Starting phenix.real_space_refine on Thu Jul 2 16:35:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxj_36703/07_2026/8jxj_36703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxj_36703/07_2026/8jxj_36703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jxj_36703/07_2026/8jxj_36703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxj_36703/07_2026/8jxj_36703.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jxj_36703/07_2026/8jxj_36703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxj_36703/07_2026/8jxj_36703.map" } resolution = 3.9 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 98 5.16 5 C 5650 2.51 5 N 1536 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9158 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4461 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 31, 'TRANS': 538} Chain breaks: 1 Chain: "B" Number of atoms: 4461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4461 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 31, 'TRANS': 538} Chain breaks: 1 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 14 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 14 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.20, per 1000 atoms: 0.24 Number of scatterers: 9158 At special positions: 0 Unit cell: (148.155, 152.388, 79.016, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 98 16.00 O 1866 8.00 N 1536 7.00 C 5650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 40 " distance=2.03 Simple disulfide: pdb=" SG CYS A 35 " - pdb=" SG CYS A 53 " distance=2.04 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 62 " distance=2.03 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A3930 " - pdb=" SG CYS A3942 " distance=2.03 Simple disulfide: pdb=" SG CYS A3937 " - pdb=" SG CYS A3955 " distance=2.03 Simple disulfide: pdb=" SG CYS A3949 " - pdb=" SG CYS A3964 " distance=2.03 Simple disulfide: pdb=" SG CYS A3972 " - pdb=" SG CYS A3981 " distance=2.03 Simple disulfide: pdb=" SG CYS A3977 " - pdb=" SG CYS A3991 " distance=2.03 Simple disulfide: pdb=" SG CYS A3993 " - pdb=" SG CYS A4007 " distance=2.03 Simple disulfide: pdb=" SG CYS A4013 " - pdb=" SG CYS A4023 " distance=2.03 Simple disulfide: pdb=" SG CYS A4019 " - pdb=" SG CYS A4032 " distance=2.03 Simple disulfide: pdb=" SG CYS A4034 " - pdb=" SG CYS A4049 " distance=2.03 Simple disulfide: pdb=" SG CYS A4336 " - pdb=" SG CYS A4344 " distance=2.03 Simple disulfide: pdb=" SG CYS A4340 " - pdb=" SG CYS A4353 " distance=2.03 Simple disulfide: pdb=" SG CYS A4355 " - pdb=" SG CYS A4369 " distance=2.03 Simple disulfide: pdb=" SG CYS A4383 " - pdb=" SG CYS A4391 " distance=2.03 Simple disulfide: pdb=" SG CYS A4385 " - pdb=" SG CYS A4401 " distance=2.03 Simple disulfide: pdb=" SG CYS A4403 " - pdb=" SG CYS A4412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 40 " distance=2.03 Simple disulfide: pdb=" SG CYS B 35 " - pdb=" SG CYS B 53 " distance=2.04 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS B 62 " distance=2.03 Simple disulfide: pdb=" SG CYS B 67 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 93 " distance=2.04 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B3930 " - pdb=" SG CYS B3942 " distance=2.03 Simple disulfide: pdb=" SG CYS B3937 " - pdb=" SG CYS B3955 " distance=2.03 Simple disulfide: pdb=" SG CYS B3949 " - pdb=" SG CYS B3964 " distance=2.03 Simple disulfide: pdb=" SG CYS B3972 " - pdb=" SG CYS B3981 " distance=2.03 Simple disulfide: pdb=" SG CYS B3977 " - pdb=" SG CYS B3991 " distance=2.03 Simple disulfide: pdb=" SG CYS B3993 " - pdb=" SG CYS B4007 " distance=2.03 Simple disulfide: pdb=" SG CYS B4013 " - pdb=" SG CYS B4023 " distance=2.03 Simple disulfide: pdb=" SG CYS B4019 " - pdb=" SG CYS B4032 " distance=2.03 Simple disulfide: pdb=" SG CYS B4034 " - pdb=" SG CYS B4049 " distance=2.03 Simple disulfide: pdb=" SG CYS B4336 " - pdb=" SG CYS B4344 " distance=2.03 Simple disulfide: pdb=" SG CYS B4340 " - pdb=" SG CYS B4353 " distance=2.03 Simple disulfide: pdb=" SG CYS B4355 " - pdb=" SG CYS B4369 " distance=2.03 Simple disulfide: pdb=" SG CYS B4383 " - pdb=" SG CYS B4391 " distance=2.03 Simple disulfide: pdb=" SG CYS B4385 " - pdb=" SG CYS B4401 " distance=2.03 Simple disulfide: pdb=" SG CYS B4403 " - pdb=" SG CYS B4412 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " " BMA E 3 " - " MAN E 5 " BETA1-3 " NAG E 1 " - " NAG E 2 " " NAG F 2 " - " BMA F 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A4701 " - " ASN A3980 " " NAG B4701 " - " ASN B3980 " " NAG C 1 " - " ASN A4070 " " NAG D 1 " - " ASN A4329 " " NAG E 1 " - " ASN B4070 " " NAG F 1 " - " ASN B4329 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 337.2 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 30 sheets defined 4.0% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 3946 through 3948 No H-bonds generated for 'chain 'A' and resid 3946 through 3948' Processing helix chain 'A' and resid 3971 through 3975 Processing helix chain 'A' and resid 4324 through 4328 removed outlier: 3.657A pdb=" N TYR A4328 " --> pdb=" O GLN A4325 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 96 through 101 Processing helix chain 'B' and resid 3946 through 3948 No H-bonds generated for 'chain 'B' and resid 3946 through 3948' Processing helix chain 'B' and resid 3958 through 3962 removed outlier: 3.602A pdb=" N THR B3962 " --> pdb=" O SER B3959 " (cutoff:3.500A) Processing helix chain 'B' and resid 4011 through 4015 removed outlier: 3.535A pdb=" N GLU B4015 " --> pdb=" O GLU B4012 " (cutoff:3.500A) Processing helix chain 'B' and resid 4324 through 4328 removed outlier: 3.653A pdb=" N TYR B4328 " --> pdb=" O GLN B4325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 73 Processing sheet with id=AA3, first strand: chain 'A' and resid 3934 through 3935 removed outlier: 3.700A pdb=" N ILE A3943 " --> pdb=" O TYR A3935 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3981 through 3984 Processing sheet with id=AA5, first strand: chain 'A' and resid 3997 through 3999 Processing sheet with id=AA6, first strand: chain 'A' and resid 4024 through 4026 Processing sheet with id=AA7, first strand: chain 'A' and resid 4038 through 4042 Processing sheet with id=AA8, first strand: chain 'A' and resid 4076 through 4077 Processing sheet with id=AA9, first strand: chain 