Starting phenix.real_space_refine on Sat Aug 23 02:58:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxj_36703/08_2025/8jxj_36703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxj_36703/08_2025/8jxj_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_36703/08_2025/8jxj_36703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxj_36703/08_2025/8jxj_36703.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jxj_36703/08_2025/8jxj_36703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxj_36703/08_2025/8jxj_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 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, 18 Unusual residues: {' CA': 4, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 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: 2.34, per 1000 atoms: 0.26 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: 1.10 Conformation dependent library (CDL) restraints added in 390.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.38 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: 1.69 Time building geometry restraints manager: 1.39 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 2.510 nonbonded pdb=" OD1 ASP A 48 " pdb="CA CA A4702 " model vdw 2.172 2.510 nonbonded pdb=" OD2 ASP B3960 " pdb="CA CA B4704 " model vdw 2.177 2.510 nonbonded pdb=" OD2 ASP A 58 " pdb="CA CA A4702 " model vdw 2.186 2.510 nonbonded pdb=" O VAL B3952 " pdb="CA CA B4704 " model vdw 2.187 2.510 ... (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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.120 Find NCS groups from input model: 0.160 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 aren 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 covalent geometry : bond 0.00424 ( 9360) covalent geometry : angle 0.79827 (12688) SS BOND : bond 0.00232 ( 42) SS BOND : angle 1.05573 ( 84) hydrogen bonds : bond 0.24369 ( 214) hydrogen bonds : angle 10.46030 ( 516) link_ALPHA1-3 : bond 0.01092 ( 2) link_ALPHA1-3 : angle 1.51381 ( 6) link_ALPHA1-6 : bond 0.00547 ( 2) link_ALPHA1-6 : angle 0.58100 ( 6) link_BETA1-3 : bond 0.00467 ( 2) link_BETA1-3 : angle 4.19848 ( 6) link_BETA1-4 : bond 0.00632 ( 6) link_BETA1-4 : angle 1.74612 ( 18) link_NAG-ASN : bond 0.00625 ( 6) link_NAG-ASN : angle 3.60778 ( 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 : 0.223 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: 0.0670 time to fit residues: 8.2980 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 : 0.361 ------------------------------------------------------------------------------- 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: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3693 r_free = 0.3693 target = 0.119257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.084431 restraints weight = 18053.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086487 restraints weight = 10288.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.087758 restraints weight = 7303.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088585 restraints weight = 5962.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.089061 restraints weight = 5291.352| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9420 Z= 0.183 Angle : 0.735 12.129 12826 Z= 0.366 Chirality : 0.050 0.338 1374 Planarity : 0.005 0.048 1664 Dihedral : 13.186 103.379 1616 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 3.78 % Allowed : 16.14 % Favored : 80.08 % 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 aren not related in a simple way. whole: -1.41 (0.25), residues: 1132 helix: -4.60 (0.56), residues: 25 sheet: -0.95 (0.32), residues: 259 loop : -0.83 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4321 TYR 0.018 0.002 TYR B4411 PHE 0.012 0.001 PHE A4323 TRP 0.015 0.001 TRP A4297 HIS 0.005 0.001 HIS B4221 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 9360) covalent geometry : angle 0.70888 (12688) SS BOND : bond 0.00359 ( 42) SS BOND : angle 1.00638 ( 84) hydrogen bonds : bond 0.04414 ( 214) hydrogen bonds : angle 7.99499 ( 516) link_ALPHA1-3 : bond 0.02250 ( 2) link_ALPHA1-3 : angle 1.57483 ( 6) link_ALPHA1-6 : bond 0.00802 ( 2) link_ALPHA1-6 : angle 1.53804 ( 6) link_BETA1-3 : bond 0.01289 ( 2) link_BETA1-3 : angle 5.87508 ( 6) link_BETA1-4 : bond 0.01000 ( 6) link_BETA1-4 : angle 2.38970 ( 18) link_NAG-ASN : bond 0.00738 ( 6) link_NAG-ASN : angle 2.72791 ( 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 94 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 56 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4217 MET cc_start: 0.8621 (mpt) cc_final: 0.7852 (mpt) REVERT: A 4386 MET cc_start: 0.8025 (pmm) cc_final: 0.7729 (pmm) REVERT: A 4400 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.7374 (mtmm) REVERT: B 91 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6792 (tttp) REVERT: B 4039 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7894 (mtpt) REVERT: B 4041 MET cc_start: 0.6136 (tpt) cc_final: 0.5848 (tpt) REVERT: B 4045 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.5128 (t80) REVERT: B 4144 MET cc_start: 0.7338 (mtp) cc_final: 0.7098 (mtt) REVERT: B 4307 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8267 (mtpm) outliers start: 38 outliers final: 21 residues processed: 90 average time/residue: 0.1005 time to fit residues: 12.8721 Evaluate side-chains 75 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 49 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ARG Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 54 LEU 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 4400 LYS 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 3960 ASP 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: 0.7980 chunk 87 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3697 r_free = 0.3697 target = 0.119440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084710 restraints weight = 18033.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086651 restraints weight = 10537.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087960 restraints weight = 7609.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088670 restraints weight = 6227.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.089157 restraints weight = 5581.546| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9420 Z= 0.166 Angle : 0.699 10.473 12826 Z= 0.348 Chirality : 0.049 0.292 1374 Planarity : 0.004 0.047 1664 Dihedral : 11.267 96.807 1610 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.28 % Allowed : 16.14 % Favored : 79.58 % 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 aren not related in a simple way. whole: -1.49 (0.25), residues: 1132 helix: -4.61 (0.55), residues: 25 sheet: -1.07 (0.30), residues: 290 loop : -0.84 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A4266 TYR 0.016 0.001 TYR A4079 PHE 0.010 0.001 PHE A4323 TRP 0.013 0.001 TRP A4297 HIS 0.005 0.001 HIS B4221 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9360) covalent geometry : angle 0.67586 (12688) SS BOND : bond 0.00309 ( 42) SS BOND : angle 0.91352 ( 84) hydrogen bonds : bond 0.03873 ( 214) hydrogen bonds : angle 7.48018 ( 516) link_ALPHA1-3 : bond 0.02299 ( 2) link_ALPHA1-3 : angle 1.62392 ( 6) link_ALPHA1-6 : bond 0.01011 ( 2) link_ALPHA1-6 : angle 1.83305 ( 6) link_BETA1-3 : bond 0.01226 ( 2) link_BETA1-3 : angle 5.12088 ( 6) link_BETA1-4 : bond 0.00834 ( 6) link_BETA1-4 : angle 2.41646 ( 18) link_NAG-ASN : bond 0.00733 ( 6) link_NAG-ASN : angle 2.32332 ( 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 101 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 58 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4217 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7881 (mpt) REVERT: B 91 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6937 (tttp) REVERT: B 4039 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7852 (mtpt) REVERT: B 4041 MET cc_start: 0.6339 (tpt) cc_final: 0.5890 (tpt) REVERT: B 4045 TYR cc_start: 0.5724 (OUTLIER) cc_final: 0.5198 (t80) REVERT: B 4144 MET cc_start: 0.7204 (mtp) cc_final: 0.6934 (mtt) REVERT: B 4307 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8178 (mtpm) outliers start: 43 outliers final: 23 residues processed: 95 average time/residue: 0.0913 time to fit residues: 12.7934 Evaluate side-chains 79 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 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 3960 ASP 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 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: 0.7980 chunk 110 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3705 r_free = 0.3705 target = 0.119960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.087205 restraints weight = 18444.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.086939 restraints weight = 10936.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.087989 restraints weight = 8989.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.088412 restraints weight = 7205.