Starting phenix.real_space_refine on Wed Apr 30 07:10:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxj_36703/04_2025/8jxj_36703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxj_36703/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxj_36703/04_2025/8jxj_36703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxj_36703/04_2025/8jxj_36703.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxj_36703/04_2025/8jxj_36703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxj_36703/04_2025/8jxj_36703.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.02, per 1000 atoms: 0.66 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: 2.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.39 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: 2.98 Time building geometry restraints manager: 2.97 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: 0.00 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: 5.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.000 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (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 TRP 0.013 0.001 TRP A4297 HIS 0.005 0.001 HIS B4221 PHE 0.018 0.001 PHE B 33 TYR 0.021 0.001 TYR B4411 ARG 0.006 0.000 ARG A 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00625 ( 6) link_NAG-ASN : angle 3.60778 ( 18) link_ALPHA1-6 : bond 0.00547 ( 2) link_ALPHA1-6 : angle 0.58100 ( 6) link_BETA1-4 : bond 0.00632 ( 6) link_BETA1-4 : angle 1.74612 ( 18) link_ALPHA1-3 : bond 0.01092 ( 2) link_ALPHA1-3 : angle 1.51381 ( 6) hydrogen bonds : bond 0.24369 ( 214) hydrogen bonds : angle 10.46030 ( 516) SS BOND : bond 0.00232 ( 42) SS BOND : angle 1.05573 ( 84) link_BETA1-3 : bond 0.00467 ( 2) link_BETA1-3 : angle 4.19848 ( 6) covalent geometry : bond 0.00424 ( 9360) covalent geometry : angle 0.79827 (12688) *********************** 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 : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4308 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7513 (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: 0.7626 (mtt) outliers start: 18 outliers final: 15 residues processed: 76 average time/residue: 0.1673 time to fit residues: 20.6306 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 : 1.286 ------------------------------------------------------------------------------- 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 96 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.0770 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- 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 ** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3714 r_free = 0.3714 target = 0.120749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085925 restraints weight = 17894.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087943 restraints weight = 10456.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.089203 restraints weight = 7511.996| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9420 Z= 0.142 Angle : 0.714 12.210 12826 Z= 0.355 Chirality : 0.049 0.338 1374 Planarity : 0.005 0.047 1664 Dihedral : 13.113 103.384 1616 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.69 % Allowed : 16.14 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.25), residues: 1132 helix: -4.59 (0.56), residues: 25 sheet: -0.85 (0.33), residues: 249 loop : -0.75 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 PHE 0.011 0.001 PHE A4323 TYR 0.016 0.001 TYR B4411 ARG 0.004 0.000 ARG A4119 Details of bonding type rmsd link_NAG-ASN : bond 0.00823 ( 6) link_NAG-ASN : angle 2.62905 ( 18) link_ALPHA1-6 : bond 0.00845 ( 2) link_ALPHA1-6 : angle 1.47699 ( 6) link_BETA1-4 : bond 0.01110 ( 6) link_BETA1-4 : angle 2.37817 ( 18) link_ALPHA1-3 : bond 0.02308 ( 2) link_ALPHA1-3 : angle 1.54627 ( 6) hydrogen bonds : bond 0.04394 ( 214) hydrogen bonds : angle 8.02140 ( 516) SS BOND : bond 0.00316 ( 42) SS BOND : angle 0.97113 ( 84) link_BETA1-3 : bond 0.01347 ( 2) link_BETA1-3 : angle 5.84189 ( 6) covalent geometry : bond 0.00310 ( 9360) covalent geometry : angle 0.68815 (12688) *********************** 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 93 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 56 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4217 MET cc_start: 0.8619 (mpt) cc_final: 0.7920 (mpt) REVERT: A 4386 MET cc_start: 0.7962 (pmm) cc_final: 0.7691 (pmm) REVERT: B 91 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6756 (tttp) REVERT: B 4039 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7914 (mtpt) REVERT: B 4041 MET cc_start: 0.6349 (tpt) cc_final: 0.6087 (tpt) REVERT: B 4045 TYR cc_start: 0.5781 (OUTLIER) cc_final: 0.5147 (t80) REVERT: B 4144 MET cc_start: 0.7226 (mtp) cc_final: 0.6992 (mtt) REVERT: B 4307 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8329 (mtpm) outliers start: 37 outliers final: 18 residues processed: 89 average time/residue: 0.2532 time to fit residues: 32.2906 Evaluate side-chains 73 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4377 VAL Chi-restraints excluded: chain A residue 4401 CYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 3962 THR Chi-restraints excluded: chain B residue 3965 ASN Chi-restraints excluded: chain B residue 3971 THR Chi-restraints excluded: chain B residue 4039 LYS Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4045 TYR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4307 LYS Chi-restraints excluded: chain B residue 4339 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 chunk 110 optimal weight: 7.9990 chunk 37 optimal weight: 0.0980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 69 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** 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 = 0.3721 r_free = 0.3721 target = 0.121042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086265 restraints weight = 18039.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.088290 restraints weight = 10469.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.089570 restraints weight = 7491.654| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9420 Z= 0.132 Angle : 0.672 10.407 12826 Z= 0.334 Chirality : 0.049 0.297 1374 Planarity : 0.005 0.047 1664 Dihedral : 10.972 95.387 1610 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.69 % Allowed : 16.63 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.25), residues: 1132 helix: -4.57 (0.57), residues: 25 sheet: -0.78 (0.33), residues: 249 loop : -0.77 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 PHE 0.009 0.001 PHE A4323 TYR 0.015 0.001 TYR A4079 ARG 0.018 0.001 ARG B4067 Details of bonding type rmsd link_NAG-ASN : bond 0.00739 ( 6) link_NAG-ASN : angle 2.33715 ( 18) link_ALPHA1-6 : bond 0.01079 ( 2) link_ALPHA1-6 : angle 1.77165 ( 6) link_BETA1-4 : bond 0.00907 ( 6) link_BETA1-4 : angle 2.36746 ( 18) link_ALPHA1-3 : bond 0.02060 ( 2) link_ALPHA1-3 : angle 1.73908 ( 6) hydrogen bonds : bond 0.03677 ( 214) hydrogen bonds : angle 7.37815 ( 516) SS BOND : bond 0.00280 ( 42) SS BOND : angle 0.86455 ( 84) link_BETA1-3 : bond 0.00987 ( 2) link_BETA1-3 : angle 4.98031 ( 6) covalent geometry : bond 0.00293 ( 9360) covalent geometry : angle 0.64875 (12688) *********************** 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 97 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4217 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.7931 (mpt) REVERT: B 91 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6957 (tttp) REVERT: B 4039 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7868 (mtpt) REVERT: B 4045 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.5190 (t80) REVERT: B 4307 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8314 (mtpm) outliers start: 37 outliers final: 21 residues processed: 91 average time/residue: 0.1966 time to fit residues: 26.6836 Evaluate side-chains 76 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 98 ASP Chi-restraints excluded: chain A residue 4047 GLU 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 10 optimal weight: 0.0470 chunk 77 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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** 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 = 0.3711 r_free = 0.3711 target = 0.120505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.085535 restraints weight = 17905.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087447 restraints weight = 10726.