Starting phenix.real_space_refine on Wed Oct 28 06:19:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xti_67233/10_2026/9xti_67233.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xti_67233/10_2026/9xti_67233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xti_67233/10_2026/9xti_67233.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xti_67233/10_2026/9xti_67233.map" model { file = "/net/cci-nas-00/data/ceres_data/9xti_67233/10_2026/9xti_67233.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xti_67233/10_2026/9xti_67233.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.034 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 4 9.91 5 S 176 5.16 5 C 16766 2.51 5 N 4542 2.21 5 O 5132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26620 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1542, 12134 Classifications: {'peptide': 1542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 54, 'TRANS': 1484} Chain: "D" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1174 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "B" Number of atoms: 12134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1542, 12134 Classifications: {'peptide': 1542} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 54, 'TRANS': 1484} Chain: "F" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1174 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 146} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.54, per 1000 atoms: 0.21 Number of scatterers: 26620 At special positions: 0 Unit cell: (164.573, 239.003, 147.206, 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 4 19.99 S 176 16.00 O 5132 8.00 N 4542 7.00 C 16766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6424 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 14 sheets defined 66.4% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 3220 through 3247 Processing helix chain 'A' and resid 3265 through 3297 removed outlier: 8.031A pdb=" N ILE A3288 " --> pdb=" O ALA A3284 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASN A3289 " --> pdb=" O GLN A3285 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP A3290 " --> pdb=" O ARG A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3298 through 3311 removed outlier: 4.441A pdb=" N TYR A3302 " --> pdb=" O ASP A3298 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A3309 " --> pdb=" O LEU A3305 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A3310 " --> pdb=" O GLN A3306 " (cutoff:3.500A) Processing helix chain 'A' and resid 3315 through 3329 Processing helix chain 'A' and resid 3330 through 3341 removed outlier: 4.141A pdb=" N GLY A3341 " --> pdb=" O ALA A3337 " (cutoff:3.500A) Processing helix chain 'A' and resid 3379 through 3403 removed outlier: 3.866A pdb=" N THR A3383 " --> pdb=" O LYS A3379 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A3384 " --> pdb=" O ASP A3380 " (cutoff:3.500A) Processing helix chain 'A' and resid 3404 through 3417 Processing helix chain 'A' and resid 3422 through 3439 Processing helix chain 'A' and resid 3440 through 3455 Processing helix chain 'A' and resid 3456 through 3464 Proline residue: A3459 - end of helix removed outlier: 3.633A pdb=" N GLY A3462 " --> pdb=" O PRO A3459 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ARG A3463 " --> pdb=" O ALA A3460 " (cutoff:3.500A) Processing helix chain 'A' and resid 3465 through 3479 removed outlier: 3.698A pdb=" N LEU A3471 " --> pdb=" O GLN A3467 " (cutoff:3.500A) Processing helix chain 'A' and resid 3482 through 3506 Processing helix chain 'A' and resid 3509 through 3518 removed outlier: 4.242A pdb=" N GLY A3518 " --> pdb=" O ASN A3514 " (cutoff:3.500A) Processing helix chain 'A' and resid 3601 through 3606 removed outlier: 3.627A pdb=" N LEU A3605 " --> pdb=" O ILE A3602 " (cutoff:3.500A) Processing helix chain 'A' and resid 3608 through 3612 Processing helix chain 'A' and resid 3651 through 3654 Processing helix chain 'A' and resid 3728 through 3755 Processing helix chain 'A' and resid 3756 through 3768 Processing helix chain 'A' and resid 3788 through 3792 Processing helix chain 'A' and resid 3793 through 3804 Processing helix chain 'A' and resid 3805 through 3844 removed outlier: 3.761A pdb=" N SER A3842 " --> pdb=" O ALA A3838 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A3843 " --> pdb=" O ALA A3839 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG A3844 " --> pdb=" O THR A3840 " (cutoff:3.500A) Processing helix chain 'A' and resid 3852 through 3859 Processing helix chain 'A' and resid 3872 through 3891 Processing helix chain 'A' and resid 3893 through 3902 Processing helix chain 'A' and resid 3904 through 3912 Processing helix chain 'A' and resid 3918 through 3933 removed outlier: 3.547A pdb=" N THR A3933 " --> pdb=" O MET A3929 " (cutoff:3.500A) Processing helix chain 'A' and resid 3936 through 3957 Processing helix chain 'A' and resid 3963 through 3981 removed outlier: 3.638A pdb=" N SER A3967 " --> pdb=" O ASP A3963 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR A3970 " --> pdb=" O SER A3966 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N GLU A3971 " --> pdb=" O SER A3967 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4001 removed outlier: 3.966A pdb=" N ARG A3989 " --> pdb=" O CYS A3985 " (cutoff:3.500A) Processing helix chain 'A' and resid 4005 through 4012 removed outlier: 4.037A pdb=" N VAL A4009 " --> pdb=" O THR A4005 " (cutoff:3.500A) Processing helix chain 'A' and resid 4012 through 4025 Processing helix chain 'A' and resid 4039 through 4043 Processing helix chain 'A' and resid 4055 through 4060 Processing helix chain 'A' and resid 4061 through 4062 No H-bonds generated for 'chain 'A' and resid 4061 through 4062' Processing helix chain 'A' and resid 4063 through 4066 Processing helix chain 'A' and resid 4067 through 4074 Processing helix chain 'A' and resid 4088 through 4113 Processing helix chain 'A' and resid 4128 through 4134 removed outlier: 3.548A pdb=" N VAL A4132 " --> pdb=" O TRP A4128 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A4134 " --> pdb=" O ARG A4130 " (cutoff:3.500A) Processing helix chain 'A' and resid 4138 through 4153 removed outlier: 3.818A pdb=" N ARG A4142 " --> pdb=" O THR A4138 " (cutoff:3.500A) Processing helix chain 'A' and resid 4155 through 4168 Processing helix chain 'A' and resid 4169 through 4171 No H-bonds generated for 'chain 'A' and resid 4169 through 4171' Processing helix chain 'A' and resid 4172 through 4177 Processing helix chain 'A' and resid 4180 through 4191 Processing helix chain 'A' and resid 4193 through 4203 Processing helix chain 'A' and resid 4204 through 4226 removed outlier: 3.670A pdb=" N TYR A4208 " --> pdb=" O GLY A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4235 through 4251 removed outlier: 4.428A pdb=" N VAL A4251 " --> pdb=" O SER A4247 " (cutoff:3.500A) Processing helix chain 'A' and resid 4251 through 4276 removed outlier: 5.507A pdb=" N SER A4260 " --> pdb=" O ARG A4256 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG A4261 " --> pdb=" O HIS A4257 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLY A4264 " --> pdb=" O SER A4260 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N THR A4265 " --> pdb=" O ARG A4261 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A4276 " --> pdb=" O CYS A4272 " (cutoff:3.500A) Processing helix chain 'A' and resid 4281 through 4300 removed outlier: 4.193A pdb=" N THR A4300 " --> pdb=" O GLU A4296 " (cutoff:3.500A) Processing helix chain 'A' and resid 4302 through 4318 Processing helix chain 'A' and resid 4327 through 4340 removed outlier: 4.110A pdb=" N ILE A4331 " --> pdb=" O THR A4327 " (cutoff:3.500A) Processing helix chain 'A' and resid 4357 through 4360 removed outlier: 3.844A pdb=" N GLU A4360 " --> pdb=" O PRO A4357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4357 through 4360' Processing helix chain 'A' and resid 4382 through 4394 removed outlier: 3.543A pdb=" N ILE A4386 " --> pdb=" O LEU A4382 " (cutoff:3.500A) Processing helix chain 'A' and resid 4396 through 4400 Processing helix chain 'A' and resid 4420 through 4428 Processing helix chain 'A' and resid 4429 through 4434 removed outlier: 3.628A pdb=" N GLU A4434 " --> pdb=" O CYS A4430 " (cutoff:3.500A) Processing helix chain 'A' and resid 4468 through 4473 Processing helix chain 'A' and resid 4474 through 4482 removed outlier: 4.146A pdb=" N VAL A4478 " --> pdb=" O LYS A4474 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A4479 " --> pdb=" O MET A4475 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A4480 " --> pdb=" O ALA A4476 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A4481 " --> pdb=" O GLY A4477 " (cutoff:3.500A) Processing helix chain 'A' and resid 4483 through 4495 removed outlier: 3.757A pdb=" N CYS A4487 " --> pdb=" O GLY A4483 " (cutoff:3.500A) Processing helix chain 'A' and resid 4497 through 4516 removed outlier: 5.708A pdb=" N HIS A4503 " --> pdb=" O LYS A4499 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A4504 " --> pdb=" O GLN A4500 " (cutoff:3.500A) Processing helix chain 'A' and resid 4518 through 4527 removed outlier: 4.170A pdb=" N LYS A4527 " --> pdb=" O GLN A4523 " (cutoff:3.500A) Processing helix chain 'A' and resid 4531 through 4550 removed outlier: 3.980A pdb=" N VAL A4535 " --> pdb=" O ASN A4531 " (cutoff:3.500A) Processing helix chain 'A' and resid 4554 through 4576 removed outlier: 3.875A pdb=" N GLU A4576 " --> pdb=" O GLU A4572 " (cutoff:3.500A) Processing helix chain 'A' and resid 4590 through 4603 removed outlier: 