1013 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.33 % Favored : 92.44 % Rotamer: Outliers : 3.02 % Allowed : 20.74 % Favored : 76.24 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.28), residues: 860 helix: -4.48 (0.96), residues: 8 sheet: -0.40 (0.30), residues: 313 loop : -0.88 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 36 HIS 0.005 0.002 HIS D 94 PHE 0.017 0.002 PHE A 107 TYR 0.018 0.002 TYR H 105 ARG 0.008 0.001 ARG D 71 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 1) link_NAG-ASN : angle 1.21329 ( 3) link_BETA1-4 : bond 0.00488 ( 1) link_BETA1-4 : angle 0.88935 ( 3) hydrogen bonds : bond 0.03369 ( 199) hydrogen bonds : angle 5.70890 ( 567) SS BOND : bond 0.00634 ( 10) SS BOND : angle 1.35835 ( 20) covalent geometry : bond 0.00564 ( 6928) covalent geometry : angle 1.02648 ( 9404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.35 seconds wall clock time: 59 minutes 37.30 seconds (3577.30 seconds total)