Starting phenix.real_space_refine on Wed Sep 17 15:42:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l6c_62852/09_2025/9l6c_62852.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l6c_62852/09_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_62852/09_2025/9l6c_62852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l6c_62852/09_2025/9l6c_62852.map" model { file = "/net/cci-nas-00/data/ceres_data/9l6c_62852/09_2025/9l6c_62852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l6c_62852/09_2025/9l6c_62852.cif" } resolution = 3.33 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= 0.020 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.91, per 1000 atoms: 0.28 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: 0.53 Conformation dependent library (CDL) restraints added in 378.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.33 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: 1.13 Time building geometry restraints manager: 0.74 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: 8.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.410 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.000 ARG A 16 TYR 0.013 0.001 TYR D 59 PHE 0.009 0.001 PHE A 107 TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS A 35 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 6928) covalent geometry : angle 0.57347 ( 9404) SS BOND : bond 0.00305 ( 10) SS BOND : angle 0.97029 ( 20) hydrogen bonds : bond 0.28428 ( 199) hydrogen bonds : angle 10.32523 ( 567) link_BETA1-4 : bond 0.00552 ( 1) link_BETA1-4 : angle 0.88947 ( 3) link_NAG-ASN : bond 0.00187 ( 1) link_NAG-ASN : angle 1.52723 ( 3) *********************** 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 : 0.271 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: 0.0811 time to fit residues: 14.9444 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 : 0.275 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0000 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.137276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121402 restraints weight = 9782.813| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.60 r_work: 0.3514 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6940 Z= 0.155 Angle : 0.573 5.288 9430 Z= 0.307 Chirality : 0.041 0.143 1016 Planarity : 0.005 0.075 1209 Dihedral : 5.688 73.296 1017 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.40 % Favored : 93.26 % Rotamer: Outliers : 2.61 % Allowed : 18.13 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 aren not related in a simple way. whole: -0.96 (0.29), residues: 860 helix: -4.91 (0.33), residues: 13 sheet: -0.28 (0.31), residues: 308 loop : -0.71 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.014 0.002 TYR D 93 PHE 0.015 0.001 PHE E 400 TRP 0.012 0.002 TRP D 107 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 6928) covalent geometry : angle 0.57130 ( 9404) SS BOND : bond 0.00468 ( 10) SS BOND : angle 1.20587 ( 20) hydrogen bonds : bond 0.04292 ( 199) hydrogen bonds : angle 6.65294 ( 567) link_BETA1-4 : bond 0.00520 ( 1) link_BETA1-4 : angle 0.58608 ( 3) link_NAG-ASN : bond 0.00451 ( 1) link_NAG-ASN : angle 0.78523 ( 3) *********************** 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 148 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8180 (t0) cc_final: 0.7943 (t0) REVERT: D 81 GLN cc_start: 0.7543 (tp40) cc_final: 0.7080 (tt0) outliers start: 19 outliers final: 14 residues processed: 139 average time/residue: 0.0810 time to fit residues: 15.3286 Evaluate side-chains 143 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 B residue 105 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 51 ILE 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 60 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.137179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121325 restraints weight = 9706.633| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.57 r_work: 0.3513 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6940 Z= 0.151 Angle : 0.541 5.161 9430 Z= 0.289 Chirality : 0.041 0.141 1016 Planarity : 0.005 0.070 1209 Dihedral : 4.746 27.604 1013 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.40 % Favored : 93.26 % Rotamer: Outliers : 2.61 % Allowed : 18.