3.669A pdb=" N ILE A4601 " --> pdb=" O LEU A4597 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN A4602 " --> pdb=" O LEU A4598 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A4603 " --> pdb=" O ASP A4599 " (cutoff:3.500A) Processing helix chain 'A' and resid 4603 through 4609 Processing helix chain 'A' and resid 4609 through 4625 Proline residue: A4621 - end of helix Processing helix chain 'A' and resid 4627 through 4639 removed outlier: 3.581A pdb=" N PHE A4638 " --> pdb=" O LEU A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4640 through 4642 No H-bonds generated for 'chain 'A' and resid 4640 through 4642' Processing helix chain 'A' and resid 4643 through 4650 Processing helix chain 'A' and resid 4652 through 4668 Processing helix chain 'A' and resid 4672 through 4685 Processing helix chain 'A' and resid 4686 through 4699 Processing helix chain 'A' and resid 4707 through 4715 Processing helix chain 'A' and resid 4717 through 4731 removed outlier: 4.401A pdb=" N PHE A4721 " --> pdb=" O PRO A4717 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4744 removed outlier: 4.386A pdb=" N ASP A4743 " --> pdb=" O LEU A4739 " (cutoff:3.500A) Processing helix chain 'A' and resid 4744 through 4753 Processing helix chain 'D' and resid 1 through 5 removed outlier: 3.870A pdb=" N GLN D 4 " --> pdb=" O MET D 1 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 21 Processing helix chain 'D' and resid 32 through 40 removed outlier: 3.797A pdb=" N LEU D 40 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 57 Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.773A pdb=" N LYS D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 94 Processing helix chain 'D' and resid 102 through 114 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'B' and resid 3220 through 3247 Processing helix chain 'B' and resid 3265 through 3297 removed outlier: 7.998A pdb=" N ILE B3288 " --> pdb=" O ALA B3284 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASN B3289 " --> pdb=" O GLN B3285 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP B3290 " --> pdb=" O ARG B3286 " (cutoff:3.500A) Processing helix chain 'B' and resid 3298 through 3311 removed outlier: 4.180A pdb=" N TYR B3302 " --> pdb=" O ASP B3298 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B3309 " --> pdb=" O LEU B3305 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B3310 " --> pdb=" O GLN B3306 " (cutoff:3.500A) Processing helix chain 'B' and resid 3315 through 3329 Processing helix chain 'B' and resid 3330 through 3343 removed outlier: 4.041A pdb=" N GLY B3341 " --> pdb=" O ALA B3337 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B3342 " --> pdb=" O ALA B3338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3379 through 3403 removed outlier: 3.928A pdb=" N THR B3383 " --> pdb=" O LYS B3379 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B3384 " --> pdb=" O ASP B3380 " (cutoff:3.500A) Processing helix chain 'B' and resid 3404 through 3417 Processing helix chain 'B' and resid 3422 through 3439 Processing helix chain 'B' and resid 3440 through 3455 Processing helix chain 'B' and resid 3456 through 3464 Proline residue: B3459 - end of helix removed outlier: 3.555A pdb=" N GLY B3462 " --> pdb=" O PRO B3459 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG B3463 " --> pdb=" O ALA B3460 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B3464 " --> pdb=" O TYR B3461 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3456 through 3464' Processing helix chain 'B' and resid 3465 through 3479 removed outlier: 3.719A pdb=" N LEU B3471 " --> pdb=" O GLN B3467 " (cutoff:3.500A) Processing helix chain 'B' and resid 3482 through 3506 Processing helix chain 'B' and resid 3509 through 3518 removed outlier: 4.318A pdb=" N GLY B3518 " --> pdb=" O ASN B3514 " (cutoff:3.500A) Processing helix chain 'B' and resid 3601 through 3606 removed outlier: 3.548A pdb=" N LEU B3605 " --> pdb=" O ILE B3602 " (cutoff:3.500A) Processing helix chain 'B' and resid 3608 through 3612 Processing helix chain 'B' and resid 3651 through 3654 Processing helix chain 'B' and resid 3728 through 3755 Processing helix chain 'B' and resid 3756 through 3769 Processing helix chain 'B' and resid 3788 through 3792 removed outlier: 3.504A pdb=" N VAL B3792 " --> pdb=" O SER B3789 " (cutoff:3.500A) Processing helix chain 'B' and resid 3793 through 3804 Processing helix chain 'B' and resid 3805 through 3844 removed outlier: 3.713A pdb=" N SER B3842 " --> pdb=" O ALA B3838 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B3843 " --> pdb=" O ALA B3839 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B3844 " --> pdb=" O THR B3840 " (cutoff:3.500A) Processing helix chain 'B' and resid 3852 through 3859 Processing helix chain 'B' and resid 3872 through 3891 Processing helix chain 'B' and resid 3893 through 3902 Processing helix chain 'B' and resid 3904 through 3912 Processing helix chain 'B' and resid 3918 through 3933 removed outlier: 3.562A pdb=" N THR B3933 " --> pdb=" O MET B3929 " (cutoff:3.500A) Processing helix chain 'B' and resid 3936 through 3957 Processing helix chain 'B' and resid 3964 through 3981 removed outlier: 6.327A pdb=" N TYR B3970 " --> pdb=" O SER B3966 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU B3971 " --> pdb=" O SER B3967 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B3981 " --> pdb=" O ASP B3977 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4001 removed outlier: 3.938A pdb=" N ARG B3989 " --> pdb=" O CYS B3985 " (cutoff:3.500A) Processing helix chain 'B' and resid 4006 through 4012 Processing helix chain 'B' and resid 4012 through 4025 Processing helix chain 'B' and resid 4038 through 4043 removed outlier: 3.706A pdb=" N THR B4043 " --> pdb=" O GLU B4040 " (cutoff:3.500A) Processing helix chain 'B' and resid 4055 through 4060 Processing helix chain 'B' and resid 4061 through 4062 No H-bonds generated for 'chain 'B' and resid 4061 through 4062' Processing helix chain 'B' and resid 4063 through 4066 Processing helix chain 'B' and resid 4067 through 4074 Processing helix chain 'B' and resid 4088 through 4112 Processing helix chain 'B' and resid 4128 through 4134 removed outlier: 3.601A pdb=" N VAL B4132 " --> pdb=" O TRP B4128 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B4134 " --> pdb=" O ARG B4130 " (cutoff:3.500A) Processing helix chain 'B' and resid 4138 through 4153 removed outlier: 3.866A pdb=" N ARG B4142 " --> pdb=" O THR B4138 " (cutoff:3.500A) Processing helix chain 'B' and resid 4155 through 4168 Processing helix chain 'B' and resid 4169 through 4171 No H-bonds generated for 'chain 'B' and resid 4169 through 4171' Processing helix chain 'B' and resid 4172 through 4177 Processing helix chain 'B' and resid 4180 through 4192 Processing helix chain 'B' and resid 4193 through 4203 Processing helix chain 'B' and resid 4204 through 4227 removed outlier: 3.598A pdb=" N TYR B4208 " --> pdb=" O GLY B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4235 through 4250 Processing helix chain 'B' and resid 4251 through 4275 removed outlier: 5.724A pdb=" N SER B4260 " --> pdb=" O ARG B4256 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG B4261 " --> pdb=" O HIS B4257 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLY B4264 " --> pdb=" O SER B4260 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N THR B4265 " --> pdb=" O ARG B4261 " (cutoff:3.500A) Processing helix chain 'B' and resid 4281 through 4299 Processing helix chain 'B' and resid 4302 through 4316 Processing helix chain 'B' and resid 4327 through 4340 removed outlier: 4.326A pdb=" N ILE B4331 " --> pdb=" O THR B4327 " (cutoff:3.500A) Processing helix chain 'B' and resid 4357 through 4360 removed outlier: 3.796A pdb=" N GLU B4360 " --> pdb=" O PRO B4357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4357 through 4360' Processing helix chain 'B' and resid 4382 through 4394 Processing helix chain 'B' and resid 4396 through 4400 Processing helix chain 'B' and resid 4420 through 4428 Processing helix chain 'B' and resid 4429 through 4434 removed outlier: 3.692A pdb=" N GLU B4434 " --> pdb=" O CYS B4430 " (cutoff:3.500A) Processing helix chain 'B' and resid 4468 through 4473 removed outlier: 3.607A pdb=" N TYR B4473 " --> pdb=" O GLU B4469 " (cutoff:3.500A) Processing helix chain 'B' and resid 4475 through 4482 removed outlier: 4.207A pdb=" N MET B4479 " --> pdb=" O MET B4475 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B4480 " --> pdb=" O ALA B4476 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B4481 " --> pdb=" O GLY B4477 " (cutoff:3.500A) Processing helix chain 'B' and resid 4483 through 4495 removed outlier: 3.918A pdb=" N CYS B4487 " --> pdb=" O GLY B4483 " (cutoff:3.500A) Processing helix chain 'B' and resid 4497 through 4516 removed outlier: 5.680A pdb=" N HIS B4503 " --> pdb=" O LYS B4499 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N LEU B4504 " --> pdb=" O GLN B4500 " (cutoff:3.500A) Processing helix chain 'B' and resid 4518 through 4527 removed outlier: 4.070A pdb=" N LYS B4527 " --> pdb=" O GLN B4523 " (cutoff:3.500A) Processing helix chain 'B' and resid 4528 through 4530 No H-bonds generated for 'chain 'B' and resid 4528 through 4530' Processing helix chain 'B' and resid 4531 through 4550 removed outlier: 4.327A pdb=" N VAL B4535 " --> pdb=" O ASN B4531 " (cutoff:3.500A) Processing helix chain 'B' and resid 4554 through 4576 removed outlier: 3.924A pdb=" N GLU B4576 " --> pdb=" O GLU B4572 " (cutoff:3.500A) Processing helix chain 'B' and resid 4590 through 