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.088338 restraints weight = 6806.205| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9420 Z= 0.146 Angle : 0.676 10.215 12826 Z= 0.334 Chirality : 0.049 0.269 1374 Planarity : 0.004 0.046 1664 Dihedral : 9.906 81.319 1609 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 4.68 % Allowed : 15.94 % 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 aren not related in a simple way. whole: -1.48 (0.25), residues: 1132 helix: -4.50 (0.68), residues: 19 sheet: -1.09 (0.31), residues: 285 loop : -0.87 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B4067 TYR 0.014 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 covalent geometry : bond 0.00326 ( 9360) covalent geometry : angle 0.65341 (12688) SS BOND : bond 0.00313 ( 42) SS BOND : angle 0.88310 ( 84) hydrogen bonds : bond 0.03449 ( 214) hydrogen bonds : angle 7.20626 ( 516) link_ALPHA1-3 : bond 0.02142 ( 2) link_ALPHA1-3 : angle 1.84675 ( 6) link_ALPHA1-6 : bond 0.00813 ( 2) link_ALPHA1-6 : angle 2.03550 ( 6) link_BETA1-3 : bond 0.01202 ( 2) link_BETA1-3 : angle 4.85646 ( 6) link_BETA1-4 : bond 0.00901 ( 6) link_BETA1-4 : angle 2.13280 ( 18) link_NAG-ASN : bond 0.00759 ( 6) link_NAG-ASN : angle 2.50880 ( 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 106 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 59 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7154 (t70) cc_final: 0.6906 (t0) REVERT: A 4217 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7926 (mpt) REVERT: B 91 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6995 (tttp) REVERT: B 4039 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7774 (mtpt) REVERT: B 4041 MET cc_start: 0.6394 (tpt) cc_final: 0.5996 (tpt) REVERT: B 4045 TYR cc_start: 0.5780 (OUTLIER) cc_final: 0.5256 (t80) REVERT: B 4174 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7576 (p0) REVERT: B 4187 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6523 (m-30) REVERT: B 4307 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8131 (mtpm) outliers start: 47 outliers final: 27 residues processed: 94 average time/residue: 0.0810 time to fit residues: 11.5757 Evaluate side-chains 86 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 52 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR 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 4201 MET Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU 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 A residue 4400 LYS 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 3960 ASP Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN 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 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: 0.0270 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3710 r_free = 0.3710 target = 0.120386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086352 restraints weight = 18227.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087997 restraints weight = 10427.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088622 restraints weight = 8188.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089032 restraints weight = 6320.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.089192 restraints weight = 6115.777| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9420 Z= 0.130 Angle : 0.646 9.850 12826 Z= 0.321 Chirality : 0.047 0.249 1374 Planarity : 0.004 0.046 1664 Dihedral : 7.944 49.798 1608 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.58 % Allowed : 16.53 % Favored : 78.88 % 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 aren not related in a simple way. whole: -1.44 (0.25), residues: 1132 helix: -4.46 (0.70), residues: 19 sheet: -1.07 (0.31), residues: 285 loop : -0.84 (0.22), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B3970 TYR 0.016 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 covalent geometry : bond 0.00291 ( 9360) covalent geometry : angle 0.62451 (12688) SS BOND : bond 0.00277 ( 42) SS BOND : angle 0.82322 ( 84) hydrogen bonds : bond 0.03197 ( 214) hydrogen bonds : angle 6.93146 ( 516) link_ALPHA1-3 : bond 0.01792 ( 2) link_ALPHA1-3 : angle 2.12026 ( 6) link_ALPHA1-6 : bond 0.00724 ( 2) link_ALPHA1-6 : angle 1.90580 ( 6) link_BETA1-3 : bond 0.01303 ( 2) link_BETA1-3 : angle 4.61939 ( 6) link_BETA1-4 : bond 0.00821 ( 6) link_BETA1-4 : angle 2.02934 ( 18) link_NAG-ASN : bond 0.00688 ( 6) link_NAG-ASN : angle 2.40140 ( 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 108 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 62 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6923 (mtm-85) REVERT: A 4217 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7905 (mpt) REVERT: B 91 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6964 (tttp) REVERT: B 4039 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7784 (mtpt) REVERT: B 4041 MET cc_start: 0.5981 (tpt) cc_final: 0.5645 (tpt) REVERT: B 4174 ASP cc_start: 0.8233 (OUTLIER) cc_final: 0.7607 (p0) REVERT: B 4307 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8109 (mtpm) REVERT: B 4384 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7160 (ttp80) outliers start: 46 outliers final: 30 residues processed: 98 average time/residue: 0.0850 time to fit residues: 12.3226 Evaluate side-chains 94 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 4326 LEU Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4400 LYS 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 3960 ASP Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 4032 CYS Chi-restraints excluded: chain B residue 4039 LYS Chi-restraints excluded: chain B residue 4043 THR 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 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 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: 0.8980 chunk 7 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3669 r_free = 0.3669 target = 0.117498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.083088 restraints weight = 18308.