'A' and resid 4086 through 4092 removed outlier: 4.206A pdb=" N THR A4088 " --> pdb=" O THR A4106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 4148 through 4152 removed outlier: 4.056A pdb=" N GLY A4148 " --> pdb=" O SER A4161 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A4167 " --> pdb=" O ASP A4162 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE A4168 " --> pdb=" O LEU A4181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 4189 through 4195 removed outlier: 3.956A pdb=" N ALA A4191 " --> pdb=" O THR A4204 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE A4212 " --> pdb=" O LEU A4225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 4235 through 4239 removed outlier: 3.561A pdb=" N GLY A4235 " --> pdb=" O SER A4249 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A4249 " --> pdb=" O GLY A4235 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA A4258 " --> pdb=" O LEU A4268 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU A4268 " --> pdb=" O ALA A4258 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 4276 through 4282 removed outlier: 4.456A pdb=" N SER A4278 " --> pdb=" O VAL A4289 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A4289 " --> pdb=" O SER A4278 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ARG A4298 " --> pdb=" O LYS A4309 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS A4309 " --> pdb=" O ARG A4298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 4343 through 4347 removed outlier: 3.509A pdb=" N LEU A4343 " --> pdb=" O ALA A4354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 4390 through 4393 Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 34 Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AB9, first strand: chain 'B' and resid 3934 through 3936 Processing sheet with id=AC1, first strand: chain 'B' and resid 3964 through 3965 removed outlier: 3.838A pdb=" N ASN B3980 " --> pdb=" O SER B3992 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 3997 through 3999 Processing sheet with id=AC3, first strand: chain 'B' and resid 4024 through 4026 Processing sheet with id=AC4, first strand: chain 'B' and resid 4039 through 4043 Processing sheet with id=AC5, first strand: chain 'B' and resid 4076 through 4077 removed outlier: 3.509A pdb=" N ARG B4321 " --> pdb=" O LEU B4059 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 4086 through 4092 removed outlier: 4.627A pdb=" N THR B4088 " --> pdb=" O THR B4106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 4146 through 4152 removed outlier: 3.656A pdb=" N GLY B4148 " --> pdb=" O SER B4161 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B4167 " --> pdb=" O ASP B4162 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE B4168 " --> pdb=" O LEU B4181 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 4189 through 4195 removed outlier: 4.278A pdb=" N ALA B4191 " --> pdb=" O THR B4204 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B4212 " --> pdb=" O LEU B4225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 4236 through 4239 removed outlier: 3.521A pdb=" N ARG B4245 " --> pdb=" O ASP B4239 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA B4258 " --> pdb=" O LEU B4268 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU B4268 " --> pdb=" O ALA B4258 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 4276 through 4282 removed outlier: 4.219A pdb=" N SER B4278 " --> pdb=" O VAL B4289 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B4295 " --> pdb=" O ALA B4290 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B4296 " --> pdb=" O VAL B4310 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 4343 through 4346 Processing sheet with id=AD3, first strand: chain 'B' and resid 4392 through 4393 214 hydrogen bonds defined for protein. 516 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: 1.40 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3029 1.34 - 1.46: 2002 1.46 - 1.58: 4217 1.58 - 1.70: 0 1.70 - 1.82: 112 Bond restraints: 9360 Sorted by residual: bond pdb=" N PHE B4125 " pdb=" CA PHE B4125 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.15e-02 7.56e+03 1.00e+01 bond pdb=" N LEU B3958 " pdb=" CA LEU B3958 " ideal model delta sigma weight residual 1.459 1.497 -0.039 1.32e-02 5.74e+03 8.59e+00 bond pdb=" N ASP B4284 " pdb=" CA ASP B4284 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.23e+00 bond pdb=" N GLU A4126 " pdb=" CA GLU A4126 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.80e+00 bond pdb=" CA SER A4127 " pdb=" CB SER A4127 " ideal model delta sigma weight residual 1.533 1.493 0.039 1.65e-02 3.67e+03 5.68e+00 ... (remaining 9355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 12133 1.81 - 3.61: 470 3.61 - 5.42: 72 5.42 - 7.23: 10 7.23 - 9.03: 3 Bond angle restraints: 12688 Sorted by residual: angle pdb=" N ASN B4124 " pdb=" CA ASN B4124 " pdb=" C ASN B4124 " ideal model delta sigma weight residual 113.18 106.83 6.35 1.21e+00 6.83e-01 2.75e+01 angle pdb=" C CYS A3937 " pdb=" CA CYS A3937 " pdb=" CB CYS A3937 " ideal model delta sigma weight residual 117.23 110.18 7.05 1.36e+00 5.41e-01 2.69e+01 angle pdb=" C GLU B3978 " pdb=" N GLN B3979 " pdb=" CA GLN B3979 " ideal model delta sigma weight residual 122.44 116.81 5.63 1.19e+00 7.06e-01 2.24e+01 angle pdb=" N ASN A4124 " pdb=" CA ASN A4124 " pdb=" C ASN A4124 " ideal model delta sigma weight residual 111.28 106.50 4.78 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N VAL B4367 " pdb=" CA VAL B4367 " pdb=" C VAL B4367 " ideal model delta sigma weight residual 113.71 109.55 4.16 9.50e-01 1.11e+00 1.91e+01 ... (remaining 12683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.74: 5477 23.74 - 47.47: 391 47.47 - 71.21: 51 71.21 - 94.94: 37 94.94 - 118.68: 16 Dihedral angle restraints: 5972 sinusoidal: 2690 harmonic: 3282 Sorted by residual: dihedral pdb=" CB CYS A3972 " pdb=" SG CYS A3972 " pdb=" SG CYS A3981 " pdb=" CB CYS A3981 " ideal model delta sinusoidal sigma weight residual -86.00 -163.37 77.37 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS B4034 " pdb=" SG CYS B4034 " pdb=" SG CYS B4049 " pdb=" CB CYS B4049 " ideal model delta sinusoidal sigma weight residual 93.00 161.21 -68.21 1 1.00e+01 1.00e-02 6.04e+01 dihedral pdb=" CB CYS A4385 " pdb=" SG CYS A4385 " pdb=" SG CYS