4600 Processing helix chain 'B' and resid 4603 through 4609 Processing helix chain 'B' and resid 4609 through 4625 Proline residue: B4621 - end of helix Processing helix chain 'B' and resid 4627 through 4639 removed outlier: 3.634A pdb=" N PHE B4638 " --> pdb=" O LEU B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4640 through 4642 No H-bonds generated for 'chain 'B' and resid 4640 through 4642' Processing helix chain 'B' and resid 4643 through 4650 Processing helix chain 'B' and resid 4652 through 4668 Processing helix chain 'B' and resid 4672 through 4685 Processing helix chain 'B' and resid 4686 through 4699 Processing helix chain 'B' and resid 4707 through 4715 Processing helix chain 'B' and resid 4717 through 4731 removed outlier: 4.421A pdb=" N PHE B4721 " --> pdb=" O PRO B4717 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4744 removed outlier: 4.403A pdb=" N ASP B4743 " --> pdb=" O LEU B4739 " (cutoff:3.500A) Processing helix chain 'B' and resid 4744 through 4753 Processing helix chain 'F' and resid 1 through 5 removed outlier: 4.223A pdb=" N GLN F 4 " --> pdb=" O MET F 1 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 32 through 40 Processing helix chain 'F' and resid 45 through 57 Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.694A pdb=" N LYS F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 102 through 114 Processing helix chain 'F' and resid 118 through 130 removed outlier: 3.569A pdb=" N VAL F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 148 Processing sheet with id=AA1, first strand: chain 'A' and resid 3250 through 3252 Processing sheet with id=AA2, first strand: chain 'A' and resid 3543 through 3546 removed outlier: 7.443A pdb=" N LYS A3718 " --> pdb=" O ILE A3571 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE A3571 " --> pdb=" O LYS A3718 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS A3720 " --> pdb=" O HIS A3569 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N HIS A3569 " --> pdb=" O CYS A3720 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP A3553 " --> pdb=" O LYS A3564 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE A3566 " --> pdb=" O LYS A3551 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LYS A3551 " --> pdb=" O ILE A3566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3543 through 3546 removed outlier: 7.443A pdb=" N LYS A3718 " --> pdb=" O ILE A3571 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE A3571 " --> pdb=" O LYS A3718 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N CYS A3720 " --> pdb=" O HIS A3569 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N HIS A3569 " --> pdb=" O CYS A3720 " (cutoff:3.500A) removed outlier: 11.965A pdb=" N GLN A3561 " --> pdb=" O ALA A3645 " (cutoff:3.500A) removed outlier: 11.019A pdb=" N ALA A3645 " --> pdb=" O GLN A3561 " (cutoff:3.500A) removed outlier: 12.147A pdb=" N VAL A3563 " --> pdb=" O GLU A3643 " (cutoff:3.500A) removed outlier: 10.909A pdb=" N GLU A3643 " --> pdb=" O VAL A3563 " (cutoff:3.500A) removed outlier: 11.179A pdb=" N LEU A3565 " --> pdb=" O MET A3641 " (cutoff:3.500A) removed outlier: 11.408A pdb=" N MET A3641 " --> pdb=" O LEU A3565 " (cutoff:3.500A) removed outlier: 10.091A pdb=" N GLY A3567 " --> pdb=" O ASN A3639 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN A3639 " --> pdb=" O GLY A3567 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS A3573 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 10.889A pdb=" N LEU A3633 " --> pdb=" O LYS A3573 " (cutoff:3.500A) removed outlier: 11.007A pdb=" N THR A3575 " --> pdb=" O LEU A3631 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N LEU A3631 " --> pdb=" O THR A3575 " (cutoff:3.500A) removed outlier: 10.995A pdb=" N LYS A3577 " --> pdb=" O ILE A3629 " (cutoff:3.500A) removed outlier: 11.975A pdb=" N ILE A3629 " --> pdb=" O LYS A3577 " (cutoff:3.500A) removed outlier: 11.300A pdb=" N GLY A3579 " --> pdb=" O VAL A3627 " (cutoff:3.500A) removed outlier: 11.660A pdb=" N VAL A3627 " --> pdb=" O GLY A3579 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A3640 " --> pdb=" O TYR A3594 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A3594 " --> pdb=" O LEU A3640 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE A3642 " --> pdb=" O LEU A3592 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU A3592 " --> pdb=" O ILE A3642 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N PHE A3644 " --> pdb=" O ILE A3590 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE A3590 " --> pdb=" O PHE A3644 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP A3646 " --> pdb=" O ARG A3588 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ARG A3588 " --> pdb=" O GLN A3619 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A3619 " --> pdb=" O ARG A3588 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A3590 " --> pdb=" O LYS A3617 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N LYS A3617 " --> pdb=" O ILE A3590 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A3592 " --> pdb=" O ALA A3615 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3657 through 3659 Processing sheet with id=AA5, first strand: chain 'A' and resid 4051 through 4052 Processing sheet with id=AA6, first strand: chain 'A' and resid 4372 through 4373 removed outlier: 3.673A pdb=" N MET A4438 " --> pdb=" O PHE A4350 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU A4408 " --> pdb=" O ILE A4415 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A4414 " --> pdb=" O ILE A4456 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 27 through 29 Processing sheet with id=AA8, first strand: chain 'B' and resid 3250 through 3252 Processing sheet with id=AA9, first strand: chain 'B' and resid 3543 through 3546 removed outlier: 7.555A pdb=" N LYS B3718 " --> pdb=" O ILE B3571 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE B3571 " --> pdb=" O LYS B3718 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLN B3560 " --> pdb=" O TYR B3556 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR B3556 " --> pdb=" O GLN B3560 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL B3562 " --> pdb=" O THR B3554 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR B3554 " --> pdb=" O VAL B3562 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS B3564 " --> pdb=" O VAL B3552 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3543 through 3546 removed outlier: 7.555A pdb=" N LYS B3718 " --> pdb=" O ILE B3571 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE B3571 " --> pdb=" O LYS B3718 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N SER B3638 " --> pdb=" O LEU B3565 " (cutoff:3.500A) removed outlier: 10.959A pdb=" N GLY B3567 " --> pdb=" O VAL B3636 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N VAL B3636 " --> pdb=" O GLY B3567 " (cutoff:3.500A) removed outlier: 9.633A pdb=" N HIS B3569 " --> pdb=" O PRO B3634 " (cutoff:3.500A) removed outlier: 10.791A pdb=" N ILE B3571 " --> pdb=" O PRO B3632 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LYS B3573 " --> pdb=" O ASP B3630 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP B3630 " --> pdb=" O LYS B3573 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR B3575 " --> pdb=" O LYS B3628 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS B3628 " --> pdb=" O THR B3575 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS B3577 " --> pdb=" O GLU B3626 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU B3626 " --> pdb=" O LYS B3577 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR B3589 " --> pdb=" O ALA B3645 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B3647 " --> pdb=" O VAL B3587 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B3587 " --> pdb=" O PHE B3647 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU B3649 " --> pdb=" O LYS B3585 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N LYS B3585 " --> pdb=" O GLU B3649 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ARG B3588 " --> pdb=" O GLN B3619 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLN B3619 " --> pdb=" O ARG B3588 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE B3590 " --> pdb=" O LYS B3617 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYS B3617 " --> pdb=" O ILE B3590 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B3592 " --> pdb=" O ALA B3615 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3657 through 3659 Processing sheet with id=AB3, first strand: chain 'B' and resid 4051 through 4052 Processing sheet with id=AB4, first strand: chain 'B' and resid 4372 through 4373 removed outlier: 4.628A pdb=" N LEU B4408 " --> pdb=" O ILE B4415 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B4414 " --> pdb=" O ILE B4456 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 27 through 29 1600 hydrogen bonds defined for protein. 