Starting phenix.real_space_refine on Mon Jul 28 15:09:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jxd_36697/07_2025/8jxd_36697.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jxd_36697/07_2025/8jxd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jxd_36697/07_2025/8jxd_36697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jxd_36697/07_2025/8jxd_36697.map" model { file = "/net/cci-nas-00/data/ceres_data/8jxd_36697/07_2025/8jxd_36697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jxd_36697/07_2025/8jxd_36697.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 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, 18 Unusual residues: {' CA': 4, 'A2G': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, F, G, H Time building chain proxies: 7.93, per 1000 atoms: 0.77 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: 2.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.40 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: 3.00 Time building geometry restraints manager: 3.27 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 2.510 nonbonded pdb=" OD2 ASP F3785 " pdb="CA CA F4704 " model vdw 2.241 2.510 nonbonded pdb=" OD2 ASP B 58 " pdb="CA CA B4702 " model vdw 2.242 2.510 nonbonded pdb=" OD2 ASP F 58 " pdb="CA CA F4702 " model vdw 2.242 2.510 nonbonded pdb=" OD1 ASP F 48 " pdb="CA CA F4702 " model vdw 2.251 2.510 ... (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: 0.05 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: 1.150 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.760 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 : 9.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP A4288 HIS 0.005 0.001 HIS A4221 PHE 0.007 0.001 PHE A4125 TYR 0.018 0.001 TYR A4392 ARG 0.004 0.000 ARG B 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00435 ( 6) link_NAG-ASN : angle 2.75089 ( 18) link_BETA1-4 : bond 0.00332 ( 4) link_BETA1-4 : angle 1.66874 ( 12) hydrogen bonds : bond 0.28342 ( 212) hydrogen bonds : angle 11.50839 ( 504) SS BOND : bond 0.00244 ( 54) SS BOND : angle 0.89819 ( 108) link_BETA1-3 : bond 0.00224 ( 2) link_BETA1-3 : angle 0.97229 ( 6) covalent geometry : bond 0.00368 (10554) covalent geometry : angle 0.65876 (14296) Misc. bond : bond 0.00046 ( 2) *********************** 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 : 1.091 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: 0.2151 time to fit residues: 40.4455 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 : 1.076 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 0.0070 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4174 r_free = 0.4174 target = 0.149271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097080 restraints weight = 18476.706| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.25 r_work: 0.3250 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10622 Z= 0.163 Angle : 0.654 7.208 14440 Z= 0.344 Chirality : 0.047 0.156 1518 Planarity : 0.005 0.051 1902 Dihedral : 9.616 67.511 1726 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.67 % Allowed : 20.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.24), residues: 1286 helix: -3.27 (1.53), residues: 12 sheet: -0.64 (0.32), residues: 278 loop : -0.45 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A4288 HIS 0.005 0.001 HIS E4221 PHE 0.014 0.002 PHE B3766 TYR 0.010 0.001 TYR E4247 ARG 0.004 0.001 ARG E3970 Details of bonding type rmsd link_NAG-ASN : bond 0.00294 ( 6) link_NAG-ASN : angle 2.75192 ( 18) link_BETA1-4 : bond 0.00699 ( 4) link_BETA1-4 : angle 2.13986 ( 12) hydrogen bonds : bond 0.05443 ( 212) hydrogen bonds : angle 7.88058 ( 504) SS BOND : bond 0.00299 ( 54) SS BOND : angle 1.16719 ( 108) link_BETA1-3 : bond 0.00893 ( 2) link_BETA1-3 : angle 2.77382 ( 6) covalent geometry : bond 0.00377 (10554) covalent geometry : angle 0.63631 (14296) Misc. bond : bond 0.00039 ( 2) *********************** 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 144 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 102 time to evaluate : 1.127 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4062 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: B 77 GLU cc_start: 0.7323 (tp30) cc_final: 0.7061 (pt0) REVERT: B 89 GLU cc_start: 0.8003 (mp0) cc_final: 0.7297 (pt0) REVERT: B 3766 PHE cc_start: 0.7022 (t80) cc_final: 0.6711 (t80) REVERT: B 3767 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.7701 (mmm-85) REVERT: E 4062 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: F 77 GLU cc_start: 0.7329 (tp30) cc_final: 0.7063 (pt0) REVERT: F 89 GLU cc_start: 0.8000 (mp0) cc_final: 0.7295 (pt0) REVERT: F 3766 PHE cc_start: 0.7382 (t80) cc_final: 0.7064 (t80) REVERT: F 3767 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.7651 (mmm-85) REVERT: F 3772 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7353 (pt0) REVERT: F 3783 GLU cc_start: 0.8629 (mp0) cc_final: 0.8383 (mp0) outliers start: 42 outliers final: 22 residues processed: 139 average time/residue: 0.2395 time to fit residues: 47.0574 Evaluate side-chains 111 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3773 CYS Chi-restraints excluded: chain B residue 3774 ILE Chi-restraints excluded: chain B residue 3797 MET 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 0.2980 chunk 64 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.149273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.097072 restraints weight = 18704.766| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.24 r_work: 0.3249 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1415 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= 0.148 Angle : 0.618 7.246 14440 Z= 0.324 Chirality : 0.046 0.175 1518 Planarity : 0.005 0.043 1902 Dihedral : 7.751 63.853 1710 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.63 % Allowed : 18.79 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1286 helix: -2.99 (1.71), residues: 12 sheet: -0.70 (0.32), residues: 282 loop : -0.48 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E4288 HIS 0.003 0.001 HIS E3927 PHE 0.007 0.001 PHE E4125 TYR 0.011 0.001 TYR A4247 ARG 0.005 0.000 ARG F3767 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 6) link_NAG-ASN : angle 2.77800 ( 18) link_BETA1-4 : bond 0.00203 ( 4) link_BETA1-4 : angle 2.15324 ( 12) hydrogen bonds : bond 0.04612 ( 212) hydrogen bonds : angle 7.12143 ( 504) SS BOND : bond 0.00323 ( 54) SS BOND : angle 0.97119 ( 108) link_BETA1-3 : bond 0.00764 ( 2) link_BETA1-3 : angle 2.35015 ( 6) covalent geometry : bond 0.00343 (10554) covalent geometry : angle 0.60259 (14296) Misc. bond : bond 0.00016 ( 2) *********************** 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 144 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 91 time to evaluate : 1.117 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: A 4062 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: B 89 GLU cc_start: 0.7741 (mp0) cc_final: 0.7317 (pt0) REVERT: B 3766 PHE cc_start: 0.7516 (t80) cc_final: 0.6974 (t80) REVERT: B 3796 GLU cc_start: 0.8536 (tp30) cc_final: 0.7895 (tp30) REVERT: E 4062 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: F 89 GLU cc_start: 0.7734 (mp0) cc_final: 0.7314 (pt0) REVERT: F 3766 PHE cc_start: 0.7868 (t80) cc_final: 0.7312 (t80) REVERT: F 3772 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7685 (pt0) REVERT: F 3783 GLU cc_start: 0.8668 (mp0) cc_final: 0.8398 (mp0) REVERT: F 3796 GLU cc_start: 0.8436 (tp30) cc_final: 0.7720 (tp30) outliers start: 53 outliers final: 29 residues processed: 140 average time/residue: 0.2193 time to fit residues: 44.1547 Evaluate side-chains 118 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 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 4174 ASP Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4339 VAL Chi-restraints excluded: chain A residue 4400 LYS 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 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 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 4400 LYS 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 105 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 124 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 53 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 98 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 GLN ** E4314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.149910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097811 restraints weight = 18401.531| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.25 r_work: 0.3260 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10622 Z= 0.120 Angle : 0.592 7.175 14440 Z= 0.310 Chirality : 0.046 0.164 1518 Planarity : 0.004 0.040 1902 Dihedral : 6.920 61.834 1708 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.81 % Allowed : 18.27 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1286 helix: -3.18 (1.58), residues: 12 sheet: -0.73 (0.32), residues: 282 loop : -0.47 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A4288 HIS 0.003 0.001 HIS E3927 PHE 0.007 0.001 PHE E4125 TYR 0.010 0.001 TYR E4247 ARG 0.007 0.000 ARG B 65 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 6) link_NAG-ASN : angle 2.75629 ( 18) link_BETA1-4 : bond 0.00251 ( 4) link_BETA1-4 : angle 2.03319 ( 12) hydrogen bonds : bond 0.03898 ( 212) hydrogen bonds : angle 6.75927 ( 504) SS BOND : bond 0.00283 ( 54) SS BOND : angle 0.93020 ( 108) link_BETA1-3 : bond 0.00799 ( 2) link_BETA1-3 : angle 2.45105 ( 6) covalent geometry : bond 0.00277 (10554) covalent geometry : angle 0.57648 (14296) Misc. bond : bond 0.00006 ( 2) *********************** 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 152 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 97 time to evaluate : 1.170 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: symmetry clash REVERT: B 77 GLU cc_start: 0.6793 (tm-30) cc_final: 0.6578 (tm-30) REVERT: B 89 GLU cc_start: 0.7761 (mp0) cc_final: 0.7346 (pt0) REVERT: B 3767 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8263 (mmm-85) REVERT: B 3796 GLU cc_start: 0.8496 (tp30) cc_final: 0.7896 (tp30) REVERT: E 4218 ASN cc_start: 0.9015 (t0) cc_final: 0.8782 (t0) REVERT: F 77 GLU cc_start: 0.6795 (tm-30) cc_final: 0.6578 (tm-30) REVERT: F 89 GLU cc_start: 0.7754 (mp0) cc_final: 0.7341 (pt0) REVERT: F 3767 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.7764 (mmm160) REVERT: F 3772 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: F 3783 GLU cc_start: 0.8687 (mp0) cc_final: 0.8345 (mp0) REVERT: F 3796 GLU cc_start: 0.8427 (tp30) cc_final: 0.7773 (tp30) outliers start: 55 outliers final: 31 residues processed: 146 average time/residue: 0.2157 time to fit residues: 46.1580 Evaluate side-chains 122 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 1.102 ------------------------------------------------------------------------------- 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 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 4174 ASP Chi-restraints excluded: chain A residue 4314 ASN Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain B residue 92 ASP 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 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 4314 ASN Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain F residue 92 ASP 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 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4130 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4087 GLN E4130 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.147905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095432 restraints weight = 18303.179| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 3.24 r_work: 0.3208 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10622 Z= 0.210 Angle : 0.641 7.220 14440 Z= 0.336 Chirality : 0.047 0.161 1518 Planarity : 0.005 0.040 1902 Dihedral : 6.312 58.758 1700 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.33 % Allowed : 17.40 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1286 helix: -2.88 (1.78), residues: 12 sheet: -0.93 (0.32), residues: 282 loop : -0.46 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E4288 HIS 0.004 0.001 HIS B3811 PHE 0.010 0.002 PHE E4202 TYR 0.013 0.002 TYR E4142 ARG 0.004 0.000 ARG A4119 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 6) link_NAG-ASN : angle 2.87856 ( 18) link_BETA1-4 : bond 0.00104 ( 4) link_BETA1-4 : angle 2.14897 ( 12) hydrogen bonds : bond 0.04157 ( 212) hydrogen bonds : angle 6.80821 ( 504) SS BOND : bond 0.00266 ( 54) SS BOND : angle 1.05460 ( 108) link_BETA1-3 : bond 0.00736 ( 2) link_BETA1-3 : angle 2.00694 ( 6) covalent geometry : bond 0.00498 (10554) covalent geometry : angle 0.62512 (14296) Misc. bond : bond 0.00027 ( 2) *********************** 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 163 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 102 time to evaluate : 1.100 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 4041 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6626 (mpt) REVERT: A 4217 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8967 (mpt) REVERT: A 4272 GLU cc_start: 0.8021 (pm20) cc_final: 0.7624 (pm20) REVERT: B 51 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8205 (mpt-90) REVERT: B 79 THR cc_start: 0.4979 (p) cc_final: 0.4759 (p) REVERT: B 89 GLU cc_start: 0.8021 (mp0) cc_final: 0.7399 (pt0) REVERT: B 3771 GLN cc_start: 0.8897 (tp-100) cc_final: 0.8654 (tp-100) REVERT: B 3783 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8642 (mm-30) REVERT: B 3796 GLU cc_start: 0.8525 (tp30) cc_final: 0.7911 (tp30) REVERT: E 4041 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6638 (mpt) REVERT: E 4217 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8977 (mpt) REVERT: E 4272 GLU cc_start: 0.8004 (pm20) cc_final: 0.7609 (pm20) REVERT: F 51 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (mpt-90) REVERT: F 79 THR cc_start: 0.4978 (p) cc_final: 0.4759 (p) REVERT: F 89 GLU cc_start: 0.8023 (mp0) cc_final: 0.7399 (pt0) REVERT: F 3772 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: F 3783 GLU cc_start: 0.8735 (mp0) cc_final: 0.8513 (mp0) REVERT: F 3796 GLU cc_start: 0.8503 (tp30) cc_final: 0.7950 (tp30) outliers start: 61 outliers final: 38 residues processed: 154 average time/residue: 0.2206 time to fit residues: 48.3375 Evaluate side-chains 134 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 89 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 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 4136 VAL 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 4339 VAL Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 92 ASP 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 4041 MET Chi-restraints excluded: chain E residue 4047 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 4136 VAL 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 4339 VAL Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain E residue 4400 LYS Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 92 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 66 optimal weight: 0.0570 chunk 68 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4130 ASN B 100 GLN B3772 GLN E4130 ASN F 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.148972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096441 restraints weight = 18367.785| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.26 r_work: 0.3222 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10622 Z= 0.141 Angle : 0.611 8.366 14440 Z= 0.320 Chirality : 0.046 0.162 1518 Planarity : 0.004 0.038 1902 Dihedral : 6.127 59.025 1700 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.46 % Allowed : 18.18 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1286 helix: -3.14 (1.61), residues: 12 sheet: -0.89 (0.32), residues: 282 loop : -0.41 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E4288 HIS 0.002 0.001 HIS E3927 PHE 0.032 0.002 PHE A4033 TYR 0.011 0.001 TYR A4142 ARG 0.010 0.001 ARG F3767 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 6) link_NAG-ASN : angle 2.81657 ( 18) link_BETA1-4 : bond 0.00153 ( 4) link_BETA1-4 : angle 1.98325 ( 12) hydrogen bonds : bond 0.03706 ( 212) hydrogen bonds : angle 6.60390 ( 504) SS BOND : bond 0.00253 ( 54) SS BOND : angle 0.95607 ( 108) link_BETA1-3 : bond 0.00774 ( 2) link_BETA1-3 : angle 2.25466 ( 6) covalent geometry : bond 0.00332 (10554) covalent geometry : angle 0.59569 (14296) Misc. bond : bond 0.00003 ( 2) *********************** 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 147 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 96 time to evaluate : 1.130 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 4217 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8861 (mpt) REVERT: A 4272 GLU cc_start: 0.7970 (pm20) cc_final: 0.7507 (pm20) REVERT: B 77 GLU cc_start: 0.6563 (tm-30) cc_final: 0.5858 (pp20) REVERT: B 89 GLU cc_start: 0.8016 (mp0) cc_final: 0.7402 (pt0) REVERT: B 3771 GLN cc_start: 0.8853 (tp-100) cc_final: 0.8159 (tp40) REVERT: B 3772 GLN cc_start: 0.8377 (pt0) cc_final: 0.8137 (pt0) REVERT: B 3783 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8572 (mm-30) REVERT: B 3796 GLU cc_start: 0.8715 (tp30) cc_final: 0.8020 (tp30) REVERT: E 4217 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8872 (mpt) REVERT: E 4272 GLU cc_start: 0.7956 (pm20) cc_final: 0.7495 (pm20) REVERT: F 77 GLU cc_start: 0.6565 (tm-30) cc_final: 0.5854 (pp20) REVERT: F 89 GLU cc_start: 0.8015 (mp0) cc_final: 0.7399 (pt0) REVERT: F 3767 ARG cc_start: 0.8479 (mmt90) cc_final: 0.7741 (mmm160) REVERT: F 3771 GLN cc_start: 0.8396 (tp40) cc_final: 0.7966 (tp40) REVERT: F 3772 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.7164 (pt0) REVERT: F 3783 GLU