Starting phenix.real_space_refine on Mon Aug 25 16:50:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nwe_49876/08_2025/9nwe_49876_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nwe_49876/08_2025/9nwe_49876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nwe_49876/08_2025/9nwe_49876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nwe_49876/08_2025/9nwe_49876.map" model { file = "/net/cci-nas-00/data/ceres_data/9nwe_49876/08_2025/9nwe_49876_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nwe_49876/08_2025/9nwe_49876_neut.cif" } resolution = 3.2 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= 0.027 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: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 6 6.06 5 S 196 5.16 5 C 18495 2.51 5 N 5008 2.21 5 O 5579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 213 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29288 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 13132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1660, 13132 Classifications: {'peptide': 1660} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 57, 'TRANS': 1598} Chain breaks: 7 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 13134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1660, 13134 Classifications: {'peptide': 1660} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 4, 'PTRANS': 57, 'TRANS': 1598} Chain breaks: 7 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1134 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Chain: "D" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1127 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain breaks: 1 Chain: "E" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 380 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "F" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 371 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" 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: "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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4643 SG CYS A3660 85.594 87.486 139.059 1.00 90.24 S ATOM 4667 SG CYS A3663 85.803 88.723 142.447 1.00 91.84 S ATOM 4735 SG CYS A3674 83.867 85.747 141.883 1.00 92.63 S ATOM 4753 SG CYS A3677 82.698 88.921 140.432 1.00 91.19 S ATOM 4808 SG CYS A3684 84.304 87.338 123.279 1.00 91.92 S ATOM 4833 SG CYS A3687 80.838 88.499 122.490 1.00 92.87 S ATOM 4944 SG CYS A3700 81.995 85.311 121.250 1.00 93.84 S ATOM 4963 SG CYS A3703 83.335 88.552 119.937 1.00 94.60 S ATOM 3615 SG CYS A3532 83.069 96.100 70.578 1.00 28.97 S ATOM 3636 SG CYS A3535 85.225 97.376 71.287 1.00 24.76 S ATOM 6232 SG CYS A3872 82.962 98.109 69.352 1.00 30.00 S ATOM 6254 SG CYS A3875 86.835 95.980 70.093 1.00 24.51 S ATOM 17775 SG CYS B3660 92.583 157.711 139.059 1.00 90.24 S ATOM 17799 SG CYS B3663 92.375 156.475 142.445 1.00 91.84 S ATOM 17867 SG CYS B3674 94.312 159.449 141.883 1.00 92.63 S ATOM 17885 SG CYS B3677 95.480 156.276 140.430 1.00 91.19 S ATOM 17940 SG CYS B3684 93.873 157.867 123.279 1.00 91.92 S ATOM 17965 SG CYS B3687 97.339 156.702 122.488 1.00 92.87 S ATOM 18076 SG CYS B3700 96.181 159.892 121.249 1.00 93.84 S ATOM 18095 SG CYS B3703 94.845 156.652 119.936 1.00 94.60 S ATOM 16747 SG CYS B3532 94.654 147.816 71.195 1.00 28.97 S ATOM 16768 SG CYS B3535 92.468 147.567 70.976 1.00 24.76 S ATOM 19364 SG CYS B3872 95.206 147.103 69.351 1.00 30.00 S ATOM 19386 SG CYS B3875 91.336 149.235 70.093 1.00 24.51 S Time building chain proxies: 7.26, per 1000 atoms: 0.25 Number of scatterers: 29288 At special positions: 0 Unit cell: (179.208, 246.28, 154.056, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 Ca 4 19.99 S 196 16.00 O 5579 8.00 N 5008 7.00 C 18495 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: 2.77 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5201 " pdb="ZN ZN A5201 " - pdb=" SG CYS A3677 " pdb="ZN ZN A5201 " - pdb=" SG CYS A3663 " pdb="ZN ZN A5201 " - pdb=" SG CYS A3674 " pdb="ZN ZN A5201 " - pdb=" SG CYS A3660 " pdb=" ZN A5202 " pdb="ZN ZN A5202 " - pdb=" SG CYS A3687 " pdb="ZN ZN A5202 " - pdb=" SG CYS A3703 " pdb="ZN ZN A5202 " - pdb=" SG CYS A3684 " pdb="ZN ZN A5202 " - pdb=" SG CYS A3700 " pdb=" ZN A5203 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3535 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3532 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3875 " pdb="ZN ZN A5203 " - pdb=" SG CYS A3872 " pdb=" ZN B5201 " pdb="ZN ZN B5201 " - pdb=" SG CYS B3677 " pdb="ZN ZN B5201 " - pdb=" SG CYS B3663 " pdb="ZN ZN B5201 " - pdb=" SG CYS B3674 " pdb="ZN ZN B5201 " - pdb=" SG CYS B3660 " pdb=" ZN B5202 " pdb="ZN ZN B5202 " - pdb=" SG CYS B3687 " pdb="ZN ZN B5202 " - pdb=" SG CYS B3703 " pdb="ZN ZN B5202 " - pdb=" SG CYS B3684 " pdb="ZN ZN B5202 " - pdb=" SG CYS B3700 " pdb=" ZN B5203 " pdb="ZN ZN B5203 " - pdb=" SG CYS B3532 " pdb="ZN ZN B5203 " - pdb=" SG CYS B3535 " pdb="ZN ZN B5203 " - pdb=" SG CYS B3875 " pdb="ZN ZN B5203 " - pdb=" SG CYS B3872 " Number of angles added : 36 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7060 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 12 sheets defined 71.