A4401 " pdb=" CB CYS A4401 " ideal model delta sinusoidal sigma weight residual 93.00 161.10 -68.10 1 1.00e+01 1.00e-02 6.02e+01 ... (remaining 5969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1065 0.056 - 0.112: 263 0.112 - 0.167: 35 0.167 - 0.223: 6 0.223 - 0.279: 5 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C1 MAN C 4 " pdb=" O3 BMA C 3 " pdb=" C2 MAN C 4 " pdb=" O5 MAN C 4 " both_signs ideal model delta sigma weight residual False 2.40 2.13 0.27 2.00e-02 2.50e+03 1.80e+02 chirality pdb=" C1 NAG E 2 " pdb=" O3 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.57e+01 chirality pdb=" C1 BMA F 3 " pdb=" O3 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.36e+01 ... (remaining 1371 not shown) Planarity restraints: 1670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C 1 " 0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.119 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.531 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.331 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG E 2 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.156 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.505 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.271 2.00e-02 2.50e+03 2.28e-01 6.53e+02 pdb=" C7 NAG F 2 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.178 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.388 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.009 2.00e-02 2.50e+03 ... (remaining 1667 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 350 2.69 - 3.25: 9398 3.25 - 3.80: 14385 3.80 - 4.35: 18868 4.35 - 4.90: 30700 Nonbonded interactions: 73701 Sorted by model distance: nonbonded pdb=" OD1 ASP B3950 " pdb="CA CA B4704 " model vdw 2.143 3.250 nonbonded pdb=" OD1 ASP A 48 " pdb="CA CA A4702 " model vdw 2.172 3.250 nonbonded pdb=" OD2 ASP B3960 " pdb="CA CA B4704 " model vdw 2.177 3.250 nonbonded pdb=" OD2 ASP A 58 " pdb="CA CA A4702 " model vdw 2.186 3.250 nonbonded pdb=" O VAL B3952 " pdb="CA CA B4704 " model vdw 2.187 3.250 ... (remaining 73696 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.680 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.004 0.044 9420 Z= 0.229 Angle : 0.818 9.033 12826 Z= 0.443 Chirality : 0.051 0.279 1374 Planarity : 0.013 0.298 1664 Dihedral : 17.725 118.679 3746 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 1.79 % Allowed : 17.93 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.25), residues: 1132 helix: -4.57 (0.61), residues: 25 sheet: -0.49 (0.34), residues: 247 loop : -0.82 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 46 TYR 0.021 0.001 TYR B4411 PHE 0.018 0.001 PHE B 33 TRP 0.013 0.001 TRP A4297 HIS 0.005 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.23 ( 9360) covalent geometry : angle 0.79827 / 0.44 (12688) SS BOND : bond 0.00232 / 0.16 ( 42) SS BOND : angle 1.05573 / 0.72 ( 84) hydrogen bonds : bond 0.24369 / 16.45 ( 214) hydrogen bonds : angle 10.46030 / 7.30 ( 516) link_ALPHA1-3 : bond 0.01092 / 0.52 ( 2) link_ALPHA1-3 : angle 1.51381 / 0.80 ( 6) link_ALPHA1-6 : bond 0.00547 / 0.26 ( 2) link_ALPHA1-6 : angle 0.58100 / 0.30 ( 6) link_BETA1-3 : bond 0.00467 / 0.24 ( 2) link_BETA1-3 : angle 4.19848 / 2.33 ( 6) link_BETA1-4 : bond 0.00632 / 0.39 ( 6) link_BETA1-4 : angle 1.74612 / 1.11 ( 18) link_NAG-ASN : bond 0.00625 / 0.33 ( 6) link_NAG-ASN : angle 3.60778 / 2.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4308 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7515 (tm-30) REVERT: B 39 TYR cc_start: 0.7767 (t80) cc_final: 0.7519 (t80) REVERT: B 4144 MET cc_start: 0.8222 (mtp) cc_final: 0.7627 (mtt) outliers start: 18 outliers final: 15 residues processed: 76 average time/residue: 0.0685 time to fit residues: 8.6252 Evaluate side-chains 68 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4377 VAL Chi-restraints excluded: chain A residue 4378 THR Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3971 THR Chi-restraints excluded: chain B residue 4130 ASN Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4339 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN A3941 ASN A4110 GLN A4131 ASN A4206 GLN A4221 HIS A4342 HIS B4131 ASN B4234 ASN ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.119320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.084005 restraints weight = 18118.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.086100 restraints weight = 10359.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.087387 restraints weight = 7365.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088136 restraints weight = 6026.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088449 restraints weight = 5388.927| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9420 Z= 0.187 Angle : 0.742 12.177 12826 Z= 0.371 Chirality : 0.049 0.335 1374 Planarity : 0.005 0.048 1664 Dihedral : 13.212 103.849 1616 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.59 % Allowed : 16.24 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.25), residues: 1132 helix: -4.51 (0.65), residues: 25 sheet: -0.95 (0.32), residues: 259 loop : -0.91 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4119 TYR 0.017 0.002 TYR B4411 PHE 0.012 0.001 PHE A4323 TRP 0.016 0.001 TRP A4297 HIS 0.005 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 9360) covalent geometry : angle 0.71544 / 0.37 (12688) SS BOND : bond 0.00375 / 0.28 ( 42) SS BOND : angle 1.05997 / 0.70 ( 84) hydrogen bonds : bond 0.04868 / 3.20 ( 214) hydrogen bonds : angle 8.02481 / 5.51 ( 516) link_ALPHA1-3 : bond 0.02361 / 1.17 ( 2) link_ALPHA1-3 : angle 1.55967 / 0.85 ( 6) link_ALPHA1-6 : bond 0.00789 / 0.38 ( 2) link_ALPHA1-6 : angle 1.37850 / 0.71 ( 6) link_BETA1-3 : bond 0.01238 / 0.64 ( 2) link_BETA1-3 : angle 5.86651 / 3.31 ( 6) link_BETA1-4 : bond 0.01051 / 0.63 ( 6) link_BETA1-4 : angle 2.40283 / 1.38 ( 18) link_NAG-ASN : bond 0.00787 / 0.42 ( 6) link_NAG-ASN : angle 2.70956 / 1.