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.29), residues: 860 helix: -5.49 (0.33), residues: 6 sheet: -0.33 (0.31), residues: 307 loop : -0.75 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 16 TYR 0.012 0.002 TYR D 93 PHE 0.014 0.001 PHE A 107 TRP 0.011 0.002 TRP D 107 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6928) covalent geometry : angle 0.53873 ( 9404) SS BOND : bond 0.00578 ( 10) SS BOND : angle 1.04867 ( 20) hydrogen bonds : bond 0.03849 ( 199) hydrogen bonds : angle 6.03019 ( 567) link_BETA1-4 : bond 0.00562 ( 1) link_BETA1-4 : angle 0.74140 ( 3) link_NAG-ASN : bond 0.00500 ( 1) link_NAG-ASN : angle 0.85645 ( 3) *********************** 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 151 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8141 (t0) cc_final: 0.7878 (t0) REVERT: H 82 MET cc_start: 0.7546 (mtm) cc_final: 0.7265 (mtp) REVERT: L 97 TYR cc_start: 0.8389 (m-80) cc_final: 0.8160 (m-80) REVERT: D 79 TYR cc_start: 0.7631 (m-10) cc_final: 0.7248 (m-10) REVERT: D 81 GLN cc_start: 0.7553 (tp40) cc_final: 0.7120 (tt0) outliers start: 19 outliers final: 18 residues processed: 143 average time/residue: 0.0789 time to fit residues: 15.3068 Evaluate side-chains 150 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3824 r_free = 0.3824 target = 0.136993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.120992 restraints weight = 9859.202| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.61 r_work: 0.3483 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6940 Z= 0.215 Angle : 0.575 6.009 9430 Z= 0.308 Chirality : 0.041 0.153 1016 Planarity : 0.005 0.065 1209 Dihedral : 4.914 29.831 1013 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.86 % Favored : 92.79 % Rotamer: Outliers : 3.98 % Allowed : 19.51 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 aren not related in a simple way. whole: -1.10 (0.28), residues: 860 helix: -5.52 (0.33), residues: 6 sheet: -0.42 (0.30), residues: 307 loop : -0.84 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 71 TYR 0.013 0.002 TYR D 93 PHE 0.018 0.002 PHE A 107 TRP 0.015 0.002 TRP F 36 HIS 0.005 0.002 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 6928) covalent geometry : angle 0.57277 ( 9404) SS BOND : bond 0.00576 ( 10) SS BOND : angle 1.23638 ( 20) hydrogen bonds : bond 0.03842 ( 199) hydrogen bonds : angle 6.02580 ( 567) link_BETA1-4 : bond 0.00380 ( 1) link_BETA1-4 : angle 0.75866 ( 3) link_NAG-ASN : bond 0.00517 ( 1) link_NAG-ASN : angle 1.30674 ( 3) *********************** 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 161 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 501 ASN cc_start: 0.8103 (t0) cc_final: 0.7824 (t0) REVERT: H 82 MET cc_start: 0.7573 (mtm) cc_final: 0.7341 (mtp) REVERT: L 4 MET cc_start: 0.6905 (tpp) cc_final: 0.6598 (mmm) REVERT: L 97 TYR cc_start: 0.8409 (m-80) cc_final: 0.8149 (m-80) REVERT: D 81 GLN cc_start: 0.7571 (tp40) cc_final: 0.7116 (tt0) outliers start: 29 outliers final: 26 residues processed: 148 average time/residue: 0.0722 time to fit residues: 14.7257 Evaluate side-chains 159 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 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 48 VAL 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 32 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 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 ** 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 = 0.3822 r_free = 0.3822 target = 0.135644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119612 restraints weight = 9895.663| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.63 r_work: 0.3487 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6940 Z= 0.183 Angle : 0.555 5.706 9430 Z= 0.298 Chirality : 0.041 0.160 1016 Planarity : 0.005 0.058 1209 Dihedral : 4.834 29.538 1013 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.63 % Favored : 93.02 % Rotamer: Outliers : 4.26 % Allowed : 19.51 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 aren not related in a simple way. whole: -1.10 (0.28), residues: 860 helix: -5.51 (0.33), residues: 6 sheet: -0.45 (0.30), residues: 307 loop : -0.83 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 72 TYR 0.020 0.002 TYR H 105 PHE 0.016 0.002 PHE A 107 TRP 0.012 0.002 TRP F 36 HIS 0.005 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 6928) covalent geometry : angle 0.55281 ( 9404) SS BOND : bond 0.00529 ( 10) SS BOND : angle 1.14381 ( 20) hydrogen bonds : bond 0.03605 ( 199) hydrogen bonds : angle 5.89863 ( 567) link_BETA1-4 : bond 0.00442 ( 1) link_BETA1-4 : angle 0.80808 ( 3) link_NAG-ASN : bond 