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 2996 through 3008 Processing helix chain 'A' and resid 3014 through 3033 removed outlier: 3.672A pdb=" N GLY A3033 " --> pdb=" O ILE A3029 " (cutoff:3.500A) Processing helix chain 'A' and resid 3039 through 3044 removed outlier: 3.645A pdb=" N ASN A3043 " --> pdb=" O VAL A3039 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU A3044 " --> pdb=" O SER A3040 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3039 through 3044' Processing helix chain 'A' and resid 3046 through 3064 Processing helix chain 'A' and resid 3073 through 3092 removed outlier: 3.777A pdb=" N SER A3077 " --> pdb=" O SER A3073 " (cutoff:3.500A) Processing helix chain 'A' and resid 3093 through 3115 removed outlier: 3.764A pdb=" N TYR A3097 " --> pdb=" O GLY A3093 " (cutoff:3.500A) Processing helix chain 'A' and resid 3156 through 3178 Proline residue: A3168 - end of helix Processing helix chain 'A' and resid 3187 through 3199 removed outlier: 4.040A pdb=" N PHE A3191 " --> pdb=" O ASP A3187 " (cutoff:3.500A) Processing helix chain 'A' and resid 3205 through 3219 Processing helix chain 'A' and resid 3220 through 3248 Processing helix chain 'A' and resid 3265 through 3286 Processing helix chain 'A' and resid 3286 through 3297 removed outlier: 4.138A pdb=" N TRP A3290 " --> pdb=" O ARG A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3297 through 3310 removed outlier: 3.794A pdb=" N LEU A3301 " --> pdb=" O ASP A3297 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A3305 " --> pdb=" O LEU A3301 " (cutoff:3.500A) removed outlier: 3.772A 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 3337 Processing helix chain 'A' and resid 3386 through 3403 Processing helix chain 'A' and resid 3404 through 3417 Processing helix chain 'A' and resid 3421 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: 4.129A pdb=" N GLY A3462 " --> pdb=" O PRO A3459 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG A3463 " --> pdb=" O ALA A3460 " (cutoff:3.500A) Processing helix chain 'A' and resid 3465 through 3479 Processing helix chain 'A' and resid 3482 through 3506 Processing helix chain 'A' and resid 3509 through 3520 Processing helix chain 'A' and resid 3532 through 3537 Processing helix chain 'A' and resid 3547 through 3550 No H-bonds generated for 'chain 'A' and resid 3547 through 3550' Processing helix chain 'A' and resid 3601 through 3606 Processing helix chain 'A' and resid 3608 through 3612 Processing helix chain 'A' and resid 3727 through 3769 removed outlier: 3.672A pdb=" N ASP A3731 " --> pdb=" O GLU A3727 " (cutoff:3.500A) Proline residue: A3758 - end of helix Processing helix chain 'A' and resid 3786 through 3791 Processing helix chain 'A' and resid 3793 through 3805 Processing helix chain 'A' and resid 3805 through 3840 Processing helix chain 'A' and resid 3850 through 3856 Processing helix chain 'A' and resid 3872 through 3891 Processing helix chain 'A' and resid 3893 through 3904 Processing helix chain 'A' and resid 3904 through 3912 Processing helix chain 'A' and resid 3918 through 3934 Processing helix chain 'A' and resid 3936 through 3958 Processing helix chain 'A' and resid 3963 through 3981 removed outlier: 3.781A pdb=" N SER A3967 " --> pdb=" O ASP A3963 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A3969 " --> pdb=" O ALA A3965 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A3970 " --> pdb=" O SER A3966 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A3971 " --> pdb=" O SER A3967 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A3981 " --> pdb=" O ASP A3977 " (cutoff:3.500A) Processing helix chain 'A' and resid 3985 through 4002 removed outlier: 3.669A pdb=" N ARG A3989 " --> pdb=" O CYS A3985 " (cutoff:3.500A) Processing helix chain 'A' and resid 4005 through 4025 removed outlier: 4.326A pdb=" N LEU