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3998 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7671 (mttp) REVERT: A 4217 MET cc_start: 0.8617 (mpt) cc_final: 0.7846 (mpt) REVERT: A 4386 MET cc_start: 0.7971 (pmm) cc_final: 0.7699 (pmm) REVERT: B 91 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6977 (tttp) REVERT: B 4039 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7866 (mtpt) REVERT: B 4041 MET cc_start: 0.6003 (tpt) cc_final: 0.5671 (tpt) REVERT: B 4045 TYR cc_start: 0.5827 (OUTLIER) cc_final: 0.5024 (t80) REVERT: B 4144 MET cc_start: 0.7336 (mtp) cc_final: 0.7095 (mtt) REVERT: B 4307 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8301 (mtpm) outliers start: 36 outliers final: 19 residues processed: 88 average time/residue: 0.0949 time to fit residues: 12.0997 Evaluate side-chains 72 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 3998 LYS Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4377 VAL Chi-restraints excluded: chain A residue 4401 CYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 3971 THR Chi-restraints excluded: chain B residue 4039 LYS Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4045 TYR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4307 LYS Chi-restraints excluded: chain B residue 4339 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 76 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4299 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 = 0.3685 r_free = 0.3685 target = 0.118544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083620 restraints weight = 18024.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085817 restraints weight = 10055.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087194 restraints weight = 7000.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088040 restraints weight = 5643.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088383 restraints weight = 4983.215| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9420 Z= 0.188 Angle : 0.717 11.096 12826 Z= 0.359 Chirality : 0.050 0.284 1374 Planarity : 0.005 0.060 1664 Dihedral : 11.311 96.485 1610 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 4.58 % Allowed : 16.04 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.25), residues: 1132 helix: -4.43 (0.80), residues: 19 sheet: -1.22 (0.29), residues: 300 loop : -0.96 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B4067 TYR 0.015 0.002 TYR A4079 PHE 0.010 0.001 PHE A4323 TRP 0.013 0.001 TRP A4297 HIS 0.006 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 9360) covalent geometry : angle 0.69378 / 0.35 (12688) SS BOND : bond 0.00342 / 0.25 ( 42) SS BOND : angle 1.01140 / 0.66 ( 84) hydrogen bonds : bond 0.04066 / 2.64 ( 214) hydrogen bonds : angle 7.54074 / 5.16 ( 516) link_ALPHA1-3 : bond 0.02288 / 1.13 ( 2) link_ALPHA1-3 : angle 1.56577 / 0.79 ( 6) link_ALPHA1-6 : bond 0.00955 / 0.47 ( 2) link_ALPHA1-6 : angle 1.83720 / 0.94 ( 6) link_BETA1-3 : bond 0.01497 / 0.77 ( 2) link_BETA1-3 : angle 5.28321 / 2.99 ( 6) link_BETA1-4 : bond 0.00865 / 0.58 ( 6) link_BETA1-4 : angle 2.37419 / 1.36 ( 18) link_NAG-ASN : bond 0.00667 / 0.35 ( 6) link_NAG-ASN : angle 2.34084 / 1.43 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 56 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: A 4217 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7846 (mpt) REVERT: B 91 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6922 (tttp) REVERT: B 4021 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6597 (mp10) REVERT: B 4039 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7800 (mtpt) REVERT: B 4041 MET cc_start: 0.5983 (tpt) cc_final: 0.5637 (tpt) REVERT: B 4045 TYR cc_start: 0.5818 (OUTLIER) cc_final: 0.5242 (t80) REVERT: B 4144 MET cc_start: 0.7380 (mtp) cc_final: 0.6947 (mtt) REVERT: B 4307 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8201 (mtpm) outliers start: 46 outliers final: 23 residues processed: 93 average time/residue: 0.0809 time to fit residues: 11.4613 Evaluate side-chains 80 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4129 SER Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4377 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 3971 THR Chi-restraints excluded: chain B residue 4021 GLN Chi-restraints excluded: chain B residue 4039 LYS Chi-restraints excluded: chain B residue 4045 TYR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4255 VAL Chi-restraints excluded: chain B residue 4307 LYS Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4385 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 87 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 109 optimal weight: 0.4980 chunk 70 optimal weight: 6.9990 chunk 53 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B4008 GLN ** B4299 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.120163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.085775 restraints weight = 18365.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087408 restraints weight = 10177.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.088221 restraints weight = 7665.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088876 restraints weight = 5940.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.088937 restraints weight = 5809.034| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9420 Z= 0.135 Angle : 0.679 10.344 12826 Z= 0.336 Chirality : 0.049 0.268 1374 Planarity : 0.004 0.046 1664 Dihedral : 9.486 76.603 1609 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.48 % Allowed : 16.43 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.25), residues: 1132 helix: -4.37 (0.83), residues: 19 sheet: -1.08 (0.31), residues: 285 loop : -0.95 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B4067 TYR 0.016 0.001 TYR A4079 PHE 0.009 0.001 PHE A4323 TRP 0.013 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 9360) covalent geometry : angle 0.65591 / 0.33 (12688) SS BOND : bond 0.00294 / 0.22 ( 42) SS BOND : angle 0.91715 / 0.61 ( 84) hydrogen bonds : bond 0.03388 / 2.18 ( 214) hydrogen bonds : angle 7.22268 / 4.94 ( 516) link_ALPHA1-3 : bond 0.02097 / 1.04 ( 2) link_ALPHA1-3 : angle 1.93647 / 0.99 ( 6) link_ALPHA1-6 : bond 0.00809 / 0.39 ( 2) link_ALPHA1-6 : angle 2.13001 / 1.14 ( 6) link_BETA1-3 : bond 0.01210 / 0.62 ( 2) link_BETA1-3 : angle 4.86138 / 2.77 ( 6) link_BETA1-4 : bond 0.00891 / 0.60 ( 6) link_BETA1-4 : angle 2.10727 / 1.19 ( 18) link_NAG-ASN : bond 0.00791 / 0.44 ( 6) link_NAG-ASN : angle 2.51744 / 1.