cc_start: 0.8763 (mp0) cc_final: 0.8487 (mp0) REVERT: F 3796 GLU cc_start: 0.8640 (tp30) cc_final: 0.8060 (tp30) outliers start: 51 outliers final: 40 residues processed: 139 average time/residue: 0.2133 time to fit residues: 43.6998 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 : 1.397 ------------------------------------------------------------------------------- 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 4035 VAL Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4047 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 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 92 ASP 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 4041 MET Chi-restraints excluded: chain E residue 4047 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 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 92 ASP 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 112 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4130 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4130 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.148136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.095502 restraints weight = 18638.360| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.29 r_work: 0.3212 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10622 Z= 0.157 Angle : 0.607 7.217 14440 Z= 0.319 Chirality : 0.046 0.163 1518 Planarity : 0.004 0.047 1902 Dihedral : 6.064 57.883 1700 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.90 % Allowed : 17.83 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.24), residues: 1286 helix: -3.06 (1.65), residues: 12 sheet: -0.90 (0.32), residues: 282 loop : -0.41 (0.21), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E4288 HIS 0.003 0.001 HIS A3927 PHE 0.024 0.002 PHE E4033 TYR 0.010 0.001 TYR E4247 ARG 0.010 0.001 ARG B3767 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 6) link_NAG-ASN : angle 2.77632 ( 18) link_BETA1-4 : bond 0.00091 ( 4) link_BETA1-4 : angle 1.97641 ( 12) hydrogen bonds : bond 0.03844 ( 212) hydrogen bonds : angle 6.52204 ( 504) SS BOND : bond 0.00230 ( 54) SS BOND : angle 1.03167 ( 108) link_BETA1-3 : bond 0.00827 ( 2) link_BETA1-3 : angle 2.14670 ( 6) covalent geometry : bond 0.00373 (10554) covalent geometry : angle 0.59098 (14296) Misc. bond : bond 0.00010 ( 2) *********************** 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 152 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 96 time to evaluate : 1.195 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: 0.0688 (OUTLIER) cc_final: -0.0352 (mtm180) REVERT: A 4041 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6388 (mpt) REVERT: A 4217 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8885 (mpt) REVERT: B 89 GLU cc_start: 0.8045 (mp0) cc_final: 0.7390 (pt0) REVERT: B 3783 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8564 (mm-30) REVERT: B 3796 GLU cc_start: 0.8807 (tp30) cc_final: 0.8097 (tp30) REVERT: E 3970 ARG cc_start: 0.0045 (OUTLIER) cc_final: -0.1239 (mtm180) REVERT: E 4041 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6386 (mpt) REVERT: E 4217 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8890 (mpt) REVERT: F 89 GLU cc_start: 0.8043 (mp0) cc_final: 0.7383 (pt0) REVERT: F 3767 ARG cc_start: 0.8377 (mmt90) cc_final: 0.7918 (mmm160) REVERT: F 3771 GLN cc_start: 0.8429 (tp40) cc_final: 0.8221 (tp40) REVERT: F 3772 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7301 (pt0) REVERT: F 3783 GLU cc_start: 0.8785 (mp0) cc_final: 0.8563 (mp0) REVERT: F 3796 GLU cc_start: 0.8689 (tp30) cc_final: 0.8044 (tp30) outliers start: 56 outliers final: 41 residues processed: 143 average time/residue: 0.1996 time to fit residues: 41.9015 Evaluate side-chains 138 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 4035 VAL Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4047 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 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 92 ASP 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 4035 VAL Chi-restraints excluded: chain E residue 4041 MET Chi-restraints excluded: chain E residue 4047 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 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 92 ASP 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 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4130 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4130 