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.085110 restraints weight = 10483.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.086387 restraints weight = 7451.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087179 restraints weight = 6096.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087550 restraints weight = 5413.333| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1823 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= 0.229 Angle : 0.713 12.269 12826 Z= 0.355 Chirality : 0.048 0.257 1374 Planarity : 0.005 0.045 1664 Dihedral : 7.791 52.069 1608 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.98 % Allowed : 16.43 % 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 aren not related in a simple way. whole: -1.64 (0.25), residues: 1132 helix: -4.42 (0.78), residues: 19 sheet: -1.26 (0.29), residues: 300 loop : -0.95 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B4067 TYR 0.018 0.002 TYR A4079 PHE 0.011 0.002 PHE A4282 TRP 0.011 0.002 TRP B4248 HIS 0.006 0.001 HIS B4221 Details of bonding type rmsd covalent geometry : bond 0.00524 ( 9360) covalent geometry : angle 0.69334 (12688) SS BOND : bond 0.00354 ( 42) SS BOND : angle 0.91700 ( 84) hydrogen bonds : bond 0.03687 ( 214) hydrogen bonds : angle 6.96892 ( 516) link_ALPHA1-3 : bond 0.01979 ( 2) link_ALPHA1-3 : angle 1.95861 ( 6) link_ALPHA1-6 : bond 0.00188 ( 2) link_ALPHA1-6 : angle 2.13314 ( 6) link_BETA1-3 : bond 0.01234 ( 2) link_BETA1-3 : angle 4.29016 ( 6) link_BETA1-4 : bond 0.00711 ( 6) link_BETA1-4 : angle 2.16307 ( 18) link_NAG-ASN : bond 0.00610 ( 6) link_NAG-ASN : angle 2.46848 ( 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 107 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 57 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8615 (pt) REVERT: A 51 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.7093 (mtm-85) REVERT: A 88 ASP cc_start: 0.6684 (t0) cc_final: 0.6412 (t0) REVERT: A 3990 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6804 (tt) REVERT: A 4217 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7922 (mpt) REVERT: B 91 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7058 (tttp) REVERT: B 4039 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7744 (mtpt) REVERT: B 4041 MET cc_start: 0.5946 (tpt) cc_final: 0.5667 (tpt) REVERT: B 4174 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.7227 (p0) REVERT: B 4187 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6502 (m-30) REVERT: B 4307 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8180 (mtpm) REVERT: B 4384 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7673 (mtp-110) outliers start: 50 outliers final: 30 residues processed: 95 average time/residue: 0.0894 time to fit residues: 12.6044 Evaluate side-chains 96 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 56 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4377 VAL Chi-restraints excluded: chain A residue 4400 LYS 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 3960 ASP Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 3992 SER Chi-restraints excluded: chain B residue 4032 CYS Chi-restraints excluded: chain B residue 4039 LYS 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 0.6980 chunk 78 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 100 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.119913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085930 restraints weight = 18226.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087444 restraints weight = 10367.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.088003 restraints weight = 8386.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088500 restraints weight = 6569.