0.00502 ( 1) link_NAG-ASN : angle 1.17189 ( 3) *********************** 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 167 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7563 (p) REVERT: E 501 ASN cc_start: 0.8063 (t0) cc_final: 0.7803 (t0) REVERT: H 82 MET cc_start: 0.7570 (mtm) cc_final: 0.7341 (mtp) REVERT: L 4 MET cc_start: 0.6814 (tpp) cc_final: 0.6452 (mmm) REVERT: L 97 TYR cc_start: 0.8371 (m-80) cc_final: 0.8149 (m-80) REVERT: D 81 GLN cc_start: 0.7564 (tp40) cc_final: 0.7109 (tt0) outliers start: 31 outliers final: 23 residues processed: 155 average time/residue: 0.0820 time to fit residues: 17.2162 Evaluate side-chains 160 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 48 VAL 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 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 90 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.136307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.120295 restraints weight = 9974.669| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.65 r_work: 0.3492 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6940 Z= 0.160 Angle : 0.544 5.348 9430 Z= 0.291 Chirality : 0.041 0.142 1016 Planarity : 0.005 0.056 1209 Dihedral : 4.796 29.159 1013 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.86 % Favored : 92.91 % Rotamer: Outliers : 4.12 % Allowed : 19.64 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 aren not related in a simple way. whole: -1.08 (0.28), residues: 860 helix: -5.48 (0.33), residues: 6 sheet: -0.44 (0.30), residues: 307 loop : -0.81 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 72 TYR 0.017 0.001 TYR H 105 PHE 0.015 0.001 PHE A 107 TRP 0.014 0.002 TRP A 52 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6928) covalent geometry : angle 0.54213 ( 9404) SS BOND : bond 0.00524 ( 10) SS BOND : angle 1.11335 ( 20) hydrogen bonds : bond 0.03362 ( 199) hydrogen bonds : angle 5.77243 ( 567) link_BETA1-4 : bond 0.00434 ( 1) link_BETA1-4 : angle 0.82020 ( 3) link_NAG-ASN : bond 0.00489 ( 1) link_NAG-ASN : angle 1.07560 ( 3) *********************** 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 165 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7555 (p) REVERT: E 501 ASN cc_start: 0.8067 (t0) cc_final: 0.7816 (t0) REVERT: H 82 MET cc_start: 0.7575 (mtm) cc_final: 0.7348 (mtp) REVERT: L 4 MET cc_start: 0.6817 (tpp) cc_final: 0.6423 (mmm) REVERT: D 81 GLN cc_start: 0.7567 (tp40) cc_final: 0.7117 (tt0) outliers start: 30 outliers final: 26 residues processed: 152 average time/residue: 0.0736 time to fit residues: 15.3786 Evaluate side-chains 160 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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 23 ARG 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 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 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 90 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 33 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.0770 chunk 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.136813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.121361 restraints weight = 9815.592| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.49 r_work: 0.3518 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6940 Z= 0.146 Angle : 0.540 5.582 9430 Z= 0.287 Chirality : 0.041 0.142 1016 Planarity : 0.005 0.056 1209 Dihedral : 4.708 28.759 1013 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.09 % Favored : 92.67 % Rotamer: Outliers : 3.98 % Allowed : 20.47 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 aren not related in a simple way. whole: -1.03 (0.28), residues: 860 helix: -4.62 (0.84), residues: 8 sheet: -0.41 (0.30), residues: 307 loop : -0.75 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 71 TYR 0.016 0.001 TYR H 105 PHE 0.014 0.001 PHE A 107 TRP 0.011 0.002 TRP A 52 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6928) covalent geometry : angle 0.53836 ( 9404) SS BOND : bond 0.00471 ( 10) SS BOND : angle 1.02406 ( 20) hydrogen bonds : bond 0.03188 ( 199) hydrogen bonds : angle 5.66548 ( 567) link_BETA1-4 : bond 0.00365 ( 1) link_BETA1-4 : angle 0.81160 ( 3) link_NAG-ASN : bond 0.00468 ( 1) link_NAG-ASN : angle 1.02143 ( 3) *********************** 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 165 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8168 (OUTLIER) cc_final: 0.7595 (p) REVERT: E 501 ASN cc_start: 