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6745 (mtm-85) REVERT: A 52 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6571 (m-30) REVERT: A 4217 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7881 (mpt) REVERT: B 91 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6857 (tttp) REVERT: B 4039 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7783 (mtpt) REVERT: B 4041 MET cc_start: 0.6409 (tpt) cc_final: 0.6012 (tpt) REVERT: B 4045 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.5660 (t80) REVERT: B 4144 MET cc_start: 0.7353 (mtp) cc_final: 0.7113 (mtt) REVERT: B 4174 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7294 (p0) REVERT: B 4187 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6636 (m-30) REVERT: B 4307 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8104 (mtpm) outliers start: 45 outliers final: 25 residues processed: 102 average time/residue: 0.0776 time to fit residues: 11.9908 Evaluate side-chains 89 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4201 MET Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 4005 ASN Chi-restraints excluded: chain B residue 4008 GLN Chi-restraints excluded: chain B residue 4039 LYS Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4045 TYR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4172 THR Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4187 ASP Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4255 VAL Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4307 LYS Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4385 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.0770 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 95 optimal weight: 0.4980 chunk 29 optimal weight: 0.0670 chunk 96 optimal weight: 0.4980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4342 HIS B4299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.120894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.086844 restraints weight = 18173.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.088479 restraints weight = 10176.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.089092 restraints weight = 8050.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.089522 restraints weight = 6295.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.089721 restraints weight = 6105.523| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9420 Z= 0.121 Angle : 0.653 9.807 12826 Z= 0.325 Chirality : 0.047 0.271 1374 Planarity : 0.004 0.046 1664 Dihedral : 7.760 50.159 1607 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 4.28 % Allowed : 17.23 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.25), residues: 1132 helix: -4.45 (0.66), residues: 25 sheet: -1.07 (0.31), residues: 285 loop : -0.88 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B4119 TYR 0.014 0.001 TYR A4079 PHE 0.012 0.001 PHE B4038 TRP 0.014 0.001 TRP A4297 HIS 0.003 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9360) covalent geometry : angle 0.63148 / 0.32 (12688) SS BOND : bond 0.00293 / 0.22 ( 42) SS BOND : angle 0.84922 / 0.56 ( 84) hydrogen bonds : bond 0.03189 / 2.03 ( 214) hydrogen bonds : angle 6.99083 / 4.79 ( 516) link_ALPHA1-3 : bond 0.01735 / 0.87 ( 2) link_ALPHA1-3 : angle 2.18585 / 1.11 ( 6) link_ALPHA1-6 : bond 0.00654 / 0.32 ( 2) link_ALPHA1-6 : angle 1.85746 / 0.98 ( 6) link_BETA1-3 : bond 0.01274 / 0.65 ( 2) link_BETA1-3 : angle 4.60306 / 2.62 ( 6) link_BETA1-4 : bond 0.00794 / 0.53 ( 6) link_BETA1-4 : angle 2.03249 / 1.15 ( 18) link_NAG-ASN : bond 0.00672 / 0.37 ( 6) link_NAG-ASN : angle 2.41244 / 1.44 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 66 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6574 (mtm-85) REVERT: A 52 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6549 (m-30) REVERT: A 3990 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7171 (tt) REVERT: A 4217 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.7870 (mpt) REVERT: B 91 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6818 (tttp) REVERT: B 4041 MET cc_start: 0.6003 (tpt) cc_final: 0.5625 (tpt) REVERT: B 4119 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7003 (ptp-170) REVERT: B 4174 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7435 (p0) REVERT: B 4307 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8196 (mtpm) REVERT: B 4384 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6859 (ttp80) outliers start: 43 outliers final: 22 residues processed: 100 average time/residue: 0.0956 time to fit residues: 13.8517 Evaluate side-chains 91 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 60 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 3990 ILE Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4201 MET Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4274 MET Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4119 ARG Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4255 VAL Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4307 LYS Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4384 ARG Chi-restraints excluded: chain B residue 4385 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4342 HIS B4008 GLN ** B4299 GLN ** 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 = 0.3673 r_free = 0.3673 target = 0.117624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083446 restraints weight = 18247.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.085450 restraints weight = 10612.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086713 restraints weight = 7572.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.087491 restraints weight = 6201.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087841 restraints weight = 5516.665| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9420 Z= 0.228 Angle : 0.710 12.156 12826 Z= 0.354 Chirality : 0.048 0.260 1374 Planarity : 0.005 0.044 1664 Dihedral : 7.705 50.945 1607 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 4.48 % Allowed : 16.53 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.25), residues: 1132 helix: -4.49 (0.64), residues: 25 sheet: -1.29 (0.29), residues: 305 loop : -0.99 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B4067 TYR 0.018 0.002 TYR A4079 PHE 0.010 0.002 PHE A4361 TRP 0.011 0.002 TRP B4248 HIS 0.006 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 ( 9360) covalent geometry : angle 0.69035 / 0.35 (12688) SS BOND : bond 0.00347 / 0.25 ( 42) SS BOND : angle 0.90658 / 0.60 ( 84) hydrogen bonds : bond 0.03621 / 2.34 ( 214) hydrogen bonds : angle 7.04205 / 4.85 ( 516) link_ALPHA1-3 : bond 0.01918 / 0.97 ( 2) link_ALPHA1-3 : angle 1.96474 / 1.01 ( 6) link_ALPHA1-6 : bond 0.00265 / 0.13 ( 2) link_ALPHA1-6 : angle 2.03747 / 1.03 ( 6) link_BETA1-3 : bond 0.01188 / 0.60 ( 2) link_BETA1-3 : angle 4.29963 / 2.42 ( 6) link_BETA1-4 : bond 0.00698 / 0.47 ( 6) link_BETA1-4 : angle 2.12031 / 1.20 ( 18) link_NAG-ASN : bond 0.00627 / 0.32 ( 6) link_NAG-ASN : angle 2.43349 / 1.