4659 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: 6.01 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8852 1.35 - 1.47: 5792 1.47 - 1.60: 12154 1.60 - 1.72: 0 1.72 - 1.84: 256 Bond restraints: 27054 Sorted by residual: bond pdb=" N LYS A4004 " pdb=" CA LYS A4004 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.09e+00 bond pdb=" N LYS B4004 " pdb=" CA LYS B4004 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.00e+00 bond pdb=" CG ARG B4319 " pdb=" CD ARG B4319 " ideal model delta sigma weight residual 1.520 1.473 0.047 3.00e-02 1.11e+03 2.48e+00 bond pdb=" CG MET B4536 " pdb=" SD MET B4536 " ideal model delta sigma weight residual 1.803 1.842 -0.039 2.50e-02 1.60e+03 2.44e+00 bond pdb=" C ILE B4003 " pdb=" N LYS B4004 " ideal model delta sigma weight residual 1.332 1.351 -0.018 1.40e-02 5.10e+03 1.74e+00 ... (remaining 27049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 36248 2.71 - 5.42: 280 5.42 - 8.14: 27 8.14 - 10.85: 8 10.85 - 13.56: 1 Bond angle restraints: 36564 Sorted by residual: angle pdb=" CB MET F 52 " pdb=" CG MET F 52 " pdb=" SD MET F 52 " ideal model delta sigma weight residual 112.70 126.26 -13.56 3.00e+00 1.11e-01 2.04e+01 angle pdb=" CA MET F 125 " pdb=" CB MET F 125 " pdb=" CG MET F 125 " ideal model delta sigma weight residual 114.10 122.98 -8.88 2.00e+00 2.50e-01 1.97e+01 angle pdb=" CG MET B4536 " pdb=" SD MET B4536 " pdb=" CE MET B4536 " ideal model delta sigma weight residual 100.90 110.05 -9.15 2.20e+00 2.07e-01 1.73e+01 angle pdb=" CG ARG B4319 " pdb=" CD ARG B4319 " pdb=" NE ARG B4319 " ideal model delta sigma weight residual 112.00 120.73 -8.73 2.20e+00 2.07e-01 1.58e+01 angle pdb=" C MET B4536 " pdb=" CA MET B4536 " pdb=" CB MET B4536 " ideal model delta sigma weight residual 110.85 117.01 -6.16 1.70e+00 3.46e-01 1.31e+01 ... (remaining 36559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15186 17.95 - 35.89: 1281 35.89 - 53.83: 179 53.83 - 71.78: 21 71.78 - 89.72: 19 Dihedral angle restraints: 16686 sinusoidal: 6778 harmonic: 9908 Sorted by residual: dihedral pdb=" CA THR A4227 " pdb=" C THR A4227 " pdb=" N LEU A4228 " pdb=" CA LEU A4228 " ideal model delta harmonic sigma weight residual -180.00 -155.37 -24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA LYS B3401 " pdb=" C LYS B3401 " pdb=" N PHE B3402 " pdb=" CA PHE B3402 " ideal model delta harmonic sigma weight residual 180.00 156.26 23.74 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ILE B4003 " pdb=" C ILE B4003 " pdb=" N LYS B4004 " pdb=" CA LYS B4004 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 16683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3043 0.039 - 0.079: 909 0.079 - 0.118: 215 0.118 - 0.157: 26 0.157 - 0.197: 7 Chirality restraints: 4200 Sorted by residual: chirality pdb=" CG LEU A4109 " pdb=" CB LEU A4109 " pdb=" CD1 LEU A4109 " pdb=" CD2 LEU A4109 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CB ILE B3726 " pdb=" CA ILE B3726 " pdb=" CG1 ILE B3726 " pdb=" CG2 ILE B3726 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.18e-01 chirality pdb=" CG LEU A4206 " pdb=" CB LEU A4206 " pdb=" CD1 LEU A4206 " pdb=" CD2 LEU A4206 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 4197 not shown) Planarity restraints: 4706 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B4003 " 0.023 2.00e-02 2.50e+03 4.60e-02 2.11e+01 pdb=" C ILE B4003 " -0.079 2.00e-02 2.50e+03 pdb=" O ILE B4003 " 0.030 2.00e-02 2.50e+03 pdb=" N LYS B4004 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A4003 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C ILE A4003 " 0.079 2.00e-02 2.50e+03 pdb=" O ILE A4003 " -0.030 2.00e-02 2.50e+03 pdb=" N LYS A4004 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B4536 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.23e+00 pdb=" C MET B4536 " -0.043 2.00e-02 2.50e+03 pdb=" O MET B4536 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B4537 " 0.015 2.00e-02 2.50e+03 ... (remaining 4703 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 406 2.69 - 3.24: 27237 3.24 - 3.80: 42331 3.80 - 4.35: 53965 4.35 - 4.90: 87820 Nonbonded interactions: 211759 Sorted by model distance: nonbonded pdb=" OG1 THR A4227 " pdb=" O GLY B3863 " model vdw 2.139 3.040 nonbonded pdb=" OD2 ASP A4648 " pdb=" OH TYR A4694 " model vdw 2.164 3.040 nonbonded pdb=" OD2 ASP B4648 " pdb=" OH TYR B4694 " model vdw 2.168 3.040 nonbonded pdb=" OG SER A4067 " pdb=" OD1 ASP A4069 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR A3436 " pdb=" OG1 THR A3479 " model vdw 2.197 3.040 ... (remaining 211754 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 'B' } ncs_group { reference = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 16.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.800 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 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 : 0.003 0.047 27054 Z= 0.139 Angle : 0.616 13.562 36564 Z= 0.326 Chirality : 0.039 0.197 4200 Planarity : 0.003 0.053 4706 Dihedral : 13.084 89.724 10262 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3374 helix: 1.52 (0.12), residues: 2050 sheet: 0.63 (0.40), residues: 156 loop : 0.05 (0.19), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B4319 TYR 0.015 0.001 TYR B3302 PHE 0.027 0.002 PHE D 66 TRP 0.038 0.002 TRP A3612 HIS 0.014 0.001 HIS A3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (27054) covalent geometry : angle 0.61633 / 0.33 (36564) hydrogen bonds : bond 0.13468 / 9.02 ( 1576) hydrogen bonds : angle 5.26323 / 3.79 ( 4659) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.936 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: A 3711 PHE cc_start: 0.4293 (m-10) cc_final: 0.4086 (m-10) REVERT: A 4089 LYS cc_start: 0.6334 (tmmt) cc_final: 0.6049 (tptt) REVERT: A 4512 PHE cc_start: 0.6351 (m-80) cc_final: 0.6104 (m-80) REVERT: D 146 MET cc_start: -0.0353 (ttm) cc_final: -0.0754 (ttm) REVERT: B 3267 ASP cc_start: 0.5870 (m-30) cc_final: 0.5619 (m-30) REVERT: B 4267 LEU cc_start: 0.7460 (pp) cc_final: 0.7180 (tp) REVERT: B 4406 MET cc_start: 0.1700 (tmm) cc_final: 0.1425 (tmm) REVERT: F 52 MET cc_start: 0.4815 (mmm) cc_final: 0.4437 (mmp) outliers start: 0 outliers final: 0 residues processed: 268 average time/residue: 0.1647 time to fit residues: 72.6690 Evaluate side-chains 203 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.2980 chunk 183 optimal weight: 0.2980 chunk 298 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3291 GLN A3390 GLN A3398 GLN A3420 ASN A3509 ASN ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3835 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3291 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4761 r_free = 0.4761 target = 0.208951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.147708 restraints weight = 60024.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.149343 restraints weight = 41838.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.148607 restraints weight = 28767.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.148978 restraints weight = 29143.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.149257 restraints weight = 24869.976| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27054 Z= 0.128 Angle : 0.558 9.036 36564 Z= 0.286 Chirality : 0.039 0.214 4200 Planarity : 0.003 0.035 4706 Dihedral : 4.033 27.795 3642 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.47 % Allowed : 5.28 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.15), residues: 3374 helix: 1.57 (0.11), residues: 2074 sheet: 0.55 (0.40), residues: 156 loop : 0.01 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B4319 TYR 0.016 0.001 TYR A4101 PHE 0.033 0.002 PHE B3402 TRP 0.014 0.001 TRP A3612 HIS 0.012 0.001 HIS A3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (27054) covalent geometry : angle 0.55848 / 0.29 (36564) hydrogen bonds : bond 0.03939 / 2.69 ( 1576) hydrogen bonds : angle 4.25085 / 3.06 ( 4659) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3323 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7530 (tt) REVERT: A 4089 LYS cc_start: 0.6562 (tmmt) cc_final: 0.6192 (tptt) REVERT: A 4383 MET cc_start: 0.0120 (ptp) cc_final: -0.1394 (mpp) REVERT: A 4406 MET cc_start: -0.0777 (tmm) cc_final: -0.1001 (ttt) REVERT: A 4512 PHE cc_start: 0.6680 (m-80) cc_final: 0.6164 (m-80) REVERT: A 4530 MET cc_start: 0.3135 (pmm) cc_final: 0.2895 (pmm) REVERT: B 3267 ASP cc_start: 0.6850 (m-30) cc_final: 0.6381 (m-30) REVERT: B 3302 TYR cc_start: 0.8082 (t80) cc_final: 0.7863 (t80) REVERT: B 4262 LEU cc_start: 0.8186 (mt) cc_final: 0.7974 (mp) REVERT: B 4298 MET cc_start: 0.5600 (tmm) cc_final: 0.5061 (tmm) REVERT: B 4596 MET cc_start: 0.6819 (tmm) cc_final: 0.6195 (ppp) REVERT: F 52 MET cc_start: 0.3457 (mmm) cc_final: 0.3168 (mmp) outliers start: 14 outliers final: 8 residues processed: 244 average time/residue: 0.1590 time to fit residues: 63.9835 Evaluate side-chains 201 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3742 LEU Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 3956 LYS Chi-restraints excluded: chain A residue 4022 LYS Chi-restraints excluded: chain A residue 4146 CYS Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 4042 LEU Chi-restraints excluded: chain F residue 137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [208, 104, 20, 234, 173, 330, 249, 24, 204, 213, 321] chunk 208 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 234 optimal weight: 0.6980 chunk 173 optimal weight: 3.9990 chunk 330 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 204 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 321 optimal weight: 20.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3306 GLN A3509 ASN A3639 ASN ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3834 GLN ** A4234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3420 ASN B3942 GLN B4268 ASN B4500 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.202413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.137723 restraints weight = 58988.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.138169 restraints weight = 41118.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.137942 restraints weight = 37506.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.138744 restraints weight = 28722.