Starting phenix.real_space_refine on Thu Jul 2 21:42:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxd_36697/07_2026/8jxd_36697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxd_36697/07_2026/8jxd_36697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jxd_36697/07_2026/8jxd_36697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxd_36697/07_2026/8jxd_36697.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jxd_36697/07_2026/8jxd_36697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxd_36697/07_2026/8jxd_36697.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 12 9.91 5 S 124 5.16 5 C 6330 2.51 5 N 1762 2.21 5 O 2106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10334 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3896 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 26, 'TRANS': 466} Chain: "B" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1170 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 14 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 14 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'A2G': 1} Classifications: {'undetermined': 1} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, F, G, H Time building chain proxies: 3.25, per 1000 atoms: 0.31 Number of scatterers: 10334 At special positions: 0 Unit cell: (150.977, 153.799, 86.071, 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 12 19.99 S 124 16.00 O 2106 8.00 N 1762 7.00 C 6330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS B 87 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B3761 " - pdb=" SG CYS B3773 " distance=2.03 Simple disulfide: pdb=" SG CYS B3768 " - pdb=" SG CYS B3786 " distance=2.03 Simple disulfide: pdb=" SG CYS B3780 " - pdb=" SG CYS B3795 " distance=2.04 Simple disulfide: pdb=" SG CYS B3800 " - pdb=" SG CYS B3812 " distance=2.03 Simple disulfide: pdb=" SG CYS B3807 " - pdb=" SG CYS B3825 " distance=2.04 Simple disulfide: pdb=" SG CYS B3819 " - pdb=" SG CYS B3834 " distance=2.03 Simple disulfide: pdb=" SG CYS E3930 " - pdb=" SG CYS E3942 " distance=2.03 Simple disulfide: pdb=" SG CYS E3937 " - pdb=" SG CYS E3955 " distance=2.03 Simple disulfide: pdb=" SG CYS E3949 " - pdb=" SG CYS E3964 " distance=2.03 Simple disulfide: pdb=" SG CYS E3972 " - pdb=" SG CYS E3981 " distance=2.03 Simple disulfide: pdb=" SG CYS E3977 " - pdb=" SG CYS E3991 " distance=2.03 Simple disulfide: pdb=" SG CYS E3993 " - pdb=" SG CYS E4007 " distance=2.03 Simple disulfide: pdb=" SG CYS E4013 " - pdb=" SG CYS E4023 " distance=2.03 Simple disulfide: pdb=" SG CYS E4019 " - pdb=" SG CYS E4032 " distance=2.03 Simple disulfide: pdb=" SG CYS E4034 " - pdb=" SG CYS E4049 " distance=2.03 Simple disulfide: pdb=" SG CYS E4336 " - pdb=" SG CYS E4344 " distance=2.03 Simple disulfide: pdb=" SG CYS E4340 " - pdb=" SG CYS E4353 " distance=2.03 Simple disulfide: pdb=" SG CYS E4355 " - pdb=" SG CYS E4369 " distance=2.03 Simple disulfide: pdb=" SG CYS E4383 " - pdb=" SG CYS E4391 " distance=2.03 Simple disulfide: pdb=" SG CYS E4385 " - pdb=" SG CYS E4401 " distance=2.03 Simple disulfide: pdb=" SG CYS E4403 " - pdb=" SG CYS E4412 " distance=2.03 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 40 " distance=2.03 Simple disulfide: pdb=" SG CYS F 35 " - pdb=" SG CYS F 53 " distance=2.04 Simple disulfide: pdb=" SG CYS F 47 " - pdb=" SG CYS F 62 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 74 " - pdb=" SG CYS F 93 " distance=2.03 Simple disulfide: pdb=" SG CYS F 87 " - pdb=" SG CYS F 103 " distance=2.03 Simple disulfide: pdb=" SG CYS F3761 " - pdb=" SG CYS F3773 " distance=2.03 Simple disulfide: pdb=" SG CYS F3768 " - pdb=" SG CYS F3786 " distance=2.03 Simple disulfide: pdb=" SG CYS F3780 " - pdb=" SG CYS F3795 " distance=2.04 Simple disulfide: pdb=" SG CYS F3800 " - pdb=" SG CYS F3812 " distance=2.03 Simple disulfide: pdb=" SG CYS F3807 " - pdb=" SG CYS F3825 " distance=2.04 Simple disulfide: pdb=" SG CYS F3819 " - pdb=" SG CYS F3834 " 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=2, symmetry=0 Links applied BETA1-3 " NAG D 2 " - " BMA D 3 " " NAG H 2 " - " BMA H 3 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A4701 " - " ASN A3980 " " NAG C 1 " - " ASN A4070 " " NAG D 1 " - " ASN A4329 " " NAG E4701 " - " ASN E3980 " " NAG G 1 " - " ASN E4070 " " NAG H 1 " - " ASN E4329 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 350.8 milliseconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2404 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 34 sheets defined 5.1% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... 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 3958 through 3962 removed outlier: 3.804A pdb=" N THR A3962 " --> pdb=" O SER A3959 " (cutoff:3.500A) Processing helix chain 'A' and resid 3971 through 3975 Processing helix chain 'A' and resid 4011 through 4015 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 97 through 102 Processing helix chain 'B' and resid 3777 through 3779 No H-bonds generated for 'chain 'B' and resid 3777 through 3779' Processing helix chain 'B' and resid 3816 through 3818 No H-bonds generated for 'chain 'B' and resid 3816 through 3818' Processing helix chain 'E' and resid 3946 through 3948 No H-bonds generated for 'chain 'E' and resid 3946 through 3948' Processing helix chain 'E' and resid 3958 through 3962 removed outlier: 3.804A pdb=" N THR E3962 " --> pdb=" O SER E3959 " (cutoff:3.500A) Processing helix chain 'E' and resid 3971 through 3975 Processing helix chain 'E' and resid 4011 through 4015 Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 97 through 102 Processing helix chain 'F' and resid 3777 through 3779 No H-bonds generated for 'chain 'F' and resid 3777 through 3779' Processing helix chain 'F' and resid 3816 through 3818 No H-bonds generated for 'chain 'F' and resid 3816 through 3818' Processing sheet with id=1, first strand: chain 'A' and resid 3934 through 3935 Processing sheet with id=2, first strand: chain 'A' and resid 3981 through 3983 Processing sheet with id=3, first strand: chain 'A' and resid 3997 through 3999 Processing sheet with id=4, first strand: chain 'A' and resid 4024 through 4026 Processing sheet with id=5, first strand: chain 'A' and resid 4040 through 4043 removed outlier: 3.738A pdb=" N GLY A4046 " --> pdb=" O THR A4043 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 4075 through 4077 removed outlier: 3.871A pdb=" N LYS A4075 " --> pdb=" O ASN A4070 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A4077 " --> pdb=" O LYS A4068 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS A4068 " --> pdb=" O SER A4077 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 4086 through 4092 removed outlier: 5.144A pdb=" N THR A4088 " --> pdb=" O THR A4106 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR A4106 " --> pdb=" O THR A4088 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A4136 " --> pdb=" O ARG A4119 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'A' and resid 4146 through 4152 removed outlier: 3.713A pdb=" N GLY A4148 " --> pdb=" O SER A4161 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL A4170 " --> pdb=" O TRP A4180 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TRP A4180 " --> pdb=" O VAL A4170 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 4189 through 4195 removed outlier: 4.452A pdb=" N THR A4204 " --> pdb=" O ALA A4190 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE A4192 " --> pdb=" O PHE A4202 