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 58 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6652 (mtm-85) REVERT: A 52 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.6802 (m-30) REVERT: A 3990 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6819 (tt) REVERT: A 4217 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7941 (mpt) REVERT: B 91 LYS cc_start: 0.7231 (OUTLIER) cc_final: 0.6903 (tttp) REVERT: B 4174 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7416 (p0) REVERT: B 4187 ASP cc_start: 0.6753 (OUTLIER) cc_final: 0.6516 (m-30) REVERT: B 4384 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7178 (ttp80) outliers start: 45 outliers final: 28 residues processed: 91 average time/residue: 0.0833 time to fit residues: 11.5544 Evaluate side-chains 90 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 54 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 3931 THR Chi-restraints excluded: chain A residue 3990 ILE Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4122 ILE Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4201 MET Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4274 MET Chi-restraints excluded: chain A residue 4326 LEU Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4377 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 4008 GLN Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4172 THR Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4187 ASP Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4255 VAL Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4384 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 0.0770 chunk 100 optimal weight: 0.5980 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B4299 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 = 0.3706 r_free = 0.3706 target = 0.120001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.085922 restraints weight = 18225.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.087600 restraints weight = 10425.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.088092 restraints weight = 8291.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088562 restraints weight = 6553.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088750 restraints weight = 6311.913| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9420 Z= 0.126 Angle : 0.655 9.687 12826 Z= 0.327 Chirality : 0.047 0.262 1374 Planarity : 0.004 0.045 1664 Dihedral : 7.278 52.714 1605 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.88 % Allowed : 17.33 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.25), residues: 1132 helix: -4.46 (0.64), residues: 25 sheet: -1.09 (0.31), residues: 285 loop : -0.93 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B4067 TYR 0.018 0.001 TYR A4079 PHE 0.009 0.001 PHE A4323 TRP 0.015 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 9360) covalent geometry : angle 0.63447 / 0.32 (12688) SS BOND : bond 0.00274 / 0.20 ( 42) SS BOND : angle 0.95311 / 0.64 ( 84) hydrogen bonds : bond 0.03143 / 2.01 ( 214) hydrogen bonds : angle 6.89067 / 4.71 ( 516) link_ALPHA1-3 : bond 0.01832 / 0.92 ( 2) link_ALPHA1-3 : angle 2.24624 / 1.15 ( 6) link_ALPHA1-6 : bond 0.00342 / 0.16 ( 2) link_ALPHA1-6 : angle 1.76603 / 0.89 ( 6) link_BETA1-3 : bond 0.01043 / 0.54 ( 2) link_BETA1-3 : angle 4.18584 / 2.37 ( 6) link_BETA1-4 : bond 0.00679 / 0.44 ( 6) link_BETA1-4 : angle 1.87861 / 1.04 ( 18) link_NAG-ASN : bond 0.00645 / 0.35 ( 6) link_NAG-ASN : angle 2.27010 / 1.32 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8543 (pt) REVERT: A 51 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6538 (mtm-85) REVERT: A 52 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6542 (m-30) REVERT: A 4217 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7965 (mpt) REVERT: B 91 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6799 (tttp) REVERT: B 4119 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7417 (ptt180) REVERT: B 4174 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7303 (p0) REVERT: B 4187 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6627 (m-30) REVERT: B 4384 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6872 (ttp80) outliers start: 39 outliers final: 24 residues processed: 91 average time/residue: 0.0874 time to fit residues: 11.6844 Evaluate side-chains 90 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4122 ILE Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4201 MET Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4274 MET Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4119 ARG Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4187 ASP Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4255 VAL Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 4384 ARG Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4402 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 16 optimal weight: 4.9990 chunk 42 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 9 optimal weight: 0.0170 chunk 81 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4342 HIS ** B4299 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.120332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.086570 restraints weight = 18021.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087942 restraints weight = 10483.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088508 restraints weight = 8559.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.088969 restraints weight = 6792.