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088688 restraints weight = 7813.992| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9420 Z= 0.150 Angle : 0.673 10.548 12826 Z= 0.333 Chirality : 0.048 0.275 1374 Planarity : 0.004 0.045 1664 Dihedral : 9.610 78.912 1608 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.98 % Allowed : 16.33 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.25), residues: 1132 helix: -4.48 (0.71), residues: 19 sheet: -1.06 (0.31), residues: 289 loop : -0.71 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 PHE 0.009 0.001 PHE A4323 TYR 0.014 0.001 TYR A4079 ARG 0.006 0.000 ARG B4067 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 6) link_NAG-ASN : angle 2.27082 ( 18) link_ALPHA1-6 : bond 0.00702 ( 2) link_ALPHA1-6 : angle 2.14407 ( 6) link_BETA1-4 : bond 0.00860 ( 6) link_BETA1-4 : angle 2.09617 ( 18) link_ALPHA1-3 : bond 0.02032 ( 2) link_ALPHA1-3 : angle 1.93961 ( 6) hydrogen bonds : bond 0.03433 ( 214) hydrogen bonds : angle 7.12444 ( 516) SS BOND : bond 0.00286 ( 42) SS BOND : angle 0.86894 ( 84) link_BETA1-3 : bond 0.01107 ( 2) link_BETA1-3 : angle 5.11175 ( 6) covalent geometry : bond 0.00336 ( 9360) covalent geometry : angle 0.65079 (12688) *********************** 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 99 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 59 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.6673 (t0) cc_final: 0.6386 (t0) REVERT: A 4217 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7907 (mpt) REVERT: B 91 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6968 (tttp) REVERT: B 4039 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7776 (mtpt) REVERT: B 4045 TYR cc_start: 0.5707 (OUTLIER) cc_final: 0.5210 (t80) REVERT: B 4174 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7400 (p0) REVERT: B 4307 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8258 (mtpm) outliers start: 40 outliers final: 27 residues processed: 90 average time/residue: 0.2138 time to fit residues: 28.4906 Evaluate side-chains 85 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 52 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 4174 ASP Chi-restraints excluded: chain A residue 4201 MET Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4236 LEU Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4377 VAL 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 4008 GLN Chi-restraints excluded: chain B residue 4039 LYS Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4045 TYR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 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 4385 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** ** 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 = 0.3686 r_free = 0.3686 target = 0.118706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085234 restraints weight = 18066.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.085758 restraints weight = 11331.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.086630 restraints weight = 9319.373| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9420 Z= 0.210 Angle : 0.690 10.046 12826 Z= 0.345 Chirality : 0.048 0.263 1374 Planarity : 0.005 0.045 1664 Dihedral : 8.206 48.797 1608 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.88 % Allowed : 16.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.25), residues: 1132 helix: -4.45 (0.74), residues: 19 sheet: -1.13 (0.30), residues: 299 loop : -0.87 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A4297 HIS 0.006 0.001 HIS B4221 PHE 0.010 0.001 PHE A4361 TYR 0.014 0.002 TYR A4079 ARG 0.006 0.001 ARG B4067 Details of bonding type rmsd link_NAG-ASN : bond 0.00658 ( 6) link_NAG-ASN : angle 2.41214 ( 18) link_ALPHA1-6 : bond 0.00571 ( 2) link_ALPHA1-6 : angle 1.90846 ( 6) link_BETA1-4 : bond 0.00820 ( 6) link_BETA1-4 : angle 2.16953 ( 18) link_ALPHA1-3 : bond 0.01984 ( 2) link_ALPHA1-3 : angle 1.92204 ( 6) hydrogen bonds : bond 0.03567 ( 214) hydrogen bonds : angle 7.03454 ( 516) SS BOND : bond 0.00334 ( 42) SS BOND : angle 0.88717 ( 84) link_BETA1-3 : bond 0.01353 ( 2) link_BETA1-3 : angle 4.71419 ( 6) covalent geometry : bond 0.00481 ( 9360) covalent geometry : angle 0.66825 (12688) *********************** 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: 49 poor density : 59 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6943 (mtm-85) REVERT: A 88 ASP cc_start: 0.6882 (t0) cc_final: 0.6580 (t0) REVERT: A 4217 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7938 (mpt) REVERT: B 91 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6958 (tttp) REVERT: B 4039 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7717 (mtpt) REVERT: B 4041 MET cc_start: 0.5972 (tpt) cc_final: 0.5534 (tpt) REVERT: B 4045 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.5288 (t80) REVERT: B 4174 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7392 (p0) REVERT: B 4187 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6482 (m-30) REVERT: B 4307 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8271 (mtpm) REVERT: B 4384 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7068 (ttp80) outliers start: 49 outliers final: 30 residues