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE A4202 " --> pdb=" O ILE A4192 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL A4194 " --> pdb=" O LEU A4200 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU A4200 " --> pdb=" O VAL A4194 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A4212 " --> pdb=" O LEU A4225 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'A' and resid 4233 through 4239 removed outlier: 3.587A pdb=" N GLY A4235 " --> pdb=" O SER A4249 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A4256 " --> pdb=" O ILE A4269 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'A' and resid 4276 through 4282 removed outlier: 6.568A pdb=" N VAL A4289 " --> pdb=" O PHE A4277 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A4279 " --> pdb=" O TYR A4287 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR A4287 " --> pdb=" O LEU A4279 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE A4281 " --> pdb=" O LYS A4285 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS A4285 " --> pdb=" O ILE A4281 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A4296 " --> pdb=" O VAL A4310 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'A' and resid 4343 through 4347 Processing sheet with id=13, first strand: chain 'A' and resid 4390 through 4393 removed outlier: 3.753A pdb=" N ASN A4390 " --> pdb=" O LYS A4402 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 32 through 34 Processing sheet with id=15, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=16, first strand: chain 'B' and resid 3765 through 3767 Processing sheet with id=17, first strand: chain 'B' and resid 3804 through 3806 Processing sheet with id=18, first strand: chain 'E' and resid 3934 through 3935 Processing sheet with id=19, first strand: chain 'E' and resid 3981 through 3983 Processing sheet with id=20, first strand: chain 'E' and resid 3997 through 3999 Processing sheet with id=21, first strand: chain 'E' and resid 4024 through 4026 Processing sheet with id=22, first strand: chain 'E' and resid 4040 through 4043 removed outlier: 3.738A pdb=" N GLY E4046 " --> pdb=" O THR E4043 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 4075 through 4077 removed outlier: 3.871A pdb=" N LYS E4075 " --> pdb=" O ASN E4070 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E4077 " --> pdb=" O LYS E4068 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS E4068 " --> pdb=" O SER E4077 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 4086 through 4092 removed outlier: 5.144A pdb=" N THR E4088 " --> pdb=" O THR E4106 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR E4106 " --> pdb=" O THR E4088 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL E4136 " --> pdb=" O ARG E4119 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 4146 through 4152 removed outlier: 3.713A pdb=" N GLY E4148 " --> pdb=" O SER E4161 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL E4170 " --> pdb=" O TRP E4180 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N TRP E4180 " --> pdb=" O VAL E4170 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'E' and resid 4189 through 4195 removed outlier: 4.452A pdb=" N THR E4204 " --> pdb=" O ALA E4190 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE E4192 " --> pdb=" O PHE E4202 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE E4202 " --> pdb=" O ILE E4192 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL E4194 " --> pdb=" O LEU E4200 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LEU E4200 " --> pdb=" O VAL E4194 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE E4212 " --> pdb=" O LEU E4225 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'E' and resid 4233 through 4239 removed outlier: 3.587A pdb=" N GLY E4235 " --> pdb=" O SER E4249 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE E4256 " --> pdb=" O ILE E4269 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'E' and resid 4276 through 4282 removed outlier: 6.568A pdb=" N VAL E4289 " --> pdb=" O PHE E4277 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU E4279 " --> pdb=" O TYR E4287 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TYR E4287 " --> pdb=" O LEU E4279 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE E4281 " --> pdb=" O LYS E4285 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N LYS E4285 " --> pdb=" O ILE E4281 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL E4296 " --> pdb=" O VAL E4310 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 4343 through 4347 Processing sheet with id=30, first strand: chain 'E' and resid 4390 through 4393 removed outlier: 3.753A pdb=" N ASN E4390 " --> pdb=" O LYS E4402 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'F' and resid 32 through 34 Processing sheet with id=32, first strand: chain 'F' and resid 71 through 73 Processing sheet with id=33, first strand: chain 'F' and resid 3765 through 3767 Processing sheet with id=34, first strand: chain 'F' and resid 3804 through 3806 212 hydrogen bonds defined for protein. 504 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.01 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: 3500 1.34 - 1.46: 2278 1.46 - 1.58: 4636 1.58 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 10554 Sorted by residual: bond pdb=" C1 A2G B4701 " pdb=" O5 A2G B4701 " ideal model delta sigma weight residual 1.385 1.420 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 A2G F4701 " pdb=" O5 A2G F4701 " ideal model delta sigma weight residual 1.385 1.420 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C2 BMA H 3 " pdb=" O2 BMA H 3 " ideal model delta sigma weight residual 1.402 1.431 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C2 BMA D 3 " pdb=" O2 BMA D 3 " ideal model delta sigma weight residual 1.402 1.431 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C3 NAG H 1 " pdb=" O3 NAG H 1 " ideal model delta sigma weight residual 1.403 1.432 -0.029 2.00e-02 2.50e+03 2.11e+00 ... (remaining 10549 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 13968 1.96 - 3.92: 288 3.92 - 5.88: 32 5.88 - 7.84: 6 7.84 - 9.80: 2 Bond angle restraints: 14296 Sorted by residual: angle pdb=" CB LYS B 91 " pdb=" CG LYS B 91 " pdb=" CD LYS B 91 " ideal model delta sigma weight residual 111.30 121.10 -9.80 2.30e+00 1.89e-01 1.82e+01 angle pdb=" CB LYS F 91 " pdb=" CG LYS F 91 " pdb=" CD LYS F 91 " ideal model delta sigma weight residual 111.30 121.10 -9.80 2.30e+00 1.89e-01 1.82e+01 angle pdb=" C ARG B3793 " pdb=" N ASP B3794 " pdb=" CA ASP B3794 " ideal model delta sigma weight residual 122.46 126.92 -4.46 1.41e+00 5.03e-01 1.00e+01 angle pdb=" C ARG F3793 " pdb=" N ASP F3794 " pdb=" CA ASP F3794 " ideal model delta sigma weight residual 122.46 126.92 -4.46 1.41e+00 5.03e-01 1.00e+01 angle pdb=" N ASP B3794 " pdb=" CA ASP B3794 " pdb=" C ASP B3794 " ideal model delta sigma weight residual 111.30 115.57 -4.27 1.36e+00 5.41e-01 9.84e+00 ... (remaining 14291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 5966 21.50 - 42.99: 594 42.99 - 64.49: 96 64.49 - 85.99: 38 85.99 - 107.48: 16 Dihedral angle restraints: 6710 sinusoidal: 2968 harmonic: 3742 Sorted by residual: dihedral pdb=" CB CYS E3937 " pdb=" SG CYS E3937 " pdb=" SG CYS E3955 " pdb=" CB CYS E3955 " ideal model delta sinusoidal sigma weight residual -86.00 -173.10 87.10 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS A3937 " pdb=" SG CYS A3937 " pdb=" SG CYS A3955 " pdb=" CB CYS A3955 " ideal model delta sinusoidal sigma weight residual -86.00 -173.10 87.10 1 1.00e+01 1.00e-02 9.11e+01 dihedral pdb=" CB CYS A3972 " pdb=" SG CYS A3972 " pdb=" SG CYS A3981 " pdb=" CB CYS A3981 " ideal model delta sinusoidal sigma weight residual 93.00 165.57 -72.57 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 6707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 982 0.039 - 0.078: 366 0.078 - 0.117: 136 0.117 - 0.156: 26 0.156 - 0.195: 8 Chirality restraints: 1518 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O3 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.61e+01 chirality pdb=" C1 BMA D 3 " pdb=" O3 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.61e+01 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.47 0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 1515 not shown) Planarity restraints: 1908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.156 2.00e-02 2.50e+03 1.28e-01 2.06e+02 pdb=" C7 NAG C 2 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.115 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.206 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.156 2.00e-02 2.50e+03 1.28e-01 2.06e+02 pdb=" C7 NAG G 2 " -0.042 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.115 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.206 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.081 2.00e-02 2.50e+03 6.63e-02 5.49e+01 pdb=" C7 NAG C 1 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.061 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.105 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.015 2.00e-02 2.50e+03 ... (remaining 1905 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2036 2.77 - 3.30: 10249 3.30 - 3.84: 16993 3.84 - 4.37: 19798 4.37 - 4.90: 33654 Nonbonded interactions: 82730 Sorted by model distance: nonbonded pdb=" OD2 ASP B3785 " pdb="CA CA B4704 " model vdw 2.241 3.250 nonbonded pdb=" OD2 ASP F3785 " pdb="CA CA F4704 " model vdw 2.241 3.250 nonbonded pdb=" OD2 ASP B 58 " pdb="CA CA B4702 " model vdw 2.242 3.250 nonbonded pdb=" OD2 ASP F 58 " pdb="CA CA F4702 " model vdw 2.242 3.250 nonbonded pdb=" OD1 ASP F 48 " pdb="CA CA F4702 " model vdw 2.251 3.250 ... (remaining 82725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.390 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 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 0.062 10622 Z= 0.172 Angle : 0.669 9.805 14440 Z= 0.351 Chirality : 0.047 0.195 1518 Planarity : 0.007 0.128 1902 Dihedral : 17.240 107.485 4144 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.45 % Allowed : 22.55 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.24), residues: 1286 helix: -3.96 (1.09), residues: 14 sheet: -0.43 (0.31), residues: 298 loop : -0.41 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.018 0.001 TYR A4392 PHE 0.007 0.001 PHE A4125 TRP 0.009 0.001 TRP A4288 HIS 0.005 0.001 HIS A4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (10554) covalent geometry : angle 0.65876 / 0.35 (14296) SS BOND : bond 0.00244 / 0.17 ( 54) SS BOND : angle 0.89819 / 0.64 ( 108) hydrogen bonds : bond 0.28342 / 18.39 ( 212) hydrogen bonds : angle 11.50839 / 7.79 ( 504) Misc. bond : bond 0.00046 / 0.02 ( 2) link_BETA1-3 : bond 0.00224 / 0.11 ( 2) link_BETA1-3 : angle 0.97229 / 0.48 ( 6) link_BETA1-4 : bond 0.00332 / 0.17 ( 4) link_BETA1-4 : angle 1.66874 / 1.16 ( 12) link_NAG-ASN : bond 0.00435 / 0.21 ( 6) link_NAG-ASN : angle 2.75089 / 1.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 106 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4062 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: B 89 GLU cc_start: 0.7862 (mp0) cc_final: 0.7265 (pt0) REVERT: B 3767 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7898 (mmm-85) REVERT: B 3798 LYS cc_start: 0.9013 (ptpt) cc_final: 0.8806 (ptpt) REVERT: E 4062 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: F 89 GLU cc_start: 0.7863 (mp0) cc_final: 0.7267 (pt0) REVERT: F 3767 ARG cc_start: 0.8104 (mmm-85) cc_final: 0.7870 (mmm-85) REVERT: F 3798 LYS cc_start: 0.9011 (ptpt) cc_final: 0.8805 (ptpt) outliers start: 28 outliers final: 22 residues processed: 132 average time/residue: 0.0783 time to fit residues: 15.1556 Evaluate side-chains 112 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3942 CYS Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4108 LEU Chi-restraints excluded: chain A residue 4237 SER Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4353 CYS Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain B residue 3773 CYS Chi-restraints excluded: chain B residue 3799 THR Chi-restraints excluded: chain E residue 3942 CYS Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4108 LEU Chi-restraints excluded: chain E residue 4237 SER Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4353 CYS Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain F residue 3773 CYS Chi-restraints excluded: chain F residue 3799 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4087 GLN A4131 ASN A4221 HIS A4390 ASN B 100 GLN B3772 GLN B3782 GLN E4131 ASN E4221 HIS E4390 ASN F 100 GLN F3782 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.147200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094761 restraints weight = 18805.639| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.27 r_work: 0.3203 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10622 Z= 0.235 Angle : 0.710 7.245 14440 Z= 0.375 Chirality : 0.049 0.163 1518 Planarity : 0.006 0.051 1902 Dihedral : 9.605 64.846 1726 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 4.63 % Allowed : 19.58 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.23), residues: 1286 helix: -3.82 (1.15), residues: 12 sheet: -0.92 (0.33), residues: 258 loop : -0.61 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E4119 TYR 0.012 0.002 TYR E4247 PHE 0.014 0.002 PHE B3766 TRP 0.018 0.002 TRP E4288 HIS 0.008 0.001 HIS E4221 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (10554) covalent geometry : angle 0.69246 / 0.37 (14296) SS BOND : bond 0.00305 / 0.19 ( 54) SS BOND : angle 1.29306 / 0.89 ( 108) hydrogen bonds : bond 0.05519 / 3.61 ( 212) hydrogen bonds : angle 7.86835 / 5.28 ( 504) Misc. bond : bond 0.00053 / 0.03 ( 2) link_BETA1-3 : bond 0.00905 / 0.45 ( 2) link_BETA1-3 : angle 2.63565 / 1.47 ( 6) link_BETA1-4 : bond 0.00496 / 0.25 ( 4) link_BETA1-4 : angle 2.15981 / 1.48 ( 12) link_NAG-ASN : bond 0.00086 / 0.04 ( 6) link_NAG-ASN : angle 2.88524 / 1.