A4014 " --> pdb=" O GLU A4010 " (cutoff:3.500A) Processing helix chain 'A' and resid 4031 through 4035 Processing helix chain 'A' and resid 4056 through 4061 Processing helix chain 'A' and resid 4067 through 4075 Processing helix chain 'A' and resid 4088 through 4113 Processing helix chain 'A' and resid 4127 through 4135 removed outlier: 3.580A pdb=" N THR A4135 " --> pdb=" O GLN A4131 " (cutoff:3.500A) Processing helix chain 'A' and resid 4138 through 4153 removed outlier: 3.721A pdb=" N ARG A4142 " --> pdb=" O THR A4138 " (cutoff:3.500A) Processing helix chain 'A' and resid 4155 through 4177 removed outlier: 5.142A pdb=" N ASP A4171 " --> pdb=" O THR A4167 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLU A4172 " --> pdb=" O SER A4168 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A4173 " --> pdb=" O TYR A4169 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER A4174 " --> pdb=" O LEU A4170 " (cutoff:3.500A) Processing helix chain 'A' and resid 4180 through 4191 Processing helix chain 'A' and resid 4193 through 4204 Processing helix chain 'A' and resid 4204 through 4224 removed outlier: 3.535A pdb=" N TYR A4208 " --> pdb=" O GLY A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4235 through 4250 Processing helix chain 'A' and resid 4251 through 4275 removed outlier: 5.377A pdb=" N SER A4260 " --> pdb=" O ARG A4256 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ARG A4261 " --> pdb=" O HIS A4257 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY A4264 " --> pdb=" O SER A4260 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N THR A4265 " --> pdb=" O ARG A4261 " (cutoff:3.500A) Processing helix chain 'A' and resid 4281 through 4300 Processing helix chain 'A' and resid 4302 through 4319 Processing helix chain 'A' and resid 4328 through 4340 Processing helix chain 'A' and resid 4357 through 4360 removed outlier: 3.688A 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: 3.632A pdb=" N ILE A4386 " --> pdb=" O LEU A4382 " (cutoff:3.500A) Processing helix chain 'A' and resid 4396 through 4401 removed outlier: 4.141A pdb=" N GLU A4401 " --> pdb=" O VAL A4397 " (cutoff:3.500A) Processing helix chain 'A' and resid 4420 through 4428 Processing helix chain 'A' and resid 4429 through 4434 removed outlier: 3.723A 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 4476 No H-bonds generated for 'chain 'A' and resid 4474 through 4476' Processing helix chain 'A' and resid 4477 through 4482 removed outlier: 3.896A pdb=" N GLN A4481 " --> pdb=" O GLY A4477 " (cutoff:3.500A) Processing helix chain 'A' and resid 4483 through 4495 Processing helix chain 'A' and resid 4497 through 4516 removed outlier: 5.514A pdb=" N HIS A4503 " --> pdb=" O LYS A4499 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU A4504 " --> pdb=" O GLN A4500 " (cutoff:3.500A) Processing helix chain 'A' and resid 4518 through 4526 Processing helix chain 'A' and resid 4527 through 4530 Processing helix chain 'A' and resid 4531 through 4550 Processing helix chain 'A' and resid 4554 through 4575 Processing helix chain 'A' and resid 4591 through 4603 Processing helix chain 'A' and resid 4603 through 4609 Processing helix chain 'A' and resid 4609 through 4624 Proline residue: A4621 - end of helix Processing helix chain 'A' and resid 4631 through 4639 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 4669 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: 4.708A pdb=" N PHE A4721 " --> pdb=" O PRO A4717 " (cutoff:3.500A) Processing helix chain 'A' and resid 4733 through 4742 Processing helix chain 'A' and resid 4744 through 4753 removed outlier: 3.898A pdb=" N GLN A4753 " --> pdb=" O HIS A4749 " (cutoff:3.500A) Processing helix chain 'A' and resid 4759 through 4772 Processing helix chain 'B' and resid 2996 through 3008 Processing helix chain 'B' and resid 3014 through 3033 removed outlier: 3.674A pdb=" N GLY B3033 " --> pdb=" O ILE B3029 " (cutoff:3.500A) Processing helix chain 'B' and resid 3039 through 3044 removed outlier: 3.643A pdb=" N ASN B3043 " --> pdb=" O VAL B3039 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU B3044 " --> pdb=" O SER B3040 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3039 through 3044' Processing helix chain 'B' and resid 3046 through 3064 Processing helix chain 'B' and resid 3073 through 3092 removed outlier: 3.775A pdb=" N SER B3077 " --> pdb=" O SER B3073 " (cutoff:3.500A) Processing helix chain 'B' and resid 3093 through 3115 removed outlier: 3.766A pdb=" N TYR B3097 " --> pdb=" O GLY B3093 " (cutoff:3.500A) Processing helix chain 'B' and resid 3156 through 3178 Proline residue: B3168 - end of helix Processing helix chain 'B' and resid 3187 through 3200 removed outlier: 4.041A pdb=" N PHE B3191 " --> pdb=" O ASP B3187 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE B3200 " --> pdb=" O GLU B3196 " (cutoff:3.500A) Processing helix chain 'B' and resid 3205 through 3219 Processing helix chain 'B' and resid 3220 through 3248 Processing helix chain 'B' and resid 3265 through 3286 Processing helix chain 'B' and resid 3286 through 3297 removed outlier: 3.925A pdb=" N TRP B3290 " --> pdb=" O ARG B3286 " (cutoff:3.500A) Processing helix chain 'B' and resid 3297 through 3310 removed outlier: 3.793A pdb=" N LEU B3301 " --> pdb=" O ASP B3297 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B3305 " --> pdb=" O LEU B3301 " (cutoff:3.500A) removed outlier: 3.770A 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 3337 Processing helix chain 'B' and resid 3386 through 3403 Processing helix chain 'B' and resid 3404 through 3417 Processing helix chain 'B' and resid 3421 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: 4.130A pdb=" N GLY B3462 " --> pdb=" O PRO B3459 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG B3463 " --> pdb=" O ALA B3460 " (cutoff:3.500A) Processing helix chain 'B' and resid 3465 through 3479 Processing helix chain 'B' and resid 3482 through 3506 Processing helix chain 'B' and resid 3509 through 3520 Processing helix chain 'B' and resid 3547 through 3550 No H-bonds generated for 'chain 'B' and resid 3547 through 3550' Processing helix chain 'B' and resid 3601 through 3606 Processing helix chain 'B' and resid 3608 through 3612 Processing helix chain 'B' and resid 3727 through 3770 removed outlier: 3.522A pdb=" N ASP B3731 " --> pdb=" O GLU B3727 " (cutoff:3.500A) Proline residue: B3758 - end of helix removed outlier: 3.703A pdb=" N ALA B3770 " --> pdb=" O LYS B3766 " (cutoff:3.500A) Processing helix chain 'B' and resid 3786 through 3792 Processing helix chain 'B' and resid 3793 through 3805 Processing helix chain 'B' and resid 3805 through 3840 Processing helix chain 'B' and resid 3850 through 3856 Processing helix chain 'B' and resid 3872 through 3891 Processing helix chain 'B' and resid 3893 through 3904 Processing helix chain 'B' and resid 3904 through 3912 Processing helix chain 'B' and resid 3918 through 3933 Processing helix chain 'B' and resid 3936 through 3955 Processing helix chain 'B' and resid 3963 through 3981 removed outlier: 3.891A pdb=" N SER B3967 " --> pdb=" O ASP B3963 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B3969 " --> pdb=" O ALA B3965 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TYR B3970 " --> pdb=" O SER B3966 " (cutoff:3.500A) Processing helix chain 'B' and resid 3985 through 4003 removed outlier: 3.982A pdb=" N ILE B4003 " --> pdb=" O MET B3999 " (cutoff:3.500A) Processing helix chain 'B' and resid 4005 through 4025 removed outlier: 3.515A pdb=" N ASN B4011 " --> pdb=" O VAL B4007 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU B4014 " --> pdb=" O GLU B4010 " (cutoff:3.500A) Processing helix chain 'B' and resid 4056 through 4061 Processing helix chain 'B' and resid 4067 through 4075 Processing helix chain 'B' and resid 4088 through 4112 Processing helix chain 'B' and resid 4128 through 4134 Processing helix chain 'B' and resid 4138 through 4153 removed outlier: 3.719A pdb=" N ARG B4142 " --> pdb=" O THR B4138 " (cutoff:3.500A) Processing helix chain 'B' and resid 4155 through 4177 removed outlier: 5.142A pdb=" N ASP B4171 " --> pdb=" O THR B4167 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N GLU B4172 " --> pdb=" O SER B4168 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B4173 " --> pdb=" O TYR B4169 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B4174 " --> pdb=" O LEU B4170 " (cutoff:3.500A) Processing helix chain 'B' and resid 4180 through 4191 Processing helix chain 'B' and resid 4193 through 4204 Processing helix chain 'B' and resid 4204 through 4224 removed outlier: 3.534A 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: 5.375A pdb=" N SER B4260 " --> pdb=" O ARG B4256 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ARG B4261 " --> pdb=" O HIS B4257 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY B4264 " --> pdb=" O SER B4260 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B4265 " --> pdb=" O ARG B4261 " (cutoff:3.500A) Processing helix chain 