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.088672 restraints weight = 6317.689| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9420 Z= 0.128 Angle : 0.646 9.146 12826 Z= 0.322 Chirality : 0.047 0.271 1374 Planarity : 0.004 0.046 1664 Dihedral : 7.295 53.425 1608 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % 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 aren not related in a simple way. whole: -1.52 (0.25), residues: 1132 helix: -4.58 (0.56), residues: 25 sheet: -1.00 (0.31), residues: 277 loop : -0.91 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B4067 TYR 0.018 0.001 TYR A4079 PHE 0.010 0.001 PHE A4323 TRP 0.014 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9360) covalent geometry : angle 0.62638 (12688) SS BOND : bond 0.00255 ( 42) SS BOND : angle 0.94566 ( 84) hydrogen bonds : bond 0.03119 ( 214) hydrogen bonds : angle 6.78197 ( 516) link_ALPHA1-3 : bond 0.01704 ( 2) link_ALPHA1-3 : angle 2.20771 ( 6) link_ALPHA1-6 : bond 0.00360 ( 2) link_ALPHA1-6 : angle 1.71961 ( 6) link_BETA1-3 : bond 0.01130 ( 2) link_BETA1-3 : angle 4.09249 ( 6) link_BETA1-4 : bond 0.00693 ( 6) link_BETA1-4 : angle 1.84607 ( 18) link_NAG-ASN : bond 0.00635 ( 6) link_NAG-ASN : angle 2.25939 ( 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 114 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 72 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6904 (mtm-85) REVERT: A 88 ASP cc_start: 0.6795 (t0) cc_final: 0.6503 (t0) REVERT: A 4217 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.7990 (mpt) REVERT: A 4306 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8128 (p0) REVERT: B 91 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6947 (tttp) REVERT: B 4144 MET cc_start: 0.7175 (mtp) cc_final: 0.6735 (mtt) REVERT: B 4174 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7608 (p0) REVERT: B 4187 ASP cc_start: 0.6884 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: B 4307 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8098 (mtpm) REVERT: B 4384 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7369 (mtp-110) outliers start: 42 outliers final: 29 residues processed: 104 average time/residue: 0.0892 time to fit residues: 13.5972 Evaluate side-chains 97 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 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 4366 THR Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3960 ASP Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 3992 SER Chi-restraints excluded: chain B residue 4032 CYS Chi-restraints excluded: chain B residue 4043 THR 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 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: 2.9990 chunk 42 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 0.0370 chunk 81 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.119875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.086280 restraints weight = 18032.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086821 restraints weight = 11097.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.087892 restraints weight = 9430.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.088479 restraints weight = 7224.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088457 restraints weight = 6334.578| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9420 Z= 0.141 Angle : 0.662 10.067 12826 Z= 0.329 Chirality : 0.047 0.223 1374 Planarity : 0.004 0.045 1664 Dihedral : 7.114 54.892 1606 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.18 % Allowed : 17.33 % 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 aren not related in a simple way. whole: -1.50 (0.25), residues: 1132 helix: -4.55 (0.58), residues: 25 sheet: -1.13 (0.30), residues: 287 loop : -0.83 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B4067 TYR 0.019 0.001 TYR A4079 PHE 0.009 0.001 PHE A3989 TRP 0.014 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9360) covalent geometry : angle 0.63904 (12688) SS BOND : bond 0.00268 ( 42) SS BOND : angle 1.32059 ( 84) hydrogen bonds : bond 0.03126 ( 214) hydrogen bonds : angle 6.78712 ( 516) link_ALPHA1-3 : bond 0.01744 ( 2) link_ALPHA1-3 : angle 2.19473 ( 6) link_ALPHA1-6 : bond 0.00309 ( 2) link_ALPHA1-6 : angle 1.77357 ( 6) link_BETA1-3 : bond 0.01073 ( 2) link_BETA1-3 : angle 3.95864 ( 6) link_BETA1-4 : bond 0.00678 ( 6) link_BETA1-4 : angle 1.81111 ( 18) link_NAG-ASN : bond 0.00600 ( 6) link_NAG-ASN : angle 2.20868 ( 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 103 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 61 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8589 (pt) REVERT: A 51 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6748 (mtm-85) REVERT: A 88 ASP cc_start: 0.6831 (t0) cc_final: 0.6578 (t0) REVERT: A 4217 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8005 (mpt) REVERT: A 4306 ASN cc_start: 0.8343 (OUTLIER) cc_final: 0.8086 (p0) REVERT: B 91 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6957 (tttp) REVERT: B 4144 MET cc_start: 0.7132 (mtp) cc_final: 0.6795 (mtt) REVERT: B 4174 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7305 (p0) REVERT: B 4187 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6468 (m-30) REVERT: B 4307 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8133 (mtpm) REVERT: B 4384 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7371 (mtp-110) outliers start: 42 outliers final: 29 residues processed: 92 average time/residue: 0.0874 time to fit residues: 11.9451 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 : 0.375 ------------------------------------------------------------------------------- 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 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 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 4339 VAL Chi-restraints excluded: chain A residue 4366 THR Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3960 ASP Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3992 SER Chi-restraints excluded: chain B residue 4032 CYS Chi-restraints excluded: chain B residue 4043 THR 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 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: 6.9990 chunk 69 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 50 optimal weight: 0.0770 chunk 112 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.121105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.087109 restraints weight = 17994.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.088606 restraints weight = 10293.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089177 restraints weight = 8363.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.089680 restraints weight = 6525.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.089863 restraints weight = 6276.877| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2142 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= 0.119 Angle : 0.637 9.196 12826 Z= 0.319 Chirality : 0.046 0.219 1374 Planarity : 0.004 0.046 1664 Dihedral : 6.781 56.384 1606 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.88 % Allowed : 17.63 % 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 aren not related in a simple way. whole: -1.45 (0.25), residues: 1132 helix: -4.51 (0.59), residues: 25 sheet: -1.27 (0.30), residues: 287 loop : -0.72 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B4067 TYR 0.016 0.001 TYR A4079 PHE 0.011 0.001 PHE A4323 TRP 0.015 0.001 TRP A4297 HIS 0.003 0.001 HIS B4221 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9360) covalent geometry : angle 0.61800 (12688) SS BOND : bond 0.00247 ( 42) SS BOND : angle 1.06633 ( 84) hydrogen bonds : bond 0.03010 ( 214) hydrogen bonds : angle 6.68198 ( 516) link_ALPHA1-3 : bond 0.01567 ( 2) link_ALPHA1-3 : angle 2.21593 ( 6) link_ALPHA1-6 : bond 0.00356 ( 2) link_ALPHA1-6 : angle 1.62338 ( 6) link_BETA1-3 : bond 0.01012 ( 2) link_BETA1-3 : angle 3.71403 ( 6) link_BETA1-4 : bond 0.00638 ( 6) link_BETA1-4 : angle 1.65567 ( 18) link_NAG-ASN : bond 0.00600 ( 6) link_NAG-ASN : angle 2.10426 ( 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 101 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 62 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6684 (mtm-85) REVERT: A 88 ASP cc_start: 0.6745 (t0) cc_final: 0.6469 (t0) REVERT: A 4217 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.7970 (mpt) REVERT: A 4306 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8085 (p0) REVERT: B 91 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6924 (tttp) REVERT: B 4174 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7284 (p0) REVERT: B 4187 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6852 (m-30) REVERT: B 4280 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8100 (m-30) REVERT: B 4307 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8157 (mtpm) REVERT: B 4384 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7493 (mtp-110) outliers start: 39 outliers final: 27 residues processed: 94 average time/residue: 0.0850 time to fit residues: 11.9115 Evaluate side-chains 96 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 74 CYS 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 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 4366 THR Chi-restraints excluded: chain A residue 4378 THR Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3960 ASP Chi-restraints excluded: chain B residue 3992 SER Chi-restraints excluded: chain B residue 4032 CYS Chi-restraints excluded: chain B residue 4043 THR 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 4280 ASP 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 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: 0.9980 chunk 17 optimal weight: 0.1980 chunk 42 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4342 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.122160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088167 restraints weight = 17924.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.089368 restraints weight = 10575.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090029 restraints weight = 8699.