0.8188 (t0) cc_final: 0.7979 (t0) REVERT: H 82 MET cc_start: 0.7740 (mtm) cc_final: 0.7514 (mtp) REVERT: L 4 MET cc_start: 0.7006 (tpp) cc_final: 0.6576 (mmm) REVERT: D 81 GLN cc_start: 0.7612 (tp40) cc_final: 0.7181 (tt0) outliers start: 29 outliers final: 27 residues processed: 154 average time/residue: 0.0759 time to fit residues: 15.9719 Evaluate side-chains 161 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR 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 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 23 ARG 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 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 67 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 0 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.136102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119965 restraints weight = 9929.384| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.65 r_work: 0.3475 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1946 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= 0.216 Angle : 0.585 6.009 9430 Z= 0.312 Chirality : 0.042 0.145 1016 Planarity : 0.005 0.055 1209 Dihedral : 4.954 30.039 1013 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.02 % Favored : 91.74 % Rotamer: Outliers : 4.53 % Allowed : 20.05 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 aren not related in a simple way. whole: -1.14 (0.28), residues: 860 helix: -4.40 (0.62), residues: 15 sheet: -0.47 (0.30), residues: 306 loop : -0.80 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 71 TYR 0.019 0.002 TYR H 105 PHE 0.018 0.002 PHE A 107 TRP 0.013 0.002 TRP F 36 HIS 0.005 0.002 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 6928) covalent geometry : angle 0.58207 ( 9404) SS BOND : bond 0.00613 ( 10) SS BOND : angle 1.26313 ( 20) hydrogen bonds : bond 0.03596 ( 199) hydrogen bonds : angle 5.85995 ( 567) link_BETA1-4 : bond 0.00300 ( 1) link_BETA1-4 : angle 0.85374 ( 3) link_NAG-ASN : bond 0.00502 ( 1) link_NAG-ASN : angle 1.37654 ( 3) *********************** 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 167 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7578 (p) REVERT: E 501 ASN cc_start: 0.8090 (t0) cc_final: 0.7851 (t0) REVERT: H 82 MET cc_start: 0.7595 (mtm) cc_final: 0.7359 (mtp) REVERT: D 81 GLN cc_start: 0.7576 (tp40) cc_final: 0.7120 (tt0) outliers start: 33 outliers final: 30 residues processed: 155 average time/residue: 0.0740 time to fit residues: 16.0741 Evaluate side-chains 165 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR 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 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 430 THR 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 48 VAL 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 37 GLN Chi-restraints excluded: chain L residue 67 SER 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 66 SER Chi-restraints excluded: chain F residue 90 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 4 optimal weight: 0.0570 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.136744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120671 restraints weight = 9878.772| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.64 r_work: 0.3499 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6940 Z= 0.146 Angle : 0.554 8.616 9430 Z= 0.293 Chirality : 0.041 0.151 1016 Planarity : 0.005 0.056 1209 Dihedral : 4.737 28.916 1013 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.51 % Favored : 93.26 % Rotamer: Outliers : 4.12 % Allowed : 20.05 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 aren not related in a simple way. whole: -1.10 (0.28), residues: 860 helix: -4.52 (0.50), residues: 15 sheet: -0.42 (0.30), residues: 314 loop : -0.77 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 71 TYR 0.016 0.001 TYR H 105 PHE 0.014 0.001 PHE A 107 TRP 0.011 0.002 TRP A 52 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6928) covalent geometry : angle 0.55211 ( 9404) SS BOND : bond 0.00463 ( 10) SS BOND : angle 1.17835 ( 20) hydrogen bonds : bond 0.03165 ( 199) hydrogen bonds : angle 5.68223 ( 567) link_BETA1-4 : bond 0.00312 ( 1) link_BETA1-4 : angle 0.81776 ( 3) link_NAG-ASN : bond 0.00477 ( 1) link_NAG-ASN : angle 1.00048 ( 3) *********************** 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 168 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8085 (OUTLIER) cc_final: 0.7517 (p) REVERT: E 501 ASN