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 101 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3947 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.8273 (t80) REVERT: A 4062 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: B 77 GLU cc_start: 0.7276 (tp30) cc_final: 0.7065 (pt0) REVERT: B 89 GLU cc_start: 0.8038 (mp0) cc_final: 0.7281 (pt0) REVERT: B 3766 PHE cc_start: 0.7141 (t80) cc_final: 0.6792 (t80) REVERT: B 3767 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.7744 (mmm-85) REVERT: B 3796 GLU cc_start: 0.8493 (tp30) cc_final: 0.7816 (tp30) REVERT: B 3798 LYS cc_start: 0.9016 (ptpt) cc_final: 0.8778 (ptpt) REVERT: E 3947 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.8270 (t80) REVERT: E 4062 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: F 77 GLU cc_start: 0.7280 (tp30) cc_final: 0.7067 (pt0) REVERT: F 89 GLU cc_start: 0.8031 (mp0) cc_final: 0.7275 (pt0) REVERT: F 3766 PHE cc_start: 0.7553 (t80) cc_final: 0.7166 (t80) REVERT: F 3767 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.8016 (mmm-85) REVERT: F 3772 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: F 3796 GLU cc_start: 0.8427 (tp30) cc_final: 0.7748 (tp30) REVERT: F 3798 LYS cc_start: 0.8953 (ptpt) cc_final: 0.8719 (ptpt) outliers start: 53 outliers final: 25 residues processed: 145 average time/residue: 0.0867 time to fit residues: 18.0530 Evaluate side-chains 116 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3926 THR Chi-restraints excluded: chain A residue 3947 TYR Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4102 VAL Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 3773 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain E residue 3926 THR Chi-restraints excluded: chain E residue 3947 TYR Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4035 VAL Chi-restraints excluded: chain E residue 4047 GLU Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4102 VAL Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4174 ASP Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 3772 GLN Chi-restraints excluded: chain F residue 3773 CYS Chi-restraints excluded: chain F residue 3797 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 61 optimal weight: 0.0570 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4130 ASN B 100 GLN E4130 ASN F 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.148046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.095902 restraints weight = 18657.727| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.26 r_work: 0.3225 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10622 Z= 0.161 Angle : 0.632 7.431 14440 Z= 0.332 Chirality : 0.047 0.168 1518 Planarity : 0.005 0.043 1902 Dihedral : 7.931 64.085 1710 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 4.98 % Allowed : 19.23 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.24), residues: 1286 helix: -3.62 (1.26), residues: 12 sheet: -0.82 (0.32), residues: 282 loop : -0.57 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A4327 TYR 0.012 0.001 TYR E4247 PHE 0.009 0.001 PHE E4125 TRP 0.012 0.002 TRP E4288 HIS 0.003 0.001 HIS B3811 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (10554) covalent geometry : angle 0.61588 / 0.33 (14296) SS BOND : bond 0.00269 / 0.18 ( 54) SS BOND : angle 0.98121 / 0.69 ( 108) hydrogen bonds : bond 0.04754 / 3.14 ( 212) hydrogen bonds : angle 7.28255 / 4.88 ( 504) Misc. bond : bond 0.00025 / 0.01 ( 2) link_BETA1-3 : bond 0.00774 / 0.39 ( 2) link_BETA1-3 : angle 2.29435 / 1.25 ( 6) link_BETA1-4 : bond 0.00149 / 0.08 ( 4) link_BETA1-4 : angle 2.14997 / 1.50 ( 12) link_NAG-ASN : bond 0.00227 / 0.11 ( 6) link_NAG-ASN : angle 2.96324 / 1.57 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 94 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3947 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.8265 (t80) REVERT: A 4062 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: B 77 GLU cc_start: 0.7029 (tp30) cc_final: 0.6764 (pt0) REVERT: B 89 GLU cc_start: 0.7998 (mp0) cc_final: 0.7287 (pt0) REVERT: B 3766 PHE cc_start: 0.7666 (t80) cc_final: 0.7132 (t80) REVERT: B 3783 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7447 (tm-30) REVERT: B 3796 GLU cc_start: 0.8495 (tp30) cc_final: 0.7898 (tp30) REVERT: E 3947 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.8262 (t80) REVERT: E 4062 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: F 77 GLU cc_start: 0.7034 (tp30) cc_final: 0.6764 (pt0) REVERT: F 89 GLU cc_start: 0.7992 (mp0) cc_final: 0.7281 (pt0) REVERT: F 3766 PHE cc_start: 0.8044 (t80) cc_final: 0.7471 (t80) REVERT: F 3772 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: F 3778 TRP cc_start: 0.6900 (m-10) cc_final: 0.6603 (m-10) REVERT: F 3783 GLU cc_start: 0.8286 (mp0) cc_final: 0.8026 (mp0) REVERT: F 3796 GLU cc_start: 0.8444 (tp30) cc_final: 0.7847 (tp30) outliers start: 57 outliers final: 30 residues processed: 143 average time/residue: 0.1007 time to fit residues: 20.7047 Evaluate side-chains 123 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3942 CYS Chi-restraints excluded: chain A residue 3947 TYR Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4088 THR Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4102 VAL Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4108 LEU Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain E residue 3942 CYS Chi-restraints excluded: chain E residue 3947 TYR Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4035 VAL Chi-restraints excluded: chain E residue 4047 GLU Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4088 THR Chi-restraints excluded: chain E residue 4089 ILE Chi-restraints excluded: chain E residue 4102 VAL Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4108 LEU Chi-restraints excluded: chain E residue 4174 ASP Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain F residue 3772 GLN Chi-restraints excluded: chain F residue 3774 ILE Chi-restraints excluded: chain F residue 3797 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 119 optimal weight: 0.4980 chunk 63 optimal weight: 20.0000 chunk 120 optimal weight: 0.0170 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4130 ASN B 100 GLN E4130 ASN F 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.148919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.096662 restraints weight = 18664.620| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.26 r_work: 0.3241 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10622 Z= 0.126 Angle : 0.595 7.198 14440 Z= 0.312 Chirality : 0.046 0.169 1518 Planarity : 0.004 0.040 1902 Dihedral : 6.916 63.093 1708 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.07 % Allowed : 17.92 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.24), residues: 1286 helix: -3.61 (1.27), residues: 12 sheet: -0.78 (0.32), residues: 282 loop : -0.49 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 65 TYR 0.010 0.001 TYR E4247 PHE 0.007 0.001 PHE E4125 TRP 0.010 0.001 TRP E4288 HIS 0.003 0.001 HIS E3927 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (10554) covalent geometry : angle 0.57931 / 0.31 (14296) SS BOND : bond 0.00255 / 0.17 ( 54) SS BOND : angle 0.96412 / 0.69 ( 108) hydrogen bonds : bond 0.03836 / 2.54 ( 212) hydrogen bonds : angle 6.73975 / 4.47 ( 504) Misc. bond : bond 0.00008 / 0.00 ( 2) link_BETA1-3 : bond 0.00793 / 0.40 ( 2) link_BETA1-3 : angle 2.34325 / 1.28 ( 6) link_BETA1-4 : bond 0.00226 / 0.12 ( 4) link_BETA1-4 : angle 2.04385 / 1.41 ( 12) link_NAG-ASN : bond 0.00314 / 0.15 ( 6) link_NAG-ASN : angle 2.77418 / 1.46 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 100 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4062 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: A 4217 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8927 (mpt) REVERT: A 4218 ASN cc_start: 0.9022 (t0) cc_final: 0.8791 (t0) REVERT: B 77 GLU cc_start: 0.7018 (tp30) cc_final: 0.6744 (pt0) REVERT: B 89 GLU cc_start: 0.7745 (mp0) cc_final: 0.7220 (pt0) REVERT: B 3767 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.7786 (mmm-85) REVERT: B 3771 GLN cc_start: 0.8915 (tp-100) cc_final: 0.8710 (tp40) REVERT: B 3783 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7603 (tm-30) REVERT: B 3796 GLU cc_start: 0.8505 (tp30) cc_final: 0.7910 (tp30) REVERT: E 4062 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: E 4217 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8937 (mpt) REVERT: E 4218 ASN cc_start: 0.9027 (t0) cc_final: 0.8792 (t0) REVERT: F 77 GLU cc_start: 0.7026 (tp30) cc_final: 0.6744 (pt0) REVERT: F 89 GLU cc_start: 0.7740 (mp0) cc_final: 0.7214 (pt0) REVERT: F 3767 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7812 (mmm-85) REVERT: F 3772 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7588 (pt0) REVERT: F 3783 GLU cc_start: 0.8235 (mp0) cc_final: 0.7976 (mp0) REVERT: F 3796 GLU cc_start: 0.8427 (tp30) cc_final: 0.7810 (tp30) outliers start: 58 outliers final: 34 residues processed: 146 average time/residue: 0.0900 time to fit residues: 19.3286 Evaluate side-chains 130 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3926 THR Chi-restraints excluded: chain A residue 3942 CYS Chi-restraints excluded: chain A residue 3964 CYS Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4102 VAL Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4147 ASP Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 3773 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain E residue 3926 THR Chi-restraints excluded: chain E residue 3942 CYS Chi-restraints excluded: chain E residue 3964 CYS Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4035 VAL Chi-restraints excluded: chain E residue 4047 GLU Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4089 ILE Chi-restraints excluded: chain E residue 4102 VAL Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4174 ASP Chi-restraints excluded: chain E residue 4217 MET Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain E residue 4400 LYS Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 3772 GLN Chi-restraints excluded: chain F residue 3773 CYS Chi-restraints excluded: chain F residue 3774 ILE Chi-restraints excluded: chain F residue 3797 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4130 ASN E4087 GLN E4130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.142656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090146 restraints weight = 18627.651| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.13 r_work: 0.3114 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 10622 Z= 0.424 Angle : 0.840 8.251 14440 Z= 0.441 Chirality : 0.055 0.177 1518 Planarity : 0.006 0.065 1902 Dihedral : 7.477 66.431 1706 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 5.33 % Allowed : 17.66 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.24), residues: 1286 helix: -3.38 (1.48), residues: 14 sheet: -1.54 (0.30), residues: 302 loop : -0.71 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A4119 TYR 0.016 0.003 TYR E4247 PHE 0.016 0.003 PHE E4202 TRP 0.024 0.003 TRP A4288 HIS 0.008 0.002 HIS A4324 Details of bonding type rmsd/Z covalent geometry : bond 0.01002 / 0.42 (10554) covalent geometry : angle 0.81869 / 0.44 (14296) SS BOND : bond 0.00403 / 0.27 ( 54) SS BOND : angle 1.54500 / 1.14 ( 108) hydrogen bonds : bond 0.05158 / 3.49 ( 212) hydrogen bonds : angle 7.47803 / 5.04 ( 504) Misc. bond : bond 0.00058 / 0.03 ( 2) link_BETA1-3 : bond 0.00698 / 0.35 ( 2) link_BETA1-3 : angle 1.89230 / 1.02 ( 6) link_BETA1-4 : bond 0.00483 / 0.24 ( 4) link_BETA1-4 : angle 2.77310 / 1.94 ( 12) link_NAG-ASN : bond 0.00482 / 0.24 ( 6) link_NAG-ASN : angle 3.53377 / 1.92 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 91 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4062 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: B 77 GLU cc_start: 0.7398 (tp30) cc_final: 0.7087 (pt0) REVERT: B 89 GLU cc_start: 0.8089 (mp0) cc_final: 0.7431 (pt0) REVERT: B 3771 GLN cc_start: 0.8623 (tp-100) cc_final: 0.8422 (tp-100) REVERT: B 3772 GLN cc_start: 0.8508 (pt0) cc_final: 0.8306 (pt0) REVERT: B 3783 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 3796 GLU cc_start: 0.8683 (tp30) cc_final: 0.8080 (tp30) REVERT: E 4062 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: F 77 GLU cc_start: 0.7403 (tp30) cc_final: 0.7089 (pt0) REVERT: F 89 GLU cc_start: 0.8089 (mp0) cc_final: 0.7433 (pt0) REVERT: F 3772 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: F 3796 GLU cc_start: 0.8665 (tp30) cc_final: 0.8073 (tp30) outliers start: 61 outliers final: 38 residues processed: 143 average time/residue: 0.0865 time to fit residues: 19.0054 Evaluate side-chains 128 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 87 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3926 THR Chi-restraints excluded: chain A residue 3942 CYS Chi-restraints excluded: chain A residue 3964 CYS Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4102 VAL Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4255 VAL Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 3773 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain B residue 3799 THR Chi-restraints excluded: chain E residue 3926 THR Chi-restraints excluded: chain E residue 3942 CYS Chi-restraints excluded: chain E residue 3964 CYS Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4041 MET Chi-restraints excluded: chain E residue 4047 GLU Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4089 ILE Chi-restraints excluded: chain E residue 4102 VAL Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4136 VAL Chi-restraints excluded: chain E residue 4255 VAL Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain E residue 4400 LYS Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 3772 GLN Chi-restraints excluded: chain F residue 3773 CYS Chi-restraints excluded: chain F residue 3774 ILE Chi-restraints excluded: chain F residue 3797 MET Chi-restraints excluded: chain F residue 3799 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 72 optimal weight: 0.0070 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4130 ASN E4130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.146795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.094190 restraints weight = 18730.874| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.27 r_work: 0.3193 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10622 Z= 0.141 Angle : 0.641 8.701 14440 Z= 0.335 Chirality : 0.047 0.162 1518 Planarity : 0.004 0.040 1902 Dihedral : 6.986 64.730 1706 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.28 % Allowed : 20.10 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.24), residues: 1286 helix: -3.30 (1.49), residues: 12 sheet: -1.06 (0.33), residues: 258 loop : -0.65 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E4048 TYR 0.013 0.001 TYR A4247 PHE 0.009 0.001 PHE E4125 TRP 0.013 0.002 TRP F 85 HIS 0.002 0.001 HIS E3927 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (10554) covalent geometry : angle 0.62408 / 0.33 (14296) SS BOND : bond 0.00383 / 0.25 ( 54) SS BOND : angle 1.06947 / 0.76 ( 108) hydrogen bonds : bond 0.03768 / 2.50 ( 212) hydrogen bonds : angle 6.95138 / 4.65 ( 504) Misc. bond : bond 0.00002 / 0.00 ( 2) link_BETA1-3 : bond 0.00875 / 0.44 ( 2) link_BETA1-3 : angle 2.38363 / 1.29 ( 6) link_BETA1-4 : bond 0.00145 / 0.07 ( 4) link_BETA1-4 : angle 2.03000 / 1.38 ( 12) link_NAG-ASN : bond 0.00262 / 0.12 ( 6) link_NAG-ASN : angle 3.03262 / 1.61 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 93 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3970 ARG cc_start: 0.0552 (OUTLIER) cc_final: -0.0511 (mtm180) REVERT: A 4062 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: A 4217 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8826 (mpt) REVERT: B 77 GLU cc_start: 0.7419 (tp30) cc_final: 0.7119 (pt0) REVERT: B 89 GLU cc_start: 0.7768 (mp0) cc_final: 0.7350 (pt0) REVERT: B 3783 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 3796 GLU cc_start: 0.8667 (tp30) cc_final: 0.8112 (tp30) REVERT: E 3970 ARG cc_start: 0.0621 (OUTLIER) cc_final: -0.0423 (mtm180) REVERT: E 4062 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: E 4217 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8835 (mpt) REVERT: F 77 GLU cc_start: 0.7428 (tp30) cc_final: 0.7121 (pt0) REVERT: F 89 GLU cc_start: 0.7765 (mp0) cc_final: 0.7349 (pt0) REVERT: F 3772 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8076 (pt0) REVERT: F 3796 GLU cc_start: 0.8639 (tp30) cc_final: 0.8098 (tp30) outliers start: 49 outliers final: 36 residues processed: 133 average time/residue: 0.0883 time to fit residues: 17.2132 Evaluate side-chains 132 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 89 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3942 CYS Chi-restraints excluded: chain A residue 3964 CYS Chi-restraints excluded: chain A residue 3970 ARG Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4102 VAL Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4147 ASP Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 3773 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain E residue 3942 CYS Chi-restraints excluded: chain E residue 3964 CYS Chi-restraints excluded: chain E residue 3970 ARG Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4035 VAL Chi-restraints excluded: chain E residue 4041 MET Chi-restraints excluded: chain E residue 4047 GLU Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4089 ILE Chi-restraints excluded: chain E residue 4102 VAL Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4136 VAL Chi-restraints excluded: chain E residue 4147 ASP Chi-restraints excluded: chain E residue 4174 ASP Chi-restraints excluded: chain E residue 4217 MET Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain E residue 4400 LYS Chi-restraints excluded: chain F residue 3772 GLN Chi-restraints excluded: chain F residue 3773 CYS Chi-restraints excluded: chain F residue 3774 ILE Chi-restraints excluded: chain F residue 3797 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 70 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4130 ASN B3771 GLN E4130 ASN F3771 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.155814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101906 restraints weight = 18213.935| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.20 r_work: 0.3166 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10622 Z= 0.159 Angle : 0.629 9.058 14440 Z= 0.329 Chirality : 0.046 0.171 1518 Planarity : 0.004 0.043 1902 Dihedral : 6.856 62.909 1706 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.63 % Allowed : 20.02 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.24), residues: 1286 helix: -3.71 (1.26), residues: 14 sheet: -1.10 (0.33), residues: 258 loop : -0.62 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A4298 TYR 0.012 0.002 TYR A4407 PHE 0.009 0.001 PHE A4323 TRP 0.014 0.002 TRP B 85 HIS 0.003 0.001 HIS E4324 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (10554) covalent geometry : angle 0.61263 / 0.32 (14296) SS BOND : bond 0.00225 / 0.15 ( 54) SS BOND : angle 1.03906 / 0.74 ( 108) hydrogen bonds : bond 0.03793 / 2.53 ( 212) hydrogen bonds : angle 6.74303 / 4.52 ( 504) Misc. bond : bond 0.00010 / 0.01 ( 2) link_BETA1-3 : bond 0.00781 / 0.39 ( 2) link_BETA1-3 : angle 2.15540 / 1.17 ( 6) link_BETA1-4 : bond 0.00032 / 0.02 ( 4) link_BETA1-4 : angle 2.05357 / 1.44 ( 12) link_NAG-ASN : bond 0.00160 / 0.07 ( 6) link_NAG-ASN : angle 2.91493 / 1.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 95 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3970 ARG cc_start: 0.0682 (OUTLIER) cc_final: -0.0025 (mtm180) REVERT: A 4062 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: A 4217 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8859 (mpt) REVERT: B 77 GLU cc_start: 0.7433 (tp30) cc_final: 0.7122 (pt0) REVERT: B 89 GLU cc_start: 0.7774 (mp0) cc_final: 0.7352 (pt0) REVERT: B 3767 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.7844 (mmm-85) REVERT: B 3772 GLN cc_start: 0.8561 (pt0) cc_final: 0.8340 (pt0) REVERT: B 3783 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 3796 GLU cc_start: 0.8656 (tp30) cc_final: 0.8097 (tp30) REVERT: E 3970 ARG cc_start: 0.0570 (OUTLIER) cc_final: -0.0249 (mtm180) REVERT: E 4062 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: E 4217 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8857 (mpt) REVERT: F 77 GLU cc_start: 0.7442 (tp30) cc_final: 0.7124 (pt0) REVERT: F 89 GLU cc_start: 0.7773 (mp0) cc_final: 0.7350 (pt0) REVERT: F 3772 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8115 (pt0) REVERT: F 3796 GLU cc_start: 0.8639 (tp30) cc_final: 0.8100 (tp30) outliers start: 53 outliers final: 36 residues processed: 138 average time/residue: 0.0824 time to fit residues: 16.6975 Evaluate side-chains 134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3942 CYS Chi-restraints excluded: chain A residue 3964 CYS Chi-restraints excluded: chain A residue 3970 ARG Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4033 PHE Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4102 VAL Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4108 LEU Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 3773 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain E residue 3942 CYS Chi-restraints excluded: chain E residue 3964 CYS Chi-restraints excluded: chain E residue 3970 ARG Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4033 PHE Chi-restraints excluded: chain E residue 4035 VAL Chi-restraints excluded: chain E residue 4041 MET Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4089 ILE Chi-restraints excluded: chain E residue 4102 VAL Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4108 LEU Chi-restraints excluded: chain E residue 4136 VAL Chi-restraints excluded: chain E residue 4217 MET Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain E residue 4400 LYS Chi-restraints excluded: chain F residue 3772 GLN Chi-restraints excluded: chain F residue 3773 CYS Chi-restraints excluded: chain F residue 3774 ILE Chi-restraints excluded: chain F residue 3797 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 127 optimal weight: 50.0000 chunk 113 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 92 optimal weight: 0.4980 chunk 58 optimal weight: 0.2980 chunk 63 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4130 ASN B3771 GLN E4130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.156495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102763 restraints weight = 18258.959| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.20 r_work: 0.3176 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10622 Z= 0.150 Angle : 0.620 8.869 14440 Z= 0.323 Chirality : 0.046 0.170 1518 Planarity : 0.004 0.041 1902 Dihedral : 6.860 63.233 1706 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.37 % Allowed : 19.84 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.24), residues: 1286 helix: -3.72 (1.24), residues: 14 sheet: -1.08 (0.33), residues: 258 loop : -0.60 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4119 TYR 0.010 0.001 TYR E4247 PHE 0.009 0.001 PHE E4323 TRP 0.015 0.002 TRP F 85 HIS 0.002 0.001 HIS E3927 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (10554) covalent geometry : angle 0.60336 / 0.32 (14296) SS BOND : bond 0.00221 / 0.15 ( 54) SS BOND : angle 1.05269 / 0.76 ( 108) hydrogen bonds : bond 0.03712 / 2.47 ( 212) hydrogen bonds : angle 6.64155 / 4.44 ( 504) Misc. bond : bond 0.00006 / 0.00 ( 2) link_BETA1-3 : bond 0.00756 / 0.38 ( 2) link_BETA1-3 : angle 2.13514 / 1.17 ( 6) link_BETA1-4 : bond 0.00050 / 0.03 ( 4) link_BETA1-4 : angle 1.95763 / 1.37 ( 12) link_NAG-ASN : bond 0.00191 / 0.09 ( 6) link_NAG-ASN : angle 2.87158 / 1.