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.138965 restraints weight = 26405.238| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 27054 Z= 0.218 Angle : 0.654 11.341 36564 Z= 0.330 Chirality : 0.043 0.252 4200 Planarity : 0.004 0.054 4706 Dihedral : 4.224 27.273 3642 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.73 % Favored : 97.18 % Rotamer: Outliers : 1.21 % Allowed : 8.68 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.15), residues: 3374 helix: 1.30 (0.11), residues: 2058 sheet: 0.64 (0.42), residues: 150 loop : -0.09 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A4439 TYR 0.019 0.002 TYR B4270 PHE 0.030 0.002 PHE D 17 TRP 0.021 0.002 TRP A3612 HIS 0.009 0.002 HIS A3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (27054) covalent geometry : angle 0.65446 / 0.33 (36564) hydrogen bonds : bond 0.04305 / 2.92 ( 1576) hydrogen bonds : angle 4.34723 / 3.13 ( 4659) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3323 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7908 (tt) REVERT: A 3711 PHE cc_start: 0.4339 (m-80) cc_final: 0.3974 (m-10) REVERT: A 3841 LYS cc_start: 0.3158 (mmtm) cc_final: 0.2820 (pttp) REVERT: A 4089 LYS cc_start: 0.6329 (tmmt) cc_final: 0.6046 (tptt) REVERT: A 4298 MET cc_start: 0.7280 (tmm) cc_final: 0.6896 (tmm) REVERT: A 4383 MET cc_start: 0.0262 (ptp) cc_final: -0.1324 (mpp) REVERT: A 4406 MET cc_start: -0.1301 (tmm) cc_final: -0.1507 (ttt) REVERT: A 4512 PHE cc_start: 0.6737 (m-80) cc_final: 0.6266 (m-80) REVERT: D 13 PHE cc_start: 0.7790 (m-10) cc_final: 0.7535 (m-10) REVERT: D 72 MET cc_start: 0.4357 (mmt) cc_final: 0.4149 (mmm) REVERT: B 3267 ASP cc_start: 0.6855 (m-30) cc_final: 0.6311 (m-30) REVERT: B 3286 ARG cc_start: 0.7818 (mmm160) cc_final: 0.7482 (mmm160) REVERT: B 3739 ILE cc_start: 0.7745 (mt) cc_final: 0.7366 (pt) REVERT: B 4077 ILE cc_start: 0.7419 (pt) cc_final: 0.6972 (mm) REVERT: B 4298 MET cc_start: 0.5788 (tmm) cc_final: 0.5377 (tmm) REVERT: B 4367 MET cc_start: -0.3766 (mmt) cc_final: -0.4154 (mtt) REVERT: B 4406 MET cc_start: 0.0891 (tmm) cc_final: 0.0496 (tmm) REVERT: B 4479 MET cc_start: 0.0124 (OUTLIER) cc_final: -0.0627 (tmm) REVERT: F 52 MET cc_start: 0.3485 (mmm) cc_final: 0.2876 (mmp) REVERT: F 73 MET cc_start: 0.6906 (tmm) cc_final: 0.5856 (tmm) REVERT: F 77 MET cc_start: 0.7273 (ppp) cc_final: 0.6810 (ppp) outliers start: 36 outliers final: 20 residues processed: 257 average time/residue: 0.1616 time to fit residues: 68.0270 Evaluate side-chains 221 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3414 CYS Chi-restraints excluded: chain A residue 3454 ILE Chi-restraints excluded: chain A residue 3742 LEU Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 4022 LYS Chi-restraints excluded: chain A residue 4044 THR Chi-restraints excluded: chain A residue 4146 CYS Chi-restraints excluded: chain A residue 4206 LEU Chi-restraints excluded: chain A residue 4217 ILE Chi-restraints excluded: chain A residue 4291 LEU Chi-restraints excluded: chain B residue 3318 VAL Chi-restraints excluded: chain B residue 3522 PHE Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3708 TYR Chi-restraints excluded: chain B residue 3767 VAL Chi-restraints excluded: chain B residue 3880 THR Chi-restraints excluded: chain B residue 4042 LEU Chi-restraints excluded: chain B residue 4245 LEU Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4479 MET Chi-restraints excluded: chain F residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [84, 227, 34, 220, 330, 180, 149, 66, 183, 267, 214] chunk 84 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 330 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 183 optimal weight: 0.0670 chunk 267 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3509 ASN ** A3596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.204411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139476 restraints weight = 58864.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.142414 restraints weight = 41198.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.142273 restraints weight = 26584.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.142525 restraints weight = 25878.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.142697 restraints weight = 23718.073| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27054 Z= 0.120 Angle : 0.524 7.501 36564 Z= 0.267 Chirality : 0.039 0.196 4200 Planarity : 0.003 0.042 4706 Dihedral : 3.966 27.519 3642 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.25 % Favored : 97.69 % Rotamer: Outliers : 1.21 % Allowed : 10.50 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3374 helix: 1.61 (0.12), residues: 2052 sheet: 0.77 (0.42), residues: 150 loop : -0.06 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B3225 TYR 0.014 0.001 TYR B3266 PHE 0.034 0.001 PHE D 17 TRP 0.014 0.001 TRP A3612 HIS 0.011 0.001 HIS B3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (27054) covalent geometry : angle 0.52357 / 0.27 (36564) hydrogen bonds : bond 0.03556 / 2.41 ( 1576) hydrogen bonds : angle 4.01608 / 2.89 ( 4659) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3841 LYS cc_start: 0.3253 (mmtm) cc_final: 0.2914 (pttp) REVERT: A 4089 LYS cc_start: 0.6358 (tmmt) cc_final: 0.6091 (tptt) REVERT: A 4383 MET cc_start: 0.0306 (ptp) cc_final: -0.1271 (mpp) REVERT: A 4488 MET cc_start: 0.2084 (ptt) cc_final: 0.1684 (ptt) REVERT: A 4512 PHE cc_start: 0.6701 (m-80) cc_final: 0.6425 (m-80) REVERT: A 4530 MET cc_start: 0.3218 (pmm) cc_final: 0.2974 (pmm) REVERT: D 72 MET cc_start: 0.4558 (mmt) cc_final: 0.3850 (mmt) REVERT: D 146 MET cc_start: -0.3387 (ttm) cc_final: -0.3604 (ttm) REVERT: B 3267 ASP cc_start: 0.7085 (m-30) cc_final: 0.6515 (m-30) REVERT: B 3794 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7433 (ptp90) REVERT: B 3829 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7013 (mm) REVERT: B 4077 ILE cc_start: 0.7302 (pt) cc_final: 0.6826 (mm) REVERT: B 4298 MET cc_start: 0.5646 (tmm) cc_final: 0.5184 (tmm) REVERT: B 4367 MET cc_start: -0.3711 (mmt) cc_final: -0.4115 (mtt) REVERT: B 4406 MET cc_start: 0.0718 (tmm) cc_final: 0.0484 (tmm) REVERT: B 4596 MET cc_start: 0.6756 (tmm) cc_final: 0.6109 (ppp) REVERT: F 52 MET cc_start: 0.3231 (mmm) cc_final: 0.2590 (mmp) REVERT: F 73 MET cc_start: 0.6834 (tmm) cc_final: 0.5877 (tmm) REVERT: F 77 MET cc_start: 0.7244 (ppp) cc_final: 0.6949 (ppp) outliers start: 36 outliers final: 16 residues processed: 248 average time/residue: 0.1655 time to fit residues: 67.8074 Evaluate side-chains 215 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3313 GLU Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3726 ILE Chi-restraints excluded: chain A residue 3956 LYS Chi-restraints excluded: chain A residue 4146 CYS Chi-restraints excluded: chain A residue 4206 LEU Chi-restraints excluded: chain A residue 4227 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3522 PHE Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3794 ARG Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 4042 LEU Chi-restraints excluded: chain B residue 4195 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [261, 334, 220, 248, 45, 62, 105, 69, 9, 316, 244] chunk 261 optimal weight: 0.5980 chunk 334 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 248 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 9 optimal weight: 0.1980 chunk 316 optimal weight: 0.0370 chunk 244 optimal weight: 0.9980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3596 ASN ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.205330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.143293 restraints weight = 59137.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.144834 restraints weight = 37992.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.143924 restraints weight = 25958.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.144308 restraints weight = 26226.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.144331 restraints weight = 25360.019| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27054 Z= 0.105 Angle : 0.507 8.673 36564 Z= 0.256 Chirality : 0.038 0.191 4200 Planarity : 0.003 0.041 4706 Dihedral : 3.816 27.467 3642 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 1.51 % Allowed : 11.34 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.15), residues: 3374 helix: 1.74 (0.12), residues: 2058 sheet: 0.79 (0.42), residues: 150 loop : -0.03 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B3286 TYR 0.014 0.001 TYR A4101 PHE 0.030 0.001 PHE F 20 TRP 0.015 0.001 TRP A3290 HIS 0.010 0.001 HIS B3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (27054) covalent geometry : angle 0.50684 / 0.26 (36564) hydrogen bonds : bond 0.03336 / 2.26 ( 1576) hydrogen bonds : angle 3.88602 / 2.79 ( 4659) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 223 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3619 GLN cc_start: 0.6412 (tm-30) cc_final: 0.6035 (tm-30) REVERT: A 3628 LYS cc_start: 0.8681 (mmmt) cc_final: 0.8440 (mmmt) REVERT: A 3841 LYS cc_start: 0.3264 (mmtm) cc_final: 0.3006 (pttp) REVERT: A 4089 LYS cc_start: 0.6512 (tmmt) cc_final: 0.6232 (tptt) REVERT: A 4383 MET cc_start: 0.0439 (ptp) cc_final: -0.1124 (mpp) REVERT: A 4512 PHE cc_start: 0.6530 (m-80) cc_final: 0.6310 (m-80) REVERT: A 4530 MET cc_start: 0.3206 (pmm) cc_final: 0.2913 (pmm) REVERT: D 72 MET cc_start: 0.4374 (mmt) cc_final: 0.3828 (mmt) REVERT: D 119 ASP cc_start: 0.7184 (p0) cc_final: 0.6842 (t70) REVERT: D 123 ASP cc_start: 0.8014 (m-30) cc_final: 0.7646 (m-30) REVERT: B 3225 ARG cc_start: 0.7920 (ttp-110) cc_final: 0.7363 (ptt-90) REVERT: B 3449 ASP cc_start: 0.7935 (t0) cc_final: 0.7709 (t0) REVERT: B 3714 MET cc_start: 0.5820 (mmp) cc_final: 0.5598 (mmp) REVERT: B 3829 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7028 (mm) REVERT: B 4298 MET cc_start: 0.5679 (tmm) cc_final: 0.5184 (tmm) REVERT: B 4367 MET cc_start: -0.3815 (mmt) cc_final: -0.4182 (mtt) REVERT: B 4438 MET cc_start: -0.1240 (tmm) cc_final: -0.3079 (mmp) REVERT: B 4596 MET cc_start: 0.6669 (tmm) cc_final: 0.6029 (ppp) REVERT: F 72 MET cc_start: 0.1389 (mmt) cc_final: 0.0943 (mmt) REVERT: F 73 MET cc_start: 0.6856 (tmm) cc_final: 0.6061 (tmm) outliers start: 45 outliers final: 28 residues processed: 253 average time/residue: 0.1622 time to fit residues: 68.0644 Evaluate side-chains 229 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3424 VAL Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3726 ILE Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3742 LEU Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4146 CYS Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4206 LEU Chi-restraints excluded: chain A residue 4227 THR Chi-restraints excluded: chain A residue 4291 LEU Chi-restraints excluded: chain A residue 4485 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3522 PHE Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3794 ARG Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3880 THR Chi-restraints excluded: chain B residue 4042 LEU Chi-restraints excluded: chain B residue 4043 THR Chi-restraints excluded: chain B residue 4195 HIS Chi-restraints excluded: chain B residue 4273 LEU Chi-restraints excluded: chain F residue 137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [144, 31, 159, 57, 253, 181, 134, 150, 45, 326, 136] chunk 144 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 253 optimal weight: 0.7980 chunk 181 optimal weight: 30.0000 chunk 134 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 326 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3509 ASN ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4053 HIS A4234 GLN A4279 GLN A4561 GLN A4600 GLN B3834 GLN F 9 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.200605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.134537 restraints weight = 58265.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.136593 restraints weight = 43497.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.136957 restraints weight = 29033.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.136981 restraints weight = 24491.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.137359 restraints weight = 24338.357| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27054 Z= 0.201 Angle : 0.614 12.238 36564 Z= 0.307 Chirality : 0.041 0.216 4200 Planarity : 0.003 0.052 4706 Dihedral : 3.982 27.330 3642 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 2.12 % Allowed : 12.11 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.15), residues: 3374 helix: 1.51 (0.11), residues: 2074 sheet: 0.61 (0.42), residues: 150 loop : -0.06 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A4522 TYR 0.016 0.002 TYR B3970 PHE 0.030 0.002 PHE F 20 TRP 0.015 0.002 TRP A3290 HIS 0.009 0.001 HIS B3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (27054) covalent geometry : angle 0.61390 / 0.31 (36564) hydrogen bonds : bond 0.03787 / 2.58 ( 1576) hydrogen bonds : angle 4.07216 / 2.92 ( 4659) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3405 LYS cc_start: 0.8664 (mttt) cc_final: 0.8335 (tttm) REVERT: A 3628 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8251 (mmpt) REVERT: A 3841 LYS cc_start: 0.3381 (mmtm) cc_final: 0.3082 (pttp) REVERT: A 4089 LYS cc_start: 0.6525 (tmmt) cc_final: 0.6270 (tptt) REVERT: A 4383 MET cc_start: 0.0461 (ptp) cc_final: -0.1051 (mpp) REVERT: A 4479 MET cc_start: 0.5686 (tmm) cc_final: 0.5478 (tpt) REVERT: A 4512 PHE cc_start: 0.6695 (m-80) cc_final: 0.6466 (m-80) REVERT: D 52 MET cc_start: 0.1210 (mmp) cc_final: 0.0512 (mmp) REVERT: B 3225 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7352 (ptt-90) REVERT: B 3583 ARG cc_start: 0.7453 (tpm170) cc_final: 0.6737 (tpm170) REVERT: B 3829 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7121 (mm) REVERT: B 3945 ASP cc_start: 0.8270 (t0) cc_final: 0.7856 (t0) REVERT: B 4295 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8306 (tt) REVERT: B 4298 MET cc_start: 0.5812 (tmm) cc_final: 0.5503 (tmm) REVERT: B 4367 MET cc_start: -0.3706 (mmt) cc_final: -0.4044 (mtt) REVERT: B 4438 MET cc_start: -0.1226 (tmm) cc_final: -0.3012 (mmp) REVERT: B 4479 MET cc_start: 0.0273 (OUTLIER) cc_final: -0.0423 (tmm) REVERT: B 4596 MET cc_start: 0.6717 (tmm) cc_final: 0.6122 (ppp) REVERT: F 52 MET cc_start: 0.3267 (mmm) cc_final: 0.2425 (mmp) REVERT: F 73 MET cc_start: 0.6570 (tmm) cc_final: 0.5985 (tmm) outliers start: 63 outliers final: 41 residues processed: 263 average time/residue: 0.1706 time to fit residues: 73.4779 Evaluate side-chains 233 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3414 CYS Chi-restraints excluded: chain A residue 3424 VAL Chi-restraints excluded: chain A residue 3454 ILE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3726 ILE Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3744 ASP Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 3884 ILE Chi-restraints excluded: chain A residue 3956 LYS Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4008 VAL Chi-restraints excluded: chain A residue 4022 LYS Chi-restraints excluded: chain A residue 4044 THR Chi-restraints excluded: chain A residue 4146 CYS Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4217 ILE Chi-restraints excluded: chain A residue 4227 THR Chi-restraints excluded: chain A residue 4291 LEU Chi-restraints excluded: chain A residue 4485 LEU Chi-restraints excluded: chain A residue 4540 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3522 PHE Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3708 TYR Chi-restraints excluded: chain B residue 3741 THR Chi-restraints excluded: chain B residue 3767 VAL Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3880 THR Chi-restraints excluded: chain B residue 3958 HIS Chi-restraints excluded: chain B residue 4042 LEU Chi-restraints excluded: chain B residue 4217 ILE Chi-restraints excluded: chain B residue 4245 LEU Chi-restraints excluded: chain B residue 4273 LEU Chi-restraints excluded: chain B residue 4295 LEU Chi-restraints excluded: chain B residue 4331 ILE Chi-restraints excluded: chain B residue 4479 MET Chi-restraints excluded: chain F residue 137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [318, 249, 59, 202, 316, 106, 309, 78, 305, 238, 32] chunk 318 optimal weight: 9.9990 chunk 249 optimal weight: 0.0010 chunk 59 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 316 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 309 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 305 optimal weight: 0.8980 chunk 238 optimal weight: 0.5980 chunk 32 optimal weight: 30.0000 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3683 GLN ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.207578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.143694 restraints weight = 58200.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.146955 restraints weight = 39398.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.147267 restraints weight = 24357.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.147432 restraints weight = 23579.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.147710 restraints weight = 23388.466| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 27054 Z= 0.114 Angle : 0.534 9.459 36564 Z= 0.269 Chirality : 0.038 0.187 4200 Planarity : 0.003 0.076 4706 Dihedral : 3.852 27.423 3642 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.34 % Favored : 97.60 % Rotamer: Outliers : 1.62 % Allowed : 12.72 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.15), residues: 3374 helix: 1.68 (0.12), residues: 2066 sheet: 0.67 (0.42), residues: 150 loop : 0.01 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3794 TYR 0.014 0.001 TYR A4169 PHE 0.034 0.001 PHE F 20 TRP 0.016 0.001 TRP A3290 HIS 0.009 0.001 HIS B3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (27054) covalent geometry : angle 0.53373 / 0.27 (36564) hydrogen bonds : bond 0.03385 / 2.30 ( 1576) hydrogen bonds : angle 3.90112 / 2.79 ( 4659) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 199 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3405 LYS cc_start: 0.8643 (mttt) cc_final: 0.8315 (tttm) REVERT: A 3628 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8258 (mmpt) REVERT: A 4089 LYS cc_start: 0.6609 (tmmt) cc_final: 0.6338 (tptt) REVERT: A 4383 MET cc_start: 0.0551 (ptp) cc_final: -0.1268 (mpp) REVERT: A 4479 MET cc_start: 0.5721 (tmm) cc_final: 0.5494 (tpt) REVERT: A 4530 MET cc_start: 0.3241 (pmm) cc_final: 0.2968 (pmm) REVERT: D 13 PHE cc_start: 0.7344 (m-10) cc_final: 0.7101 (m-80) REVERT: D 52 MET cc_start: 0.1121 (mmp) cc_final: 0.0295 (mmp) REVERT: B 3225 ARG cc_start: 0.7875 (ttp-110) cc_final: 0.7409 (ptt-90) REVERT: B 3265 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6165 (tp40) REVERT: B 3267 ASP cc_start: 0.7231 (m-30) cc_final: 0.6754 (p0) REVERT: B 3291 GLN cc_start: 0.7811 (tt0) cc_final: 0.7525 (tp-100) REVERT: B 3583 ARG cc_start: 0.7390 (tpm170) cc_final: 0.6843 (tpm170) REVERT: B 3688 ARG cc_start: 0.6453 (mmp80) cc_final: 0.6199 (mmp80) REVERT: B 3829 