processed: 97 average time/residue: 0.1819 time to fit residues: 25.9409 Evaluate side-chains 92 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 53 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4366 THR Chi-restraints excluded: chain A residue 4377 VAL 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 4032 CYS Chi-restraints excluded: chain B residue 4039 LYS Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4045 TYR Chi-restraints excluded: chain B residue 4086 ILE Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4172 THR Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 4187 ASP Chi-restraints excluded: chain B residue 4201 MET Chi-restraints excluded: chain B residue 4255 VAL Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain B residue 4307 LYS Chi-restraints excluded: chain B residue 4339 VAL Chi-restraints excluded: chain B residue 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 26 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** 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 = 0.3708 r_free = 0.3708 target = 0.120183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.086427 restraints weight = 17938.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087791 restraints weight = 10526.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088238 restraints weight = 8580.531| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1728 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= 0.134 Angle : 0.654 14.119 12826 Z= 0.324 Chirality : 0.047 0.272 1374 Planarity : 0.004 0.045 1664 Dihedral : 7.439 49.915 1608 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.38 % Allowed : 16.83 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1132 helix: -4.51 (0.58), residues: 25 sheet: -0.87 (0.32), residues: 269 loop : -0.88 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 PHE 0.009 0.001 PHE A4323 TYR 0.017 0.001 TYR A4079 ARG 0.005 0.000 ARG B4067 Details of bonding type rmsd link_NAG-ASN : bond 0.00684 ( 6) link_NAG-ASN : angle 2.40618 ( 18) link_ALPHA1-6 : bond 0.00321 ( 2) link_ALPHA1-6 : angle 1.85611 ( 6) link_BETA1-4 : bond 0.00726 ( 6) link_BETA1-4 : angle 1.94985 ( 18) link_ALPHA1-3 : bond 0.01762 ( 2) link_ALPHA1-3 : angle 2.14231 ( 6) hydrogen bonds : bond 0.03108 ( 214) hydrogen bonds : angle 6.80159 ( 516) SS BOND : bond 0.00274 ( 42) SS BOND : angle 0.78703 ( 84) link_BETA1-3 : bond 0.01096 ( 2) link_BETA1-3 : angle 4.36201 ( 6) covalent geometry : bond 0.00303 ( 9360) covalent geometry : angle 0.63370 (12688) *********************** 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 105 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 61 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6795 (mtm-85) REVERT: A 88 ASP cc_start: 0.7013 (t0) cc_final: 0.6661 (t0) REVERT: A 4217 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7949 (mpt) REVERT: B 91 LYS cc_start: 0.7287 (OUTLIER) cc_final: 0.6960 (tttp) REVERT: B 4039 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7785 (mtpt) REVERT: B 4119 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7060 (ptp-170) REVERT: B 4144 MET cc_start: 0.7047 (mtp) cc_final: 0.6646 (mtt) REVERT: B 4174 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7394 (p0) REVERT: B 4307 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8202 (mtpm) outliers start: 44 outliers final: 27 residues processed: 95 average time/residue: 0.2146 time to fit residues: 29.8231 Evaluate side-chains 92 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4377 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 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 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 4119 ARG Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4172 THR Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 25 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** 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 = 0.3698 r_free = 0.3698 target = 0.119407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085874 restraints weight = 18139.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.086677 restraints weight = 11175.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.087518 restraints weight = 9273.350| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9420 Z= 0.165 Angle : 0.667 11.723 12826 Z= 0.334 Chirality : 0.047 0.258 1374 Planarity : 0.004 0.045 1664 Dihedral : 7.284 52.231 1606 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 4.48 % Allowed : 16.