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3970 ARG cc_start: 0.0656 (OUTLIER) cc_final: 0.0201 (mtm180) REVERT: A 4041 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6443 (mpt) REVERT: A 4062 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 4217 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8909 (mpt) REVERT: B 77 GLU cc_start: 0.7513 (tp30) cc_final: 0.7122 (pt0) REVERT: B 89 GLU cc_start: 0.7760 (mp0) cc_final: 0.7371 (pt0) REVERT: B 3766 PHE cc_start: 0.7682 (t80) cc_final: 0.7331 (t80) REVERT: B 3767 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7890 (mmm-85) REVERT: B 3772 GLN cc_start: 0.8532 (pt0) cc_final: 0.8278 (pt0) REVERT: B 3783 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7682 (tm-30) REVERT: B 3796 GLU cc_start: 0.8672 (tp30) cc_final: 0.8156 (tp30) REVERT: E 3970 ARG cc_start: 0.0709 (OUTLIER) cc_final: -0.0084 (mtm180) REVERT: E 4041 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6445 (mpt) REVERT: E 4062 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: E 4217 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8910 (mpt) REVERT: F 77 GLU cc_start: 0.7521 (tp30) cc_final: 0.7122 (pt0) REVERT: F 89 GLU cc_start: 0.7759 (mp0) cc_final: 0.7369 (pt0) REVERT: F 3771 GLN cc_start: 0.9023 (tp40) cc_final: 0.8818 (tp-100) REVERT: F 3796 GLU cc_start: 0.8657 (tp30) cc_final: 0.8163 (tp30) outliers start: 50 outliers final: 35 residues processed: 134 average time/residue: 0.0893 time to fit residues: 17.2863 Evaluate side-chains 134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3942 CYS Chi-restraints excluded: chain A residue 3964 CYS Chi-restraints excluded: chain A residue 3970 ARG Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4033 PHE Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4102 VAL Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4108 LEU Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 3773 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain E residue 3942 CYS Chi-restraints excluded: chain E residue 3964 CYS Chi-restraints excluded: chain E residue 3970 ARG Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4033 PHE Chi-restraints excluded: chain E residue 4035 VAL Chi-restraints excluded: chain E residue 4041 MET Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4089 ILE Chi-restraints excluded: chain E residue 4102 VAL Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4108 LEU Chi-restraints excluded: chain E residue 4136 VAL Chi-restraints excluded: chain E residue 4147 ASP Chi-restraints excluded: chain E residue 4217 MET Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain E residue 4400 LYS Chi-restraints excluded: chain F residue 3773 CYS Chi-restraints excluded: chain F residue 3774 ILE Chi-restraints excluded: chain F residue 3797 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 127 optimal weight: 40.0000 chunk 1 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4130 ASN ** B3782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4130 ASN F3772 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.155971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.102209 restraints weight = 18256.764| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.19 r_work: 0.3164 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10622 Z= 0.170 Angle : 0.626 8.974 14440 Z= 0.327 Chirality : 0.047 0.171 1518 Planarity : 0.004 0.041 1902 Dihedral : 7.119 63.092 1706 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.55 % Allowed : 19.23 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.24), residues: 1286 helix: -4.00 (1.03), residues: 12 sheet: -1.13 (0.33), residues: 258 loop : -0.60 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E4119 TYR 0.014 0.002 TYR E4142 PHE 0.009 0.001 PHE E4323 TRP 0.015 0.002 TRP B 85 HIS 0.003 0.001 HIS E4324 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (10554) covalent geometry : angle 0.60953 / 0.32 (14296) SS BOND : bond 0.00214 / 0.14 ( 54) SS BOND : angle 1.07234 / 0.77 ( 108) hydrogen bonds : bond 0.03761 / 2.51 ( 212) hydrogen bonds : angle 6.60508 / 4.42 ( 504) Misc. bond : bond 0.00012 / 0.01 ( 2) link_BETA1-3 : bond 0.00741 / 0.37 ( 2) link_BETA1-3 : angle 1.98672 / 1.10 ( 6) link_BETA1-4 : bond 0.00023 / 0.01 ( 4) link_BETA1-4 : angle 1.95457 / 1.37 ( 12) link_NAG-ASN : bond 0.00151 / 0.07 ( 6) link_NAG-ASN : angle 2.87315 / 1.52 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 93 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3970 ARG cc_start: 0.0561 (OUTLIER) cc_final: 0.0080 (mtm180) REVERT: A 4041 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6454 (mpt) REVERT: A 4062 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: A 4217 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8909 (mpt) REVERT: B 77 GLU cc_start: 0.7293 (tp30) cc_final: 0.6889 (pt0) REVERT: B 89 GLU cc_start: 0.7803 (mp0) cc_final: 0.7385 (pt0) REVERT: B 3766 PHE cc_start: 0.7518 (t80) cc_final: 0.7232 (t80) REVERT: B 3783 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 3796 GLU cc_start: 0.8661 (tp30) cc_final: 0.8130 (tp30) REVERT: E 3970 ARG cc_start: 0.0675 (OUTLIER) cc_final: 0.0188 (mtm180) REVERT: E 4041 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6450 (mpt) REVERT: E 4062 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: E 4217 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8914 (mpt) REVERT: F 77 GLU cc_start: 0.7296 (tp30) cc_final: 0.6890 (pt0) REVERT: F 89 GLU cc_start: 0.7801 (mp0) cc_final: 0.7383 (pt0) REVERT: F 3771 GLN cc_start: 0.8876 (tp40) cc_final: 0.8670 (tp-100) REVERT: F 3783 GLU cc_start: 0.8689 (mp0) cc_final: 0.8479 (mp0) REVERT: F 3796 GLU cc_start: 0.8806 (tp30) cc_final: 0.8236 (tp30) outliers start: 52 outliers final: 36 residues processed: 132 average time/residue: 0.0776 time to fit residues: 14.9511 Evaluate side-chains 131 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3926 THR Chi-restraints excluded: chain A residue 3942 CYS Chi-restraints excluded: chain A residue 3964 CYS Chi-restraints excluded: chain A residue 3970 ARG Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4033 PHE Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4102 VAL Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4108 LEU Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4147 ASP Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 3773 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain E residue 3926 THR Chi-restraints excluded: chain E residue 3942 CYS Chi-restraints excluded: chain E residue 3964 CYS Chi-restraints excluded: chain E residue 3970 ARG Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4033 PHE Chi-restraints excluded: chain E residue 4035 VAL Chi-restraints excluded: chain E residue 4041 MET Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4089 ILE Chi-restraints excluded: chain E residue 4102 VAL Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4108 LEU Chi-restraints