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089107 restraints weight = 6500.202| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 9420 Z= 0.130 Angle : 0.654 10.368 12826 Z= 0.326 Chirality : 0.047 0.256 1374 Planarity : 0.004 0.045 1664 Dihedral : 7.003 53.623 1605 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.69 % Allowed : 17.23 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.25), residues: 1132 helix: -4.47 (0.63), residues: 25 sheet: -1.11 (0.31), residues: 287 loop : -0.89 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B4067 TYR 0.020 0.001 TYR A4079 PHE 0.009 0.001 PHE A4323 TRP 0.015 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9360) covalent geometry : angle 0.63296 / 0.32 (12688) SS BOND : bond 0.00286 / 0.21 ( 42) SS BOND : angle 1.18068 / 0.69 ( 84) hydrogen bonds : bond 0.03065 / 1.96 ( 214) hydrogen bonds : angle 6.88748 / 4.69 ( 516) link_ALPHA1-3 : bond 0.01672 / 0.84 ( 2) link_ALPHA1-3 : angle 2.23096 / 1.15 ( 6) link_ALPHA1-6 : bond 0.00354 / 0.17 ( 2) link_ALPHA1-6 : angle 1.75180 / 0.88 ( 6) link_BETA1-3 : bond 0.01091 / 0.55 ( 2) link_BETA1-3 : angle 3.99539 / 2.26 ( 6) link_BETA1-4 : bond 0.00668 / 0.42 ( 6) link_BETA1-4 : angle 1.77101 / 0.97 ( 18) link_NAG-ASN : bond 0.00602 / 0.33 ( 6) link_NAG-ASN : angle 2.20402 / 1.28 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8582 (pt) REVERT: A 51 ARG cc_start: 0.6880 (OUTLIER) cc_final: 0.6475 (mtm-85) REVERT: A 52 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.6645 (m-30) REVERT: A 4217 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7926 (mpt) REVERT: A 4306 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8084 (p0) REVERT: B 91 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6921 (tttp) REVERT: B 4119 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7099 (ptp-170) REVERT: B 4174 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7397 (p0) REVERT: B 4187 ASP cc_start: 0.7078 (OUTLIER) cc_final: 0.6833 (m-30) REVERT: B 4384 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6928 (ttp80) outliers start: 37 outliers final: 24 residues processed: 92 average time/residue: 0.0832 time to fit residues: 11.3009 Evaluate side-chains 93 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 59 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 3931 THR Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4122 ILE Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4201 MET Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4274 MET Chi-restraints excluded: chain A residue 4306 ASN Chi-restraints excluded: chain A residue 4326 LEU Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4119 ARG Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4172 THR Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4187 ASP Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4255 VAL Chi-restraints excluded: chain B residue 4384 ARG Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4402 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 66 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 0.2980 chunk 22 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 112 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4342 HIS ** B4299 GLN ** 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 = 0.3703 r_free = 0.3703 target = 0.119884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.084585 restraints weight = 18016.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086778 restraints weight = 10156.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088171 restraints weight = 7142.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.089020 restraints weight = 5788.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.089434 restraints weight = 5123.507| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9420 Z= 0.143 Angle : 0.652 8.686 12826 Z= 0.327 Chirality : 0.046 0.216 1374 Planarity : 0.004 0.044 1664 Dihedral : 6.871 54.941 1604 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 4.18 % Allowed : 17.23 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.25), residues: 1132 helix: -4.48 (0.62), residues: 25 sheet: -1.08 (0.31), residues: 287 loop : -0.88 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B4119 TYR 0.019 0.001 TYR A4079 PHE 0.010 0.001 PHE A4323 TRP 0.012 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9360) covalent geometry : angle 0.63312 / 0.32 (12688) SS BOND : bond 0.00276 / 0.20 ( 42) SS BOND : angle 1.10247 / 0.64 ( 84) hydrogen bonds : bond 0.03162 / 2.03 ( 214) hydrogen bonds : angle 6.82851 / 4.64 ( 516) link_ALPHA1-3 : bond 0.01654 / 0.84 ( 2) link_ALPHA1-3 : angle 2.17257 / 1.12 ( 6) link_ALPHA1-6 : bond 0.00311 / 0.15 ( 2) link_ALPHA1-6 : angle 1.71670 / 0.86 ( 6) link_BETA1-3 : bond 0.01002 / 0.51 ( 2) link_BETA1-3 : angle 3.81346 / 2.16 ( 6) link_BETA1-4 : bond 0.00623 / 0.41 ( 6) link_BETA1-4 : angle 1.72424 / 0.93 ( 18) link_NAG-ASN : bond 0.00559 / 0.30 ( 6) link_NAG-ASN : angle 2.14351 / 1.22 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 65 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8614 (pt) REVERT: A 51 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6476 (mtm-85) REVERT: A 52 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6717 (m-30) REVERT: A 3998 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.7126 (ptpp) REVERT: A 4217 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.7922 (mpt) REVERT: A 4306 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.8138 (p0) REVERT: B 91 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6921 (tttp) REVERT: B 4119 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.7060 (ptp-170) REVERT: B 4174 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7394 (p0) REVERT: B 4187 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6900 (m-30) REVERT: B 4280 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8096 (m-30) REVERT: B 4384 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7189 (ttp80) outliers start: 42 outliers final: 28 residues processed: 94 average time/residue: 0.0884 time to fit residues: 12.2783 Evaluate side-chains 98 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 3931 THR Chi-restraints excluded: chain A residue 3998 LYS Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4122 ILE Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4201 MET Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4274 MET Chi-restraints excluded: chain A residue 4306 ASN Chi-restraints excluded: chain A residue 4326 LEU Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4366 THR Chi-restraints excluded: chain A residue 4378 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3992 SER Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4119 ARG Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4172 THR Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4187 ASP Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4255 VAL Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4280 ASP Chi-restraints excluded: chain B residue 4384 ARG Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4402 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.0670 chunk 112 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4342 HIS ** B4299 GLN ** 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 = 0.3713 r_free = 0.3713 target = 0.120515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.085518 restraints weight = 17906.