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.25), residues: 1132 helix: -4.41 (0.75), residues: 19 sheet: -1.15 (0.30), residues: 291 loop : -0.81 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4297 HIS 0.005 0.001 HIS B4221 PHE 0.010 0.001 PHE A3989 TYR 0.021 0.001 TYR A4079 ARG 0.005 0.000 ARG B4067 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 6) link_NAG-ASN : angle 2.33896 ( 18) link_ALPHA1-6 : bond 0.00313 ( 2) link_ALPHA1-6 : angle 1.84562 ( 6) link_BETA1-4 : bond 0.00704 ( 6) link_BETA1-4 : angle 1.94093 ( 18) link_ALPHA1-3 : bond 0.01811 ( 2) link_ALPHA1-3 : angle 2.11624 ( 6) hydrogen bonds : bond 0.03229 ( 214) hydrogen bonds : angle 6.73933 ( 516) SS BOND : bond 0.00295 ( 42) SS BOND : angle 0.81440 ( 84) link_BETA1-3 : bond 0.01163 ( 2) link_BETA1-3 : angle 4.12631 ( 6) covalent geometry : bond 0.00375 ( 9360) covalent geometry : angle 0.64879 (12688) *********************** 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 110 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8574 (pt) REVERT: A 51 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6743 (mtm-85) REVERT: A 88 ASP cc_start: 0.7181 (t0) cc_final: 0.6911 (t0) REVERT: A 4217 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7940 (mpt) REVERT: B 91 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6952 (tttp) REVERT: B 4144 MET cc_start: 0.7152 (mtp) cc_final: 0.6803 (mtt) REVERT: B 4174 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7416 (p0) REVERT: B 4187 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6512 (m-30) REVERT: B 4307 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8170 (mtpm) REVERT: B 4384 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7112 (ttp80) outliers start: 45 outliers final: 31 residues processed: 100 average time/residue: 0.1902 time to fit residues: 27.7652 Evaluate side-chains 95 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 56 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4377 VAL 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 4008 GLN 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 65 optimal weight: 0.0000 chunk 4 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 98 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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** B4008 GLN ** B4299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.120215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.087114 restraints weight = 18432.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.087215 restraints weight = 11564.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088084 restraints weight = 9178.359| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1954 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= 0.136 Angle : 0.663 11.231 12826 Z= 0.331 Chirality : 0.047 0.264 1374 Planarity : 0.004 0.045 1664 Dihedral : 7.136 53.792 1606 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.98 % Allowed : 17.63 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1132 helix: -4.50 (0.59), residues: 25 sheet: -1.01 (0.31), residues: 281 loop : -0.80 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 PHE 0.009 0.001 PHE A4323 TYR 0.021 0.001 TYR A4079 ARG 0.005 0.000 ARG B4119 Details of bonding type rmsd link_NAG-ASN : bond 0.00619 ( 6) link_NAG-ASN : angle 2.24103 ( 18) link_ALPHA1-6 : bond 0.00311 ( 2) link_ALPHA1-6 : angle 1.77482 ( 6) link_BETA1-4 : bond 0.00679 ( 6) link_BETA1-4 : angle 1.82926 ( 18) link_ALPHA1-3 : bond 0.01742 ( 2) link_ALPHA1-3 : angle 2.18112 ( 6) hydrogen bonds : bond 0.03052 ( 214) hydrogen bonds : angle 6.69403 ( 516) SS BOND : bond 0.00260 ( 42) SS BOND : angle 0.95990 ( 84) link_BETA1-3 : bond 0.01102 ( 2) link_BETA1-3 : angle 4.03208 ( 6) covalent geometry : bond 0.00308 ( 9360) covalent geometry : angle 0.64445 (12688) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 62 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8552 (pt) REVERT: A 51 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6646 (mtm-85) REVERT: A 88 ASP cc_start: 0.7047 (t0) cc_final: 0.6804 (t0) REVERT: A 4217 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7983 (mpt) REVERT: B 91 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6920 (tttp) REVERT: B 4008 GLN cc_start: 0.4402 (OUTLIER) cc_final: 0.3977 (pm20) REVERT: B 4119 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7127 (ptp-170) REVERT: B 4144 MET cc_start: 0.7186 (mtp) cc_final: 0.6867 (mtt) REVERT: B 4174 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7406 (p0) REVERT: B 4307 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8158 (mtpm) REVERT: B 4384 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7106 (ttp80) outliers start: 40 outliers final: 29 residues processed: 92 average time/residue: 0.2097 time to fit residues: 28.1013 Evaluate side-chains 97 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4377 VAL 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 3965 ASN Chi-restraints excluded: chain B residue 3971 THR Chi-restraints excluded: chain B residue 4008 GLN 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 4119 ARG Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4172 THR Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 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 72 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 33 optimal weight: 0.0370 chunk 26 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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** 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 = 0.3713 r_free = 0.3713 target = 0.120460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.087692 restraints weight = 17974.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.087755 restraints weight = 11409.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.088547 restraints weight = 9074.960| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9420 Z= 0.127 Angle : 0.650 10.778 12826 Z= 0.326 Chirality : 0.046 0.222 1374 Planarity : 0.004 0.045 1664 Dihedral : 6.954 54.371 1605 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.78 % Allowed : 17.83 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.25), residues: 1132 helix: -4.48 (0.60), residues: 25 sheet: -1.07 (0.32), residues: 271 loop : -0.79 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 PHE 0.009 0.001 PHE A4323 TYR 0.018 0.001 TYR A4079 ARG 0.005 0.000 ARG B4119 Details of bonding type rmsd link_NAG-ASN : bond 0.00595 ( 6) link_NAG-ASN : angle 2.18008 ( 18) link_ALPHA1-6 : bond 0.00321 ( 2) link_ALPHA1-6 : angle 1.72359 ( 6) link_BETA1-4 : bond 0.00672 ( 6) link_BETA1-4 : angle 1.74991 ( 18) link_ALPHA1-3 : bond 0.01698 ( 2) link_ALPHA1-3 : angle 2.20440 ( 6) hydrogen bonds : bond 0.03012 ( 214) hydrogen bonds : angle 6.64086 ( 516) SS BOND : bond 0.00246 ( 42) SS BOND : angle 0.91232 ( 84) link_BETA1-3 : bond 0.01085 ( 2) link_BETA1-3 : angle 3.92199 ( 6) covalent geometry : bond 0.00288 ( 9360) covalent geometry : angle 0.63229 (12688) *********************** 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 97 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 59 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8628 (pt) REVERT: A 51 ARG cc_start: 0.7093 (OUTLIER) cc_final: 0.6755 (mtm-85) REVERT: A 88 ASP cc_start: 0.7024 (t0) cc_final: 0.6787 (t0) REVERT: A 4217 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.7992 (mpt) REVERT: B 91 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6905 (tttp) REVERT: B 4008 GLN cc_start: 0.4497 (OUTLIER) cc_final: 0.3965 (pm20) REVERT: B 4119 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.7224 (ptp-170) REVERT: B 4144 MET cc_start: 0.7151 (mtp) cc_final: 0.6840 (mtt) REVERT: B 4174 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7388 (p0) REVERT: B 4307 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8149 (mtpm) REVERT: B 4384 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7115 (ttp80) outliers start: 38 outliers final: 26 residues processed: 88 average time/residue: 0.1995 time to fit residues: 25.3842 Evaluate side-chains 93 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 58 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 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 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 4008 GLN 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 4119 ARG Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 50 optimal weight: 0.0040 chunk 78 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 68 optimal weight: 0.0010 chunk 13 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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** B4008 GLN B4299 GLN ** B4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.121072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.088095 restraints weight = 18173.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.088189 restraints weight = 11467.