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090694 restraints weight = 6856.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090777 restraints weight = 6531.347| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2274 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= 0.110 Angle : 0.624 8.775 12826 Z= 0.314 Chirality : 0.046 0.219 1374 Planarity : 0.004 0.045 1664 Dihedral : 6.551 55.232 1605 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.39 % Allowed : 18.03 % 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 aren not related in a simple way. whole: -1.34 (0.25), residues: 1132 helix: -5.06 (0.31), residues: 19 sheet: -1.23 (0.30), residues: 297 loop : -0.63 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B4067 TYR 0.014 0.001 TYR A4079 PHE 0.010 0.001 PHE A4323 TRP 0.016 0.001 TRP A4297 HIS 0.003 0.001 HIS B4221 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9360) covalent geometry : angle 0.60691 (12688) SS BOND : bond 0.00231 ( 42) SS BOND : angle 0.95218 ( 84) hydrogen bonds : bond 0.02904 ( 214) hydrogen bonds : angle 6.61235 ( 516) link_ALPHA1-3 : bond 0.01505 ( 2) link_ALPHA1-3 : angle 2.17997 ( 6) link_ALPHA1-6 : bond 0.00351 ( 2) link_ALPHA1-6 : angle 1.62326 ( 6) link_BETA1-3 : bond 0.00934 ( 2) link_BETA1-3 : angle 3.54059 ( 6) link_BETA1-4 : bond 0.00622 ( 6) link_BETA1-4 : angle 1.59909 ( 18) link_NAG-ASN : bond 0.00533 ( 6) link_NAG-ASN : angle 2.04663 ( 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 102 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 68 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6613 (mtm-85) REVERT: A 88 ASP cc_start: 0.6712 (t0) cc_final: 0.6443 (t0) REVERT: A 4217 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8007 (mpt) REVERT: A 4306 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.8037 (p0) REVERT: B 91 LYS cc_start: 0.7247 (OUTLIER) cc_final: 0.6922 (tttp) REVERT: B 4174 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7688 (p0) REVERT: B 4187 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6891 (m-30) REVERT: B 4307 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8166 (mtpm) REVERT: B 4384 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7528 (mtp-110) outliers start: 34 outliers final: 23 residues processed: 95 average time/residue: 0.0925 time to fit residues: 13.0085 Evaluate side-chains 92 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 54 LEU 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 4274 MET Chi-restraints excluded: chain A residue 4306 ASN Chi-restraints excluded: chain A residue 4326 LEU Chi-restraints excluded: chain A residue 4366 THR Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3960 ASP Chi-restraints excluded: chain B residue 4032 CYS 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 4307 LYS 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: 0.9980 chunk 70 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 104 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4342 HIS B4008 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087383 restraints weight = 17736.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.089093 restraints weight = 10217.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.089583 restraints weight = 7995.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.089910 restraints weight = 6313.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090062 restraints weight = 6056.285| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9420 Z= 0.135 Angle : 0.678 17.167 12826 Z= 0.336 Chirality : 0.046 0.213 1374 Planarity : 0.004 0.044 1664 Dihedral : 6.599 55.674 1604 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.69 % Allowed : 18.33 % Favored : 77.99 % 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 aren not related in a simple way. whole: -1.34 (0.25), residues: 1132 helix: -5.09 (0.30), residues: 19 sheet: -1.24 (0.30), residues: 297 loop : -0.63 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B4067 TYR 0.016 0.001 TYR A4079 PHE 0.010 0.001 PHE A4282 TRP 0.014 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9360) covalent geometry : angle 0.65535 (12688) SS BOND : bond 0.00249 ( 42) SS BOND : angle 1.55768 ( 84) hydrogen bonds : bond 0.03022 ( 214) hydrogen bonds : angle 6.62912 ( 516) link_ALPHA1-3 : bond 0.01518 ( 2) link_ALPHA1-3 : angle 2.12389 ( 6) link_ALPHA1-6 : bond 0.00327 ( 2) link_ALPHA1-6 : angle 1.66095 ( 6) link_BETA1-3 : bond 0.01035 ( 2) link_BETA1-3 : angle 3.48202 ( 6) link_BETA1-4 : bond 0.00624 ( 6) link_BETA1-4 : angle 1.60392 ( 18) link_NAG-ASN : bond 0.00530 ( 6) link_NAG-ASN : angle 2.00139 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1606.46 seconds wall clock time: 28 minutes 36.69 seconds (1716.69 seconds total)