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087639 restraints weight = 10244.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.089014 restraints weight = 7261.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.089715 restraints weight = 5907.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090331 restraints weight = 5278.428| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9420 Z= 0.133 Angle : 0.646 8.480 12826 Z= 0.324 Chirality : 0.046 0.211 1374 Planarity : 0.004 0.044 1664 Dihedral : 6.741 56.350 1604 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.78 % Allowed : 17.63 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.25), residues: 1132 helix: -4.47 (0.63), residues: 25 sheet: -1.02 (0.31), residues: 281 loop : -0.83 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B4067 TYR 0.017 0.001 TYR A4079 PHE 0.009 0.001 PHE A4323 TRP 0.014 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9360) covalent geometry : angle 0.62737 / 0.32 (12688) SS BOND : bond 0.00259 / 0.19 ( 42) SS BOND : angle 1.03643 / 0.62 ( 84) hydrogen bonds : bond 0.03057 / 1.96 ( 214) hydrogen bonds : angle 6.80470 / 4.63 ( 516) link_ALPHA1-3 : bond 0.01637 / 0.83 ( 2) link_ALPHA1-3 : angle 2.15107 / 1.10 ( 6) link_ALPHA1-6 : bond 0.00316 / 0.15 ( 2) link_ALPHA1-6 : angle 1.68531 / 0.84 ( 6) link_BETA1-3 : bond 0.00995 / 0.51 ( 2) link_BETA1-3 : angle 3.67980 / 2.08 ( 6) link_BETA1-4 : bond 0.00627 / 0.40 ( 6) link_BETA1-4 : angle 1.71116 / 0.92 ( 18) link_NAG-ASN : bond 0.00557 / 0.30 ( 6) link_NAG-ASN : angle 2.14430 / 1.22 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8592 (pt) REVERT: A 51 ARG cc_start: 0.6856 (OUTLIER) cc_final: 0.6452 (mtm-85) REVERT: A 52 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: A 3998 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.7072 (ptpp) REVERT: A 4217 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7947 (mpt) REVERT: A 4306 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8124 (p0) REVERT: B 91 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6859 (tttp) REVERT: B 4119 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7178 (ptp-170) REVERT: B 4174 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7405 (p0) REVERT: B 4187 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6869 (m-30) REVERT: B 4384 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7172 (ttp80) outliers start: 38 outliers final: 25 residues processed: 87 average time/residue: 0.0838 time to fit residues: 10.9106 Evaluate side-chains 95 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 59 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 51 ARG Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 3931 THR Chi-restraints excluded: chain A residue 3998 LYS Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4122 ILE Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4201 MET Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4274 MET Chi-restraints excluded: chain A residue 4306 ASN Chi-restraints excluded: chain A residue 4326 LEU Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4366 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4119 ARG Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4172 THR Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4187 ASP Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4255 VAL Chi-restraints excluded: chain B residue 4384 ARG Chi-restraints excluded: chain B residue 4385 CYS Chi-restraints excluded: chain B residue 4402 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 112 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4342 HIS ** B4299 GLN ** 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 = 0.3715 r_free = 0.3715 target = 0.120553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.085859 restraints weight = 17727.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.088010 restraints weight = 10067.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.089394 restraints weight = 7104.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090262 restraints weight = 5758.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.090758 restraints weight = 5075.461| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9420 Z= 0.133 Angle : 0.667 18.365 12826 Z= 0.329 Chirality : 0.046 0.208 1374 Planarity : 0.004 0.044 1664 Dihedral : 6.782 58.193 1604 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.98 % Allowed : 17.73 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.25), residues: 1132 helix: -4.45 (0.63), residues: 25 sheet: -1.13 (0.31), residues: 271 loop : -0.84 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B4067 TYR 0.017 0.001 TYR A4079 PHE 0.010 0.001 PHE A4125 TRP 0.012 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 9360) covalent geometry : angle 0.64919 / 0.32 (12688) SS BOND : bond 0.00257 / 0.19 ( 42) SS BOND : angle 0.99066 / 0.59 ( 84) hydrogen bonds : bond 0.03061 / 1.97 ( 214) hydrogen bonds : angle 6.77307 / 4.60 ( 516) link_ALPHA1-3 : bond 0.01601 / 0.81 ( 2) link_ALPHA1-3 : angle 2.14672 / 1.10 ( 6) link_ALPHA1-6 : bond 0.00305 / 0.15 ( 2) link_ALPHA1-6 : angle 1.69276 / 0.85 ( 6) link_BETA1-3 : bond 0.01000 / 0.51 ( 2) link_BETA1-3 : angle 3.58641 / 2.03 ( 6) link_BETA1-4 : bond 0.00634 / 0.40 ( 6) link_BETA1-4 : angle 1.74801 / 0.93 ( 18) link_NAG-ASN : bond 0.00541 / 0.29 ( 6) link_NAG-ASN : angle 2.28565 / 1.30 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1616.80 seconds wall clock time: 28 minutes 47.23 seconds (1727.23 seconds total)