excluded: chain E residue 4136 VAL Chi-restraints excluded: chain E residue 4147 ASP Chi-restraints excluded: chain E residue 4217 MET Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain E residue 4400 LYS Chi-restraints excluded: chain F residue 3773 CYS Chi-restraints excluded: chain F residue 3774 ILE Chi-restraints excluded: chain F residue 3797 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 100 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 115 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4130 ASN B3782 GLN E4130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.144631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.090571 restraints weight = 18048.284| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.20 r_work: 0.3108 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 10622 Z= 0.330 Angle : 0.754 8.301 14440 Z= 0.395 Chirality : 0.051 0.176 1518 Planarity : 0.005 0.044 1902 Dihedral : 7.226 64.889 1706 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.72 % Allowed : 19.14 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.24), residues: 1286 helix: -4.15 (0.94), residues: 12 sheet: -1.63 (0.31), residues: 286 loop : -0.67 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E4119 TYR 0.014 0.002 TYR A4079 PHE 0.014 0.002 PHE E4202 TRP 0.022 0.002 TRP E4288 HIS 0.004 0.001 HIS E4387 Details of bonding type rmsd/Z covalent geometry : bond 0.00778 / 0.33 (10554) covalent geometry : angle 0.73526 / 0.39 (14296) SS BOND : bond 0.00310 / 0.21 ( 54) SS BOND : angle 1.38750 / 1.02 ( 108) hydrogen bonds : bond 0.04483 / 3.03 ( 212) hydrogen bonds : angle 7.04511 / 4.74 ( 504) Misc. bond : bond 0.00035 / 0.02 ( 2) link_BETA1-3 : bond 0.00742 / 0.37 ( 2) link_BETA1-3 : angle 1.71391 / 0.96 ( 6) link_BETA1-4 : bond 0.00273 / 0.14 ( 4) link_BETA1-4 : angle 2.37240 / 1.67 ( 12) link_NAG-ASN : bond 0.00496 / 0.24 ( 6) link_NAG-ASN : angle 3.26668 / 1.75 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 81 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3947 TYR cc_start: 0.8553 (t80) cc_final: 0.8280 (t80) REVERT: A 3970 ARG cc_start: 0.0920 (OUTLIER) cc_final: 0.0474 (mtm180) REVERT: A 4062 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7195 (mp0) REVERT: A 4217 MET cc_start: 0.9313 (OUTLIER) cc_final: 0.9098 (mpt) REVERT: B 89 GLU cc_start: 0.7677 (mp0) cc_final: 0.7276 (pt0) REVERT: B 3767 ARG cc_start: 0.8449 (mmm-85) cc_final: 0.8176 (mmm-85) REVERT: B 3772 GLN cc_start: 0.8601 (pt0) cc_final: 0.8393 (pt0) REVERT: B 3783 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 3796 GLU cc_start: 0.8737 (tp30) cc_final: 0.8196 (tp30) REVERT: E 3947 TYR cc_start: 0.8553 (t80) cc_final: 0.8279 (t80) REVERT: E 3970 ARG cc_start: 0.1407 (OUTLIER) cc_final: 0.0941 (mtm180) REVERT: E 4062 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: E 4217 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.9099 (mpt) REVERT: F 89 GLU cc_start: 0.7676 (mp0) cc_final: 0.7274 (pt0) REVERT: F 3771 GLN cc_start: 0.8818 (tp40) cc_final: 0.8105 (tp-100) REVERT: F 3783 GLU cc_start: 0.8669 (mp0) cc_final: 0.8466 (mp0) REVERT: F 3796 GLU cc_start: 0.8722 (tp30) cc_final: 0.8054 (tp30) outliers start: 54 outliers final: 44 residues processed: 126 average time/residue: 0.0783 time to fit residues: 15.0087 Evaluate side-chains 127 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 77 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3926 THR Chi-restraints excluded: chain A residue 3942 CYS Chi-restraints excluded: chain A residue 3964 CYS Chi-restraints excluded: chain A residue 3970 ARG Chi-restraints excluded: chain A residue 3980 ASN Chi-restraints excluded: chain A residue 4033 PHE Chi-restraints excluded: chain A residue 4035 VAL Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4047 GLU Chi-restraints excluded: chain A residue 4062 GLU Chi-restraints excluded: chain A residue 4089 ILE Chi-restraints excluded: chain A residue 4102 VAL Chi-restraints excluded: chain A residue 4106 THR Chi-restraints excluded: chain A residue 4108 LEU Chi-restraints excluded: chain A residue 4136 VAL Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4363 THR Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 3773 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3782 GLN Chi-restraints excluded: chain B residue 3797 MET Chi-restraints excluded: chain E residue 3926 THR Chi-restraints excluded: chain E residue 3942 CYS Chi-restraints excluded: chain E residue 3964 CYS Chi-restraints excluded: chain E residue 3970 ARG Chi-restraints excluded: chain E residue 3980 ASN Chi-restraints excluded: chain E residue 4033 PHE Chi-restraints excluded: chain E residue 4035 VAL Chi-restraints excluded: chain E residue 4041 MET Chi-restraints excluded: chain E residue 4047 GLU Chi-restraints excluded: chain E residue 4062 GLU Chi-restraints excluded: chain E residue 4089 ILE Chi-restraints excluded: chain E residue 4102 VAL Chi-restraints excluded: chain E residue 4106 THR Chi-restraints excluded: chain E residue 4108 LEU Chi-restraints excluded: chain E residue 4136 VAL Chi-restraints excluded: chain E residue 4147 ASP Chi-restraints excluded: chain E residue 4217 MET Chi-restraints excluded: chain E residue 4314 ASN Chi-restraints excluded: chain E residue 4339 VAL Chi-restraints excluded: chain E residue 4363 THR Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain E residue 4400 LYS Chi-restraints excluded: chain F residue 3773 CYS Chi-restraints excluded: chain F residue 3774 ILE Chi-restraints excluded: chain F residue 3797 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 101 optimal weight: 0.2980 chunk 81 optimal weight: 0.0070 chunk 65 optimal weight: 0.0670 chunk 72 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 3 optimal weight: 0.2980 chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 overall best weight: 0.1534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4130 ASN B3771 GLN ** B3782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.153047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.099938 restraints weight = 18154.167| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.09 r_work: 0.3183 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10622 Z= 0.123 Angle : 0.668 13.951 14440 Z= 0.347 Chirality : 0.046 0.177 1518 Planarity : 0.005 0.084 1902 Dihedral : 6.850 64.757 1706 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.20 % Allowed : 20.28 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.25), residues: 1286 helix: -4.43 (0.75), residues: 12 sheet: -1.15 (0.34), residues: 258 loop : -0.59 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F3767 TYR 0.013 0.002 TYR A4121 PHE 0.018 0.001 PHE F3766 TRP 0.010 0.001 TRP A4093 HIS 0.002 0.001 HIS E3927 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (10554) covalent geometry : angle 0.63999 / 0.34 (14296) SS BOND : bond 0.00267 / 0.18 ( 54) SS BOND : angle 1.82412 / 1.32 ( 108) hydrogen bonds : bond 0.03658 / 2.49 ( 212) hydrogen bonds : angle 6.69622 / 4.49 ( 504) Misc. bond : bond 0.00013 / 0.01 ( 2) link_BETA1-3 : bond 0.00611 / 0.31 ( 2) link_BETA1-3 : angle 2.08916 / 1.18 ( 6) link_BETA1-4 : bond 0.00229 / 0.11 ( 4) link_BETA1-4 : angle 1.88414 / 1.33 ( 12) link_NAG-ASN : bond 0.00313 / 0.14 ( 6) link_NAG-ASN : angle 2.96253 / 1.57 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.06 seconds wall clock time: 42 minutes 32.68 seconds (2552.68 seconds total)