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.088988 restraints weight = 9066.061| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9420 Z= 0.116 Angle : 0.642 10.577 12826 Z= 0.322 Chirality : 0.046 0.219 1374 Planarity : 0.004 0.044 1664 Dihedral : 6.790 54.563 1605 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.69 % Allowed : 18.03 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.25), residues: 1132 helix: -4.45 (0.62), residues: 25 sheet: -1.14 (0.31), residues: 281 loop : -0.70 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A4297 HIS 0.003 0.001 HIS B4221 PHE 0.009 0.001 PHE A4323 TYR 0.017 0.001 TYR A4079 ARG 0.005 0.000 ARG B4067 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 6) link_NAG-ASN : angle 2.12955 ( 18) link_ALPHA1-6 : bond 0.00334 ( 2) link_ALPHA1-6 : angle 1.67467 ( 6) link_BETA1-4 : bond 0.00653 ( 6) link_BETA1-4 : angle 1.67851 ( 18) link_ALPHA1-3 : bond 0.01606 ( 2) link_ALPHA1-3 : angle 2.20694 ( 6) hydrogen bonds : bond 0.02920 ( 214) hydrogen bonds : angle 6.58521 ( 516) SS BOND : bond 0.00235 ( 42) SS BOND : angle 0.88829 ( 84) link_BETA1-3 : bond 0.01050 ( 2) link_BETA1-3 : angle 3.82286 ( 6) covalent geometry : bond 0.00260 ( 9360) covalent geometry : angle 0.62469 (12688) ********************** 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 99 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 62 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8576 (pt) REVERT: A 51 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6767 (mtm-85) REVERT: A 88 ASP cc_start: 0.6997 (t0) cc_final: 0.6766 (t0) REVERT: A 4011 ASN cc_start: 0.8866 (t0) cc_final: 0.8479 (t0) REVERT: A 4217 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7994 (mpt) REVERT: A 4306 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8049 (p0) REVERT: B 91 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6977 (tttp) REVERT: B 4008 GLN cc_start: 0.5245 (OUTLIER) cc_final: 0.4345 (pm20) REVERT: B 4119 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7773 (ptt180) REVERT: B 4174 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7209 (p0) REVERT: B 4307 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8212 (mtpm) REVERT: B 4384 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6900 (ttp80) outliers start: 37 outliers final: 25 residues processed: 91 average time/residue: 0.2139 time to fit residues: 28.2609 Evaluate side-chains 95 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 4306 ASN 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 3971 THR Chi-restraints excluded: chain B residue 4008 GLN 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 4119 ARG Chi-restraints excluded: chain B residue 4147 ASP Chi-restraints excluded: chain B residue 4154 VAL Chi-restraints excluded: chain B residue 4158 ILE Chi-restraints excluded: chain B residue 4174 ASP Chi-restraints excluded: chain B residue 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 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 82 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** ** B4008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.120663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087784 restraints weight = 18063.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088057 restraints weight = 10907.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088886 restraints weight = 8549.900| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2145 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= 0.133 Angle : 0.644 10.410 12826 Z= 0.324 Chirality : 0.046 0.217 1374 Planarity : 0.004 0.044 1664 Dihedral : 6.738 55.237 1604 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.59 % Allowed : 18.23 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1132 helix: -4.44 (0.62), residues: 25 sheet: -1.15 (0.31), residues: 281 loop : -0.70 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4297 HIS 0.004 0.001 HIS B4221 PHE 0.009 0.001 PHE A4323 TYR 0.017 0.001 TYR A4079 ARG 0.004 0.000 ARG B4067 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 6) link_NAG-ASN : angle 2.09306 ( 18) link_ALPHA1-6 : bond 0.00316 ( 2) link_ALPHA1-6 : angle 1.69480 ( 6) link_BETA1-4 : bond 0.00629 ( 6) link_BETA1-4 : angle 1.66697 ( 18) link_ALPHA1-3 : bond 0.01621 ( 2) link_ALPHA1-3 : angle 2.15315 ( 6) hydrogen bonds : bond 0.02975 ( 214) hydrogen bonds : angle 6.56789 ( 516) SS BOND : bond 0.00246 ( 42) SS BOND : angle 0.89316 ( 84) link_BETA1-3 : bond 0.01014 ( 2) link_BETA1-3 : angle 3.72205 ( 6) covalent geometry : bond 0.00302 ( 9360) covalent geometry : angle 0.62790 (12688) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3320.90 seconds wall clock time: 60 minutes 9.48 seconds (3609.48 seconds total)