cc_start: 0.8087 (t0) cc_final: 0.7845 (t0) REVERT: H 82 MET cc_start: 0.7573 (mtm) cc_final: 0.7345 (mtp) REVERT: L 4 MET cc_start: 0.6941 (mmm) cc_final: 0.6602 (mmm) REVERT: D 81 GLN cc_start: 0.7560 (tp40) cc_final: 0.7108 (tt0) outliers start: 30 outliers final: 28 residues processed: 154 average time/residue: 0.0765 time to fit residues: 16.3691 Evaluate side-chains 166 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR 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 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 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 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 67 SER 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 66 SER Chi-restraints excluded: chain F residue 90 GLN 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 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3835 r_free = 0.3835 target = 0.136722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.120636 restraints weight = 9774.069| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.64 r_work: 0.3497 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6940 Z= 0.156 Angle : 0.555 7.772 9430 Z= 0.294 Chirality : 0.041 0.152 1016 Planarity : 0.005 0.056 1209 Dihedral : 4.697 29.016 1013 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.21 % Favored : 92.56 % Rotamer: Outliers : 4.26 % Allowed : 20.19 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 aren not related in a simple way. whole: -1.08 (0.28), residues: 860 helix: -4.53 (0.49), residues: 15 sheet: -0.41 (0.30), residues: 313 loop : -0.76 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 71 TYR 0.017 0.001 TYR H 105 PHE 0.014 0.001 PHE A 107 TRP 0.011 0.002 TRP D 107 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6928) covalent geometry : angle 0.55220 ( 9404) SS BOND : bond 0.00485 ( 10) SS BOND : angle 1.22116 ( 20) hydrogen bonds : bond 0.03201 ( 199) hydrogen bonds : angle 5.65980 ( 567) link_BETA1-4 : bond 0.00352 ( 1) link_BETA1-4 : angle 0.86018 ( 3) link_NAG-ASN : bond 0.00456 ( 1) link_NAG-ASN : angle 1.06772 ( 3) ********************** 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 170 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 THR cc_start: 0.8092 (OUTLIER) cc_final: 0.7524 (p) REVERT: E 501 ASN cc_start: 0.8089 (t0) cc_final: 0.7840 (t0) REVERT: H 82 MET cc_start: 0.7552 (mtm) cc_final: 0.7331 (mtp) REVERT: D 81 GLN cc_start: 0.7554 (tp40) cc_final: 0.7102 (tt0) outliers start: 31 outliers final: 28 residues processed: 156 average time/residue: 0.0785 time to fit residues: 17.0179 Evaluate side-chains 168 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 28 THR 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 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 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 67 SER 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 66 SER Chi-restraints excluded: chain F residue 90 GLN 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 47 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.137396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.121308 restraints weight = 9821.122| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.64 r_work: 0.3507 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6940 Z= 0.136 Angle : 0.556 9.219 9430 Z= 0.290 Chirality : 0.041 0.151 1016 Planarity : 0.005 0.057 1209 Dihedral : 4.583 28.370 1013 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.16 % Favored : 93.60 % Rotamer: Outliers : 4.26 % Allowed : 20.60 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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 aren not related in a simple way. whole: -1.07 (0.28), residues: 860 helix: -4.61 (0.44), residues: 15 sheet: -0.39 (0.30), residues: 313 loop : -0.76 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 71 TYR 0.015 0.001 TYR H 105 PHE 0.013 0.001 PHE A 107 TRP 0.010 0.001 TRP D 107 HIS 0.004 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6928) covalent geometry : angle 0.55414 ( 9404) SS BOND : bond 0.00457 ( 10) SS BOND : angle 1.07499 ( 20) hydrogen bonds : bond 0.03038 ( 199) hydrogen bonds : angle 5.57369 ( 567) link_BETA1-4 : bond 0.00348 ( 1) link_BETA1-4 : angle 0.85031 ( 3) link_NAG-ASN : bond 0.00448 ( 1) link_NAG-ASN : angle 0.93375 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1717.89 seconds wall clock time: 30 minutes 13.69 seconds (1813.69 seconds total)