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7153 (mm) REVERT: B 3945 ASP cc_start: 0.8181 (t0) cc_final: 0.7787 (t0) REVERT: B 4161 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7143 (tp40) REVERT: B 4295 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8363 (tt) REVERT: B 4298 MET cc_start: 0.5789 (tmm) cc_final: 0.5536 (tmm) REVERT: B 4367 MET cc_start: -0.3841 (mmt) cc_final: -0.4149 (mtt) REVERT: B 4438 MET cc_start: -0.1261 (tmm) cc_final: -0.3065 (mmp) REVERT: B 4479 MET cc_start: 0.0027 (OUTLIER) cc_final: -0.0558 (tmm) REVERT: B 4596 MET cc_start: 0.6804 (tmm) cc_final: 0.6310 (ppp) REVERT: F 72 MET cc_start: 0.1064 (mmt) cc_final: 0.0620 (mmt) REVERT: F 73 MET cc_start: 0.6400 (tmm) cc_final: 0.6064 (tmm) outliers start: 48 outliers final: 31 residues processed: 237 average time/residue: 0.1621 time to fit residues: 63.1536 Evaluate side-chains 218 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3424 VAL Chi-restraints excluded: chain A residue 3521 GLU Chi-restraints excluded: chain A residue 3523 ASP Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3726 ILE Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 3956 LYS Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4022 LYS Chi-restraints excluded: chain A residue 4044 THR Chi-restraints excluded: chain A residue 4146 CYS Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4227 THR Chi-restraints excluded: chain A residue 4291 LEU Chi-restraints excluded: chain A residue 4485 LEU Chi-restraints excluded: chain A residue 4540 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain B residue 3265 GLN Chi-restraints excluded: chain B residue 3522 PHE Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3880 THR Chi-restraints excluded: chain B residue 3958 HIS Chi-restraints excluded: chain B residue 4042 LEU Chi-restraints excluded: chain B residue 4105 TRP Chi-restraints excluded: chain B residue 4195 HIS Chi-restraints excluded: chain B residue 4273 LEU Chi-restraints excluded: chain B residue 4295 LEU Chi-restraints excluded: chain B residue 4479 MET Chi-restraints excluded: chain F residue 137 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [255, 47, 163, 3, 248, 225, 0, 245, 288, 212, 267] chunk 255 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 248 optimal weight: 0.7980 chunk 225 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 245 optimal weight: 0.5980 chunk 288 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.201292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.136390 restraints weight = 58125.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.139253 restraints weight = 39770.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.138585 restraints weight = 25959.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.138786 restraints weight = 25737.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.138929 restraints weight = 24290.739| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27054 Z= 0.141 Angle : 0.560 12.195 36564 Z= 0.281 Chirality : 0.039 0.199 4200 Planarity : 0.003 0.070 4706 Dihedral : 3.821 27.370 3642 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 1.82 % Allowed : 12.75 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.15), residues: 3374 helix: 1.71 (0.12), residues: 2052 sheet: 0.98 (0.44), residues: 138 loop : -0.01 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A3597 TYR 0.015 0.001 TYR A4169 PHE 0.031 0.002 PHE D 20 TRP 0.012 0.001 TRP A3290 HIS 0.009 0.001 HIS B3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (27054) covalent geometry : angle 0.56010 / 0.28 (36564) hydrogen bonds : bond 0.03467 / 2.37 ( 1576) hydrogen bonds : angle 3.91523 / 2.80 ( 4659) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3405 LYS cc_start: 0.8616 (mttt) cc_final: 0.8329 (tttm) REVERT: A 3628 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8306 (mmpt) REVERT: A 3973 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 4089 LYS cc_start: 0.6548 (tmmt) cc_final: 0.6316 (tptt) REVERT: A 4383 MET cc_start: 0.0489 (ptp) cc_final: -0.1122 (mpp) REVERT: A 4488 MET cc_start: 0.2053 (ptt) cc_final: 0.1784 (ptt) REVERT: A 4530 MET cc_start: 0.3449 (pmm) cc_final: 0.3079 (pmm) REVERT: D 52 MET cc_start: 0.1201 (mmp) cc_final: 0.0921 (mmm) REVERT: B 3225 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7440 (ptt-90) REVERT: B 3265 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6305 (tp40) REVERT: B 3267 ASP cc_start: 0.7158 (m-30) cc_final: 0.6792 (p0) REVERT: B 3291 GLN cc_start: 0.7824 (tt0) cc_final: 0.7557 (tt0) REVERT: B 3739 ILE cc_start: 0.8410 (mt) cc_final: 0.8136 (tt) REVERT: B 3829 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7276 (mm) REVERT: B 3945 ASP cc_start: 0.8203 (t0) cc_final: 0.7776 (t0) REVERT: B 4295 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8159 (tt) REVERT: B 4367 MET cc_start: -0.3710 (mmt) cc_final: -0.4045 (mtt) REVERT: B 4438 MET cc_start: -0.1319 (tmm) cc_final: -0.2959 (mmp) REVERT: B 4479 MET cc_start: 0.0244 (OUTLIER) cc_final: -0.0433 (tmm) REVERT: F 72 MET cc_start: 0.1179 (mmt) cc_final: 0.0735 (mmt) REVERT: F 73 MET cc_start: 0.6423 (tmm) cc_final: 0.6120 (tmm) outliers start: 54 outliers final: 37 residues processed: 243 average time/residue: 0.1666 time to fit residues: 66.7635 Evaluate side-chains 228 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3414 CYS Chi-restraints excluded: chain A residue 3424 VAL Chi-restraints excluded: chain A residue 3454 ILE Chi-restraints excluded: chain A residue 3521 GLU Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3726 ILE Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 3956 LYS Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3973 LEU Chi-restraints excluded: chain A residue 4022 LYS Chi-restraints excluded: chain A residue 4044 THR Chi-restraints excluded: chain A residue 4146 CYS Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4206 LEU Chi-restraints excluded: chain A residue 4227 THR Chi-restraints excluded: chain A residue 4291 LEU Chi-restraints excluded: chain A residue 4485 LEU Chi-restraints excluded: chain A residue 4540 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain B residue 3265 GLN Chi-restraints excluded: chain B residue 3522 PHE Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3726 ILE Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3880 THR Chi-restraints excluded: chain B residue 3958 HIS Chi-restraints excluded: chain B residue 4042 LEU Chi-restraints excluded: chain B residue 4105 TRP Chi-restraints excluded: chain B residue 4217 ILE Chi-restraints excluded: chain B residue 4220 LEU Chi-restraints excluded: chain B residue 4273 LEU Chi-restraints excluded: chain B residue 4295 LEU Chi-restraints excluded: chain B residue 4331 ILE Chi-restraints excluded: chain B residue 4479 MET Chi-restraints excluded: chain F residue 9 GLN Chi-restraints excluded: chain F residue 137 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [5, 3, 142, 177, 332, 144, 70, 334, 137, 87, 7] chunk 5 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 332 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 334 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3291 GLN B4279 GLN F 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.200967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.136541 restraints weight = 58450.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137588 restraints weight = 44063.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.137674 restraints weight = 31794.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.138109 restraints weight = 28049.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.138343 restraints weight = 26650.737| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27054 Z= 0.142 Angle : 0.570 14.849 36564 Z= 0.285 Chirality : 0.039 0.200 4200 Planarity : 0.003 0.064 4706 Dihedral : 3.827 27.441 3642 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.43 % Favored : 97.51 % Rotamer: Outliers : 1.75 % Allowed : 13.36 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.15), residues: 3374 helix: 1.71 (0.12), residues: 2056 sheet: 0.97 (0.44), residues: 138 loop : 0.04 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3286 TYR 0.022 0.001 TYR A3556 PHE 0.031 0.002 PHE F 20 TRP 0.016 0.001 TRP A3455 HIS 0.009 0.001 HIS B3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (27054) covalent geometry : angle 0.57015 / 0.29 (36564) hydrogen bonds : bond 0.03414 / 2.33 ( 1576) hydrogen bonds : angle 3.93257 / 2.81 ( 4659) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3225 ARG cc_start: 0.6789 (ptm160) cc_final: 0.6380 (ptm-80) REVERT: A 3405 LYS cc_start: 0.8624 (mttt) cc_final: 0.8368 (tttm) REVERT: A 3628 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8317 (mmpt) REVERT: A 3973 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7998 (mm) REVERT: A 4089 LYS cc_start: 0.6556 (tmmt) cc_final: 0.6300 (tptt) REVERT: A 4232 LEU cc_start: 0.7976 (tt) cc_final: 0.7747 (mt) REVERT: A 4383 MET cc_start: 0.0503 (ptp) cc_final: -0.1060 (mpp) REVERT: A 4530 MET cc_start: 0.3515 (pmm) cc_final: 0.3245 (pmm) REVERT: D 13 PHE cc_start: 0.7417 (m-10) cc_final: 0.7207 (m-80) REVERT: D 52 MET cc_start: 0.1017 (mmp) cc_final: 0.0802 (mmm) REVERT: B 3225 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7420 (ptt-90) REVERT: B 3265 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6262 (tp40) REVERT: B 3267 ASP cc_start: 0.7154 (m-30) cc_final: 0.6884 (p0) REVERT: B 3583 ARG cc_start: 0.7109 (tpm170) cc_final: 0.6898 (tpm170) REVERT: B 3739 ILE cc_start: 0.8437 (mt) cc_final: 0.8141 (tt) REVERT: B 3829 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7420 (mm) REVERT: B 3945 ASP cc_start: 0.8204 (t0) cc_final: 0.7781 (t0) REVERT: B 4161 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7185 (mm-40) REVERT: B 4367 MET cc_start: -0.3627 (mmt) cc_final: -0.4083 (mtt) REVERT: B 4438 MET cc_start: -0.1411 (tmm) cc_final: -0.3029 (mmp) REVERT: B 4479 MET cc_start: 0.0269 (OUTLIER) cc_final: -0.0441 (tmm) REVERT: B 4596 MET cc_start: 0.6990 (tmm) cc_final: 0.6449 (ppp) REVERT: F 72 MET cc_start: 0.1323 (mmt) cc_final: 0.0886 (mmt) outliers start: 52 outliers final: 39 residues processed: 240 average time/residue: 0.1623 time to fit residues: 63.5252 Evaluate side-chains 228 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3414 CYS Chi-restraints excluded: chain A residue 3424 VAL Chi-restraints excluded: chain A residue 3454 ILE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3726 ILE Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3744 ASP Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 3956 LYS Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3973 LEU Chi-restraints excluded: chain A residue 4022 LYS Chi-restraints excluded: chain A residue 4044 THR Chi-restraints excluded: chain A residue 4146 CYS Chi-restraints excluded: chain A residue 4155 ILE Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4206 LEU Chi-restraints excluded: chain A residue 4227 THR Chi-restraints excluded: chain A residue 4291 LEU Chi-restraints excluded: chain A residue 4485 LEU Chi-restraints excluded: chain A residue 4540 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain B residue 3265 GLN Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3295 ILE Chi-restraints excluded: chain B residue 3522 PHE Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3726 ILE Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3880 THR Chi-restraints excluded: chain B residue 3958 HIS Chi-restraints excluded: chain B residue 4042 LEU Chi-restraints excluded: chain B residue 4105 TRP Chi-restraints excluded: chain B residue 4195 HIS Chi-restraints excluded: chain B residue 4217 ILE Chi-restraints excluded: chain B residue 4273 LEU Chi-restraints excluded: chain B residue 4295 LEU Chi-restraints excluded: chain B residue 4331 ILE Chi-restraints excluded: chain B residue 4479 MET Chi-restraints excluded: chain F residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [161, 69, 18, 12, 302, 181, 253, 319, 308, 105, 17] chunk 161 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 302 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 319 optimal weight: 6.9990 chunk 308 optimal weight: 0.3980 chunk 105 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A3285 GLN ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4500 GLN ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.201722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.137613 restraints weight = 58430.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.140202 restraints weight = 39509.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.139601 restraints weight = 29067.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.139967 restraints weight = 27064.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140240 restraints weight = 24449.545| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27054 Z= 0.126 Angle : 0.570 13.108 36564 Z= 0.282 Chirality : 0.039 0.226 4200 Planarity : 0.003 0.078 4706 Dihedral : 3.792 27.457 3642 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.40 % Favored : 97.54 % Rotamer: Outliers : 1.65 % Allowed : 13.49 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.15), residues: 3374 helix: 1.75 (0.12), residues: 2068 sheet: 0.96 (0.45), residues: 138 loop : 0.03 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A3225 TYR 0.014 0.001 TYR A3556 PHE 0.031 0.001 PHE F 20 TRP 0.014 0.001 TRP A3290 HIS 0.008 0.001 HIS B3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (27054) covalent geometry : angle 0.57026 / 0.28 (36564) hydrogen bonds : bond 0.03387 / 2.29 ( 1576) hydrogen bonds : angle 3.90097 / 2.78 ( 4659) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6748 Ramachandran restraints generated. 3374 Oldfield, 0 Emsley, 3374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3405 LYS cc_start: 0.8603 (mttt) cc_final: 0.8377 (tttm) REVERT: A 3628 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8338 (mmpt) REVERT: A 3973 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8033 (mm) REVERT: A 4089 LYS cc_start: 0.6569 (tmmt) cc_final: 0.6309 (tptt) REVERT: A 4232 LEU cc_start: 0.7870 (tt) cc_final: 0.7665 (mt) REVERT: A 4383 MET cc_start: 0.0519 (ptp) cc_final: -0.1036 (mpp) REVERT: D 52 MET cc_start: 0.1185 (mmp) cc_final: 0.0443 (mmp) REVERT: D 119 ASP cc_start: 0.7196 (p0) cc_final: 0.6809 (t70) REVERT: B 3265 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6427 (tp40) REVERT: B 3583 ARG cc_start: 0.7182 (tpm170) cc_final: 0.6930 (tpm170) REVERT: B 3739 ILE cc_start: 0.8489 (mt) cc_final: 0.8181 (tt) REVERT: B 3829 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7436 (mm) REVERT: B 3945 ASP cc_start: 0.8175 (t0) cc_final: 0.7749 (t0) REVERT: B 4161 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7203 (mm-40) REVERT: B 4367 MET cc_start: -0.3651 (mmt) cc_final: -0.4088 (mtt) REVERT: B 4438 MET cc_start: -0.1536 (tmm) cc_final: -0.3105 (mmp) REVERT: B 4479 MET cc_start: 0.0255 (OUTLIER) cc_final: -0.0431 (tmm) REVERT: B 4596 MET cc_start: 0.7008 (tmm) cc_final: 0.6447 (ppp) REVERT: F 72 MET cc_start: 0.1236 (mmt) cc_final: 0.0939 (mmt) outliers start: 49 outliers final: 37 residues processed: 234 average time/residue: 0.1619 time to fit residues: 62.0873 Evaluate side-chains 230 residues out of total 2972 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3414 CYS Chi-restraints excluded: chain A residue 3424 VAL Chi-restraints excluded: chain A residue 3523 ASP Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3636 VAL Chi-restraints excluded: chain A residue 3739 ILE Chi-restraints excluded: chain A residue 3744 ASP Chi-restraints excluded: chain A residue 3767 VAL Chi-restraints excluded: chain A residue 3956 LYS Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3973 LEU Chi-restraints excluded: chain A residue 4008 VAL Chi-restraints excluded: chain A residue 4022 LYS Chi-restraints excluded: chain A residue 4044 THR Chi-restraints excluded: chain A residue 4146 CYS Chi-restraints excluded: chain A residue 4193 SER Chi-restraints excluded: chain A residue 4227 THR Chi-restraints excluded: chain A residue 4291 LEU Chi-restraints excluded: chain A residue 4485 LEU Chi-restraints excluded: chain A residue 4540 LEU Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain B residue 3265 GLN Chi-restraints excluded: chain B residue 3287 THR Chi-restraints excluded: chain B residue 3295 ILE Chi-restraints excluded: chain B residue 3522 PHE Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3575 THR Chi-restraints excluded: chain B residue 3627 VAL Chi-restraints excluded: chain B residue 3647 PHE Chi-restraints excluded: chain B residue 3726 ILE Chi-restraints excluded: chain B residue 3829 LEU Chi-restraints excluded: chain B residue 3880 THR Chi-restraints excluded: chain B residue 3958 HIS Chi-restraints excluded: chain B residue 4042 LEU Chi-restraints excluded: chain B residue 4105 TRP Chi-restraints excluded: chain B residue 4195 HIS Chi-restraints excluded: chain B residue 4273 LEU Chi-restraints excluded: chain B residue 4295 LEU Chi-restraints excluded: chain B residue 4331 ILE Chi-restraints excluded: chain B residue 4479 MET Chi-restraints excluded: chain F residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: [157, 277, 275, 47, 151, 111, 124, 92, 175, 133, 42] chunk 157 optimal weight: 0.9990 chunk 277 optimal weight: 0.5980 chunk 275 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 chunk 42 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A3285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3397 ASN B4034 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.201646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.139838 restraints weight = 58432.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.141066 restraints weight = 38367.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.139893 restraints weight = 27935.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140307 restraints weight = 29884.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.140741 restraints weight = 25568.573| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27054 Z= 0.114 Angle : 0.553 11.553 36564 Z= 0.277 Chirality : 0.039 0.208 4200 Planarity : 0.003 0.066 4706 Dihedral : 3.742 27.463 3642 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 1.41 % Allowed : 13.39 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.15), residues: 3374 helix: 1.83 (0.12), residues: 2070 sheet: 0.70 (0.44), residues: 146 loop : 0.09 (0.19), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A3225 TYR 0.016 0.001 TYR B3266 PHE 0.031 0.001 PHE F 20 TRP 0.015 0.001 TRP A3290 HIS 0.008 0.001 HIS B3429 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (27054) covalent geometry : angle 0.55326 / 0.28 (36564) hydrogen bonds : bond 0.03266 / 2.21 ( 1576) hydrogen bonds : angle 3.86282 / 2.76 ( 4659) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5444.29 seconds wall clock time: 94 minutes 39.53 seconds (5679.53 seconds total)