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.148073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.095403 restraints weight = 18451.805| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 3.29 r_work: 0.3209 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10622 Z= 0.157 Angle : 0.622 10.282 14440 Z= 0.325 Chirality : 0.046 0.165 1518 Planarity : 0.004 0.039 1902 Dihedral : 6.057 57.977 1700 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.72 % Allowed : 18.18 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1286 helix: -3.15 (1.59), residues: 12 sheet: -0.87 (0.32), residues: 278 loop : -0.41 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A4288 HIS 0.003 0.001 HIS E4324 PHE 0.024 0.001 PHE E4033 TYR 0.013 0.001 TYR E4407 ARG 0.006 0.001 ARG B3767 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 6) link_NAG-ASN : angle 2.77593 ( 18) link_BETA1-4 : bond 0.00062 ( 4) link_BETA1-4 : angle 1.93860 ( 12) hydrogen bonds : bond 0.03674 ( 212) hydrogen bonds : angle 6.45152 ( 504) SS BOND : bond 0.00224 ( 54) SS BOND : angle 1.02992 ( 108) link_BETA1-3 : bond 0.00816 ( 2) link_BETA1-3 : angle 2.11267 ( 6) covalent geometry : bond 0.00374 (10554) covalent geometry : angle 0.60648 (14296) Misc. bond : bond 0.00008 ( 2) *********************** 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 149 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 95 time to evaluate : 1.203 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: 0.0674 (OUTLIER) cc_final: -0.0372 (mtm180) REVERT: A 4041 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6561 (mpt) REVERT: A 4217 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8816 (mpt) REVERT: B 77 GLU cc_start: 0.6214 (tm-30) cc_final: 0.5698 (pp20) REVERT: B 89 GLU cc_start: 0.8052 (mp0) cc_final: 0.7402 (pt0) REVERT: B 3766 PHE cc_start: 0.7707 (t80) cc_final: 0.7451 (t80) REVERT: B 3771 GLN cc_start: 0.8585 (tp40) cc_final: 0.8162 (tp40) REVERT: B 3783 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8525 (mm-30) REVERT: B 3796 GLU cc_start: 0.8822 (tp30) cc_final: 0.8231 (tp30) REVERT: E 3970 ARG cc_start: 0.0740 (OUTLIER) cc_final: -0.0281 (mtm180) REVERT: E 4041 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6556 (mpt) REVERT: E 4217 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8820 (mpt) REVERT: F 68 GLU cc_start: 0.7088 (pm20) cc_final: 0.6851 (pm20) REVERT: F 77 GLU cc_start: 0.6208 (tm-30) cc_final: 0.5691 (pp20) REVERT: F 89 GLU cc_start: 0.8050 (mp0) cc_final: 0.7396 (pt0) REVERT: F 3771 GLN cc_start: 0.8437 (tp40) cc_final: 0.8079 (tp40) REVERT: F 3772 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7177 (pt0) REVERT: F 3783 GLU cc_start: 0.8773 (mp0) cc_final: 0.8561 (mp0) REVERT: F 3796 GLU cc_start: 0.8763 (tp30) cc_final: 0.8088 (tp30) outliers start: 54 outliers final: 43 residues processed: 141 average time/residue: 0.2501 time to fit residues: 52.5282 Evaluate side-chains 142 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 92 time to evaluate : 1.146 ------------------------------------------------------------------------------- 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 4035 VAL Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4047 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 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 4339 VAL Chi-restraints excluded: chain A residue 4375 LEU Chi-restraints excluded: chain A residue 4400 LYS Chi-restraints excluded: chain B residue 92 ASP 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 4035 VAL Chi-restraints excluded: chain E residue 4041 MET Chi-restraints excluded: chain E residue 4047 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 4136 VAL 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 4339 VAL Chi-restraints excluded: chain E residue 4375 LEU Chi-restraints excluded: chain E residue 4400 LYS Chi-restraints excluded: chain F residue 92 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 75 optimal weight: 0.0050 chunk 65 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 0.0050 overall best weight: 0.