'B' and resid 4281 through 4300 removed outlier: 3.529A pdb=" N THR B4300 " --> pdb=" O GLU B4296 " (cutoff:3.500A) Processing helix chain 'B' and resid 4302 through 4319 Processing helix chain 'B' and resid 4328 through 4340 Processing helix chain 'B' and resid 4357 through 4360 removed outlier: 3.689A 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 removed outlier: 3.631A pdb=" N ILE B4386 " --> pdb=" O LEU B4382 " (cutoff:3.500A) Processing helix chain 'B' and resid 4396 through 4401 removed outlier: 4.139A pdb=" N GLU B4401 " --> pdb=" O VAL B4397 " (cutoff:3.500A) Processing helix chain 'B' and resid 4420 through 4428 Processing helix chain 'B' and resid 4429 through 4434 removed outlier: 3.722A pdb=" N GLU B4434 " --> pdb=" O CYS B4430 " (cutoff:3.500A) Processing helix chain 'B' and resid 4468 through 4473 Processing helix chain 'B' and resid 4474 through 4476 No H-bonds generated for 'chain 'B' and resid 4474 through 4476' Processing helix chain 'B' and resid 4477 through 4482 removed outlier: 3.896A pdb=" N GLN B4481 " --> pdb=" O GLY B4477 " (cutoff:3.500A) Processing helix chain 'B' and resid 4483 through 4495 Processing helix chain 'B' and resid 4497 through 4516 removed outlier: 5.511A pdb=" N HIS B4503 " --> pdb=" O LYS B4499 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N LEU B4504 " --> pdb=" O GLN B4500 " (cutoff:3.500A) Processing helix chain 'B' and resid 4518 through 4526 Processing helix chain 'B' and resid 4527 through 4530 Processing helix chain 'B' and resid 4531 through 4550 Processing helix chain 'B' and resid 4554 through 4576 removed outlier: 3.537A pdb=" N GLU B4576 " --> pdb=" O GLU B4572 " (cutoff:3.500A) Processing helix chain 'B' and resid 4591 through 4603 removed outlier: 3.718A pdb=" N VAL B4595 " --> pdb=" O LYS B4591 " (cutoff:3.500A) Processing helix chain 'B' and resid 4603 through 4609 Processing helix chain 'B' and resid 4609 through 4624 Proline residue: B4621 - end of helix Processing helix chain 'B' and resid 4631 through 4637 Processing helix chain 'B' and resid 4637 through 4643 removed outlier: 3.514A pdb=" N TYR B4641 " --> pdb=" O ARG B4637 " (cutoff:3.500A) Processing helix chain 'B' and resid 4643 through 4650 removed outlier: 3.654A pdb=" N ASP B4648 " --> pdb=" O PHE B4644 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B4649 " --> pdb=" O ASP B4645 " (cutoff:3.500A) Processing helix chain 'B' and resid 4652 through 4669 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: 4.708A pdb=" N PHE B4721 " --> pdb=" O PRO B4717 " (cutoff:3.500A) Processing helix chain 'B' and resid 4733 through 4742 Processing helix chain 'B' and resid 4744 through 4753 removed outlier: 3.902A pdb=" N GLN B4753 " --> pdb=" O HIS B4749 " (cutoff:3.500A) Processing helix chain 'B' and resid 4759 through 4772 Processing helix chain 'C' and resid 6 through 21 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 45 through 56 Processing helix chain 'C' and resid 59 through 63 Processing helix chain 'C' and resid 65 through 77 removed outlier: 4.142A pdb=" N LYS C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 102 through 114 Processing helix chain 'C' and resid 118 through 130 Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'D' and resid 6 through 21 Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 65 through 79 Processing helix chain 'D' and resid 79 through 95 removed outlier: 4.857A pdb=" N ARG D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 118 through 130 Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'E' and resid 291 through 296 Processing helix chain 'E' and resid 302 through 329 Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 302 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 3249 through 3252 Processing sheet with id=AA2, first strand: chain 'A' and resid 3545 through 3546 removed outlier: 4.157A pdb=" N LYS A3573 " --> pdb=" O TYR A3716 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS A3718 " --> pdb=" O ILE A3571 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE A3571 " --> pdb=" O LYS A3718 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A3553 " --> pdb=" O LYS A3564 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ILE A3566 " --> pdb=" O LYS A3551 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LYS A3551 " --> pdb=" O ILE A3566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 3545 through 3546 removed outlier: 4.157A pdb=" N LYS A3573 " --> pdb=" O TYR A3716 