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4156 r_free = 0.4156 target = 0.148557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095895 restraints weight = 18543.691| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.28 r_work: 0.3221 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10622 Z= 0.133 Angle : 0.603 9.218 14440 Z= 0.316 Chirality : 0.046 0.166 1518 Planarity : 0.004 0.045 1902 Dihedral : 5.980 57.831 1700 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1286 helix: -2.98 (1.71), residues: 12 sheet: -0.85 (0.32), residues: 278 loop : -0.38 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E4288 HIS 0.002 0.001 HIS E3927 PHE 0.022 0.001 PHE E4033 TYR 0.010 0.001 TYR A4121 ARG 0.008 0.000 ARG F3767 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 6) link_NAG-ASN : angle 2.70378 ( 18) link_BETA1-4 : bond 0.00116 ( 4) link_BETA1-4 : angle 1.87992 ( 12) hydrogen bonds : bond 0.03619 ( 212) hydrogen bonds : angle 6.38907 ( 504) SS BOND : bond 0.00224 ( 54) SS BOND : angle 1.01558 ( 108) link_BETA1-3 : bond 0.00757 ( 2) link_BETA1-3 : angle 2.07407 ( 6) covalent geometry : bond 0.00315 (10554) covalent geometry : angle 0.58780 (14296) Misc. bond : bond 0.00002 ( 2) *********************** 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 156 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 98 time to evaluate : 1.147 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: 0.0621 (OUTLIER) cc_final: -0.0203 (mtm180) REVERT: A 4041 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6571 (mpt) REVERT: A 4217 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8801 (mpt) REVERT: B 77 GLU cc_start: 0.6190 (tm-30) cc_final: 0.5598 (pp20) REVERT: B 89 GLU cc_start: 0.8020 (mp0) cc_final: 0.7398 (pt0) REVERT: B 3766 PHE cc_start: 0.7732 (t80) cc_final: 0.7478 (t80) REVERT: B 3771 GLN cc_start: 0.8641 (tp40) cc_final: 0.8212 (tp40) REVERT: B 3783 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8592 (mm-30) REVERT: B 3792 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8069 (mm-30) REVERT: B 3796 GLU cc_start: 0.8826 (tp30) cc_final: 0.8278 (tp30) REVERT: E 3970 ARG cc_start: 0.0763 (OUTLIER) cc_final: 0.0008 (mtm180) REVERT: E 4041 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6580 (mpt) REVERT: E 4217 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8809 (mpt) REVERT: F 68 GLU cc_start: 0.7091 (pm20) cc_final: 0.6867 (pm20) REVERT: F 77 GLU cc_start: 0.6182 (tm-30) cc_final: 0.5586 (pp20) REVERT: F 89 GLU cc_start: 0.8019 (mp0) cc_final: 0.7396 (pt0) REVERT: F 3771 GLN cc_start: 0.8319 (tp40) cc_final: 0.7593 (tp40) REVERT: F 3772 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: F 3783 GLU cc_start: 0.8771 (mp0) cc_final: 0.8532 (mp0) REVERT: F 3796 GLU cc_start: 0.8808 (tp30) cc_final: 0.8079 (tp30) outliers start: 58 outliers final: 44 residues processed: 147 average time/residue: 0.1871 time to fit residues: 41.4219 Evaluate side-chains 144 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 93 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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 4035 VAL Chi-restraints excluded: chain A residue 4041 MET Chi-restraints excluded: chain A residue 4047 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 4136 VAL Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4255 VAL 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 92 ASP 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 4035 VAL Chi-restraints excluded: chain E residue 4041 MET Chi-restraints excluded: chain E residue 4047 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 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 4255 VAL 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 92 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4130 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4130 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.148925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.096299 restraints weight = 18376.104| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.29 r_work: 0.3226 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10622 Z= 0.131 Angle : 0.595 8.914 14440 Z= 0.312 Chirality : 0.046 0.168 1518 Planarity : 0.004 0.038 1902 Dihedral : 5.921 57.632 1700 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.90 % Allowed : 17.83 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.24), residues: 1286 helix: -3.16 (1.58), residues: 12 sheet: -0.85 (0.32), residues: 278 loop : -0.35 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A4288 HIS 0.003 0.001 HIS E3927 PHE 0.021 0.001 PHE E4033 TYR 0.013 0.001 TYR A4142 ARG 0.004 0.000 ARG B3767 Details of bonding type rmsd link_NAG-ASN : bond 0.00206 ( 6) link_NAG-ASN : angle 2.64218 ( 18) link_BETA1-4 : bond 0.00106 ( 