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS A3718 " --> pdb=" O ILE A3571 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE A3571 " --> pdb=" O LYS A3718 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLN A3560 " --> pdb=" O GLU A3643 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N GLU A3643 " --> pdb=" O GLN A3560 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A3562 " --> pdb=" O MET A3641 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET A3641 " --> pdb=" O VAL A3562 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A3564 " --> pdb=" O ASN A3639 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASN A3639 " --> pdb=" O LYS A3564 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE A3566 " --> pdb=" O ALA A3637 " (cutoff:3.500A) removed outlier: 11.203A pdb=" N ALA A3637 " --> pdb=" O ILE A3566 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N SER A3568 " --> pdb=" O ILE A3635 " (cutoff:3.500A) removed outlier: 10.773A pdb=" N ILE A3635 " --> pdb=" O SER A3568 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N THR A3570 " --> pdb=" O LEU A3633 " (cutoff:3.500A) removed outlier: 10.959A pdb=" N LEU A3633 " --> pdb=" O THR A3570 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A3572 " --> pdb=" O LEU A3631 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A3640 " --> pdb=" O TYR A3594 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR A3594 " --> pdb=" O LEU A3640 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A3642 " --> pdb=" O LEU A3592 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A3592 " --> pdb=" O ILE A3642 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE A3644 " --> pdb=" O ILE A3590 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE A3590 " --> pdb=" O PHE A3644 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP A3646 " --> pdb=" O ARG A3588 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ARG A3588 " --> pdb=" O GLN A3619 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN A3619 " --> pdb=" O ARG A3588 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE A3590 " --> pdb=" O LYS A3617 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS A3617 " --> pdb=" O ILE A3590 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A3592 " --> pdb=" O ALA A3615 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 3658 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: 7.063A pdb=" N PHE A4350 " --> pdb=" O MET A4438 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE A4440 " --> pdb=" O PHE A4350 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N THR A4352 " --> pdb=" O ILE A4440 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR A4442 " --> pdb=" O THR A4352 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU A4354 " --> pdb=" O TYR A4442 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N MET A4444 " --> pdb=" O GLU A4354 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU A4408 " --> pdb=" O ILE A4415 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A4414 " --> pdb=" O ILE A4456 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 3249 through 3252 Processing sheet with id=AA8, first strand: chain 'B' and resid 3543 through 3546 removed outlier: 3.628A pdb=" N LYS B3573 " --> pdb=" O TYR B3716 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LYS B3718 " --> pdb=" O ILE B3571 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE B3571 " --> pdb=" O LYS B3718 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP B3553 " --> pdb=" O LYS B3564 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE B3566 " --> pdb=" O LYS B3551 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N LYS B3551 " --> pdb=" O ILE B3566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 3543 through 3546 removed outlier: 3.628A pdb=" N LYS B3573 " --> pdb=" O TYR B3716 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N LYS B3718 " --> pdb=" O ILE B3571 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ILE B3571 " --> pdb=" O LYS B3718 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN B3560 " --> pdb=" O GLU B3643 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU B3643 " --> pdb=" O GLN B3560 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL B3562 " --> pdb=" O MET B3641 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET B3641 " --> pdb=" O VAL B3562 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS B3564 " --> pdb=" O ASN B3639 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN B3639 " --> pdb=" O LYS B3564 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ILE B3566 " --> pdb=" O ALA B3637 " (cutoff:3.500A) removed outlier: 11.203A pdb=" N ALA B3637 " --> pdb=" O ILE B3566 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N SER B3568 " --> pdb=" O ILE B3635 " (cutoff:3.500A) removed outlier: 10.769A pdb=" N ILE B3635 " --> pdb=" O SER B3568 " (cutoff:3.500A) removed outlier: 9.849A pdb=" N THR B3570 " --> pdb=" O LEU B3633 " (cutoff:3.500A) removed outlier: 10.959A pdb=" N LEU B3633 " --> pdb=" O THR B3570 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N SER B3572 " --> pdb=" O LEU B3631 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU B3640 " --> pdb=" O TYR B3594 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR B3594 " --> pdb=" O LEU B3640 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE B3642 " --> pdb=" O LEU B3592 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU B3592 " --> pdb=" O ILE B3642 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE B3644 " --> pdb=" O ILE B3590 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B3590 " --> pdb=" O PHE B3644 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP B3646 " --> pdb=" O ARG B3588 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ARG B3588 " --> pdb=" O GLN B3619 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN B3619 " --> pdb=" O ARG B3588 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE B3590 " --> pdb=" O LYS B3617 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS B3617 " --> pdb=" O ILE B3590 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B3592 " --> pdb=" O ALA B3615 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3658 through 3659 Processing sheet with id=AB2, first strand: chain 'B' and resid 4051 through 4052 removed outlier: 3.617A pdb=" N LEU B4119 " --> pdb=" O ILE B4052 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 4372 through 4373 removed outlier: 7.061A pdb=" N PHE B4350 " --> pdb=" O MET B4438 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE B4440 " --> pdb=" O PHE B4350 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N THR B4352 " --> pdb=" O ILE B4440 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR B4442 " --> pdb=" O THR B4352 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU B4354 " --> pdb=" O TYR B4442 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N MET B4444 " --> pdb=" O GLU B4354 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU B4408 " --> pdb=" O ILE B4415 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B4414 " --> pdb=" O ILE B4456 " (cutoff:3.500A) 1888 hydrogen bonds defined for protein. 5553 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: 7.02 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5006 1.29 - 1.43: 7074 1.43 - 1.56: 17378 1.56 - 1.70: 1 1.70 - 1.83: 292 Bond restraints: 29751 Sorted by residual: bond pdb=" C THR B4013 " pdb=" O THR B4013 " ideal model delta sigma weight residual 1.236 1.167 0.070 1.15e-02 7.56e+03 3.69e+01 bond pdb=" C LEU B4023 " pdb=" O LEU B4023 " ideal model delta sigma weight residual 1.236 1.167 0.070 1.15e-02 7.56e+03 3.67e+01 bond pdb=" C LEU A3968 " pdb=" O LEU A3968 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.28e-02 6.10e+03 3.56e+01 bond pdb=" CA LYS D 14 " pdb=" C LYS D 14 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.30e-02 5.92e+03 3.49e+01 bond pdb=" CA LYS C 14 " pdb=" C LYS C 14 " ideal model delta sigma weight residual 1.523 1.447 0.077 1.30e-02 5.92e+03 3.47e+01 ... (remaining 29746 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.87: 40010 4.87 - 9.73: 159 9.73 - 14.60: 15 14.60 - 19.46: 2 19.46 - 24.33: 1 Bond angle restraints: 40187 Sorted by residual: angle pdb=" C VAL A3792 " pdb=" N ASN A3793 " pdb=" CA ASN A3793 " ideal model delta sigma weight residual 120.71 96.38 24.33 1.42e+00 4.96e-01 2.93e+02 angle pdb=" CA VAL A3792 " pdb=" C VAL A3792 " pdb=" N ASN A3793 " ideal model delta sigma weight residual 115.26 99.42 15.84 1.11e+00 8.12e-01 2.04e+02 angle pdb=" O VAL A3792 " pdb=" C VAL A3792 " pdb=" N ASN A3793 " ideal model delta sigma weight residual 122.54 136.41 -13.87 1.03e+00 9.43e-01 1.81e+02 angle pdb=" C GLN A3969 " pdb=" CA GLN A3969 " pdb=" CB GLN A3969 " ideal model delta sigma weight residual 110.96 91.86 19.10 1.54e+00 4.22e-01 1.54e+02 angle pdb=" N ILE C 86 " pdb=" CA ILE C 86 " pdb=" C ILE C 86 " ideal model delta sigma weight residual 111.09 97.20 13.89 1.25e+00 6.40e-01 1.23e+02 ... (remaining 40182 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 16677 17.99 - 35.99: 1288 35.99 - 53.98: 289 53.98 - 71.97: 71 71.97 - 89.97: 20 Dihedral angle restraints: 18345 sinusoidal: 7490 harmonic: 10855 Sorted by residual: dihedral pdb=" C GLN A3969 " pdb=" N GLN A3969 " pdb=" CA GLN A3969 " pdb=" CB GLN A3969 " ideal model delta harmonic sigma weight residual -122.60 -101.52 -21.08 0 2.50e+00 1.60e-01 7.11e+01 dihedral pdb=" CD ARG A3286 " pdb=" NE ARG A3286 " pdb=" CZ ARG A3286 " pdb=" NH1 ARG A3286 " ideal model delta sinusoidal sigma weight residual 0.00 -64.42 64.42 1 1.00e+01 1.00e-02 5.45e+01 dihedral pdb=" C TYR B3750 " pdb=" N TYR B3750 " pdb=" CA TYR B3750 " pdb=" CB TYR B3750 " ideal model delta harmonic sigma weight residual -122.60 -106.07 -16.53 0 2.50e+00 1.60e-01 4.37e+01 ... (remaining 18342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3621 0.082 - 0.165: 872 0.165 - 0.247: 133 0.247 - 0.329: 7 0.329 - 0.412: 3 Chirality restraints: 4636 Sorted by residual: chirality pdb=" CA TYR B3750 " pdb=" N TYR B3750 " pdb=" C TYR B3750 " pdb=" CB TYR B3750 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA PHE A4134 " pdb=" N PHE A4134 " pdb=" C PHE A4134 " pdb=" CB PHE A4134 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CA ILE B4052 " pdb=" N ILE B4052 " pdb=" C ILE B4052 " pdb=" CB ILE B4052 " both_signs ideal model delta sigma weight residual False 2.43 2.78 -0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 4633 not shown) Planarity restraints: 5141 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A3286 " 0.981 9.50e-02 1.11e+02 4.40e-01 1.17e+02 pdb=" NE ARG A3286 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG A3286 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A3286 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A3286 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A3792 " -0.026 2.00e-02 2.50e+03 6.64e-02 4.41e+01 pdb=" C VAL A3792 " 0.114 2.00e-02 2.50e+03 pdb=" O VAL A3792 " -0.048 2.00e-02 2.50e+03 pdb=" N ASN A3793 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A4319 " 0.560 9.50e-02 1.11e+02 2.51e-01 3.85e+01 pdb=" NE ARG A4319 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG A4319 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A4319 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A4319 " 0.018 2.00e-02 2.50e+03 ... (remaining 5138 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 30 2.15 - 2.84: 9141 2.84 - 3.53: 43898 3.53 - 4.21: 67163 4.21 - 4.90: 119147 Nonbonded interactions: 239379 Sorted by model distance: nonbonded pdb=" CD ARG A3825 " pdb=" CD2 LEU B4228 " model vdw 1.463 3.860 nonbonded pdb=" CD2 LEU A4228 " pdb=" CD ARG B3825 " model vdw 1.478 3.860 nonbonded pdb=" CD2 TYR A3750 " pdb=" CD1 LEU B4232 " model vdw 1.607 3.760 nonbonded pdb=" CB ARG A3825 " pdb=" CD1 LEU B4228 " model vdw 1.612 3.860 nonbonded pdb=" CD1 LEU A4228 " pdb=" CB ARG B3825 " model vdw 1.621 3.860 ... (remaining 239374 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2993 through 4036 or resid 4044 through 5203)) selection = (chain 'B' and (resid 2993 through 4575 or resid 4590 through 5203)) } ncs_group { reference = (chain 'C' and (resid 5 through 29 or resid 31 through 202)) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 287 through 331) 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.480 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 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 : 0.013 0.705 29775 Z= 0.723 Angle : 1.448 65.857 40223 Z= 0.907 Chirality : 0.070 0.412 4636 Planarity : 0.011 0.440 5141 Dihedral : 14.048 89.968 11285 Min Nonbonded Distance : 1.463 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.23 % Allowed : 11.20 % Favored : 86.57 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.14), residues: 3656 helix: 0.78 (0.10), residues: 2371 sheet: 0.66 (0.43), residues: 153 loop : -0.73 (0.18), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B4256 TYR 0.068 0.004 TYR B4622 PHE 0.026 0.003 PHE B4498 TRP 0.022 0.002 TRP A4128 HIS 0.012 0.002 HIS B3866 Details of bonding type rmsd covalent geometry : bond 0.00967 (29751) covalent geometry : angle 1.26489 (40187) hydrogen bonds : bond 0.13974 ( 1868) hydrogen bonds : angle 6.28855 ( 5553) metal coordination : bond 0.29016 ( 24) metal coordination : angle 23.61581 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 565 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3570 THR cc_start: 0.8392 (m) cc_final