4) link_BETA1-4 : angle 1.84114 ( 12) hydrogen bonds : bond 0.03598 ( 212) hydrogen bonds : angle 6.31344 ( 504) SS BOND : bond 0.00222 ( 54) SS BOND : angle 0.99627 ( 108) link_BETA1-3 : bond 0.00748 ( 2) link_BETA1-3 : angle 1.98918 ( 6) covalent geometry : bond 0.00309 (10554) covalent geometry : angle 0.58036 (14296) Misc. bond : bond 0.00002 ( 2) ********************** 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 159 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 103 time to evaluate : 1.333 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: A 3970 ARG cc_start: 0.0608 (OUTLIER) cc_final: -0.0233 (mtm180) REVERT: A 4041 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6722 (mpt) REVERT: A 4217 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8792 (mpt) REVERT: B 77 GLU cc_start: 0.6207 (tm-30) cc_final: 0.5606 (pp20) REVERT: B 89 GLU cc_start: 0.7994 (mp0) cc_final: 0.7406 (pt0) REVERT: B 3766 PHE cc_start: 0.7724 (t80) cc_final: 0.7484 (t80) REVERT: B 3771 GLN cc_start: 0.8662 (tp40) cc_final: 0.8228 (tp40) REVERT: B 3783 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8565 (mm-30) REVERT: B 3796 GLU cc_start: 0.8816 (tp30) cc_final: 0.8284 (tp30) REVERT: E 3970 ARG cc_start: 0.0729 (OUTLIER) cc_final: -0.0049 (mtm180) REVERT: E 4041 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6728 (mpt) REVERT: E 4217 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8804 (mpt) REVERT: F 68 GLU cc_start: 0.7117 (pm20) cc_final: 0.6879 (pm20) REVERT: F 77 GLU cc_start: 0.6202 (tm-30) cc_final: 0.5596 (pp20) REVERT: F 89 GLU cc_start: 0.7991 (mp0) cc_final: 0.7403 (pt0) REVERT: F 3771 GLN cc_start: 0.8243 (tp40) cc_final: 0.7231 (tp40) REVERT: F 3772 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: F 3783 GLU cc_start: 0.8671 (mp0) cc_final: 0.8450 (mp0) REVERT: F 3796 GLU cc_start: 0.8818 (tp30) cc_final: 0.8111 (tp30) outliers start: 56 outliers final: 42 residues processed: 151 average time/residue: 0.2061 time to fit residues: 46.6421 Evaluate side-chains 143 residues out of total 1144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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 4035 VAL Chi-restraints excluded: chain A residue 4041 MET 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 4136 VAL Chi-restraints excluded: chain A residue 4174 ASP Chi-restraints excluded: chain A residue 4217 MET Chi-restraints excluded: chain A residue 4255 VAL 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 92 ASP 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 4035 VAL Chi-restraints excluded: chain E residue 4041 MET 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 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 4255 VAL 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 92 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 88 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4130 ASN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E4130 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.146481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.093755 restraints weight = 18345.877| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.25 r_work: 0.3188 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2924 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= 0.231 Angle : 0.659 8.455 14440 Z= 0.346 Chirality : 0.048 0.168 1518 Planarity : 0.005 0.039 1902 Dihedral : 6.234 58.773 1700 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.90 % Allowed : 17.05 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.24), residues: 1286 helix: -2.99 (1.70), residues: 12 sheet: -0.90 (0.34), residues: 258 loop : -0.50 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E4288 HIS 0.003 0.001 HIS E4324 PHE 0.024 0.002 PHE F3766 TYR 0.014 0.002 TYR A4287 ARG 0.007 0.001 ARG F3767 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 6) link_NAG-ASN : angle 2.90404 ( 18) link_BETA1-4 : bond 0.00109 ( 4) link_BETA1-4 : angle 2.01925 ( 12) hydrogen bonds : bond 0.04083 ( 212) hydrogen bonds : angle 6.52689 ( 504) SS BOND : bond 0.00267 ( 54) SS BOND : angle 1.17877 ( 108) link_BETA1-3 : bond 0.00705 ( 2) link_BETA1-3 : angle 1.87306 ( 6) covalent geometry : bond 0.00547 (10554) covalent geometry : angle 0.64256 (14296) Misc. bond : bond 0.00012 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5884.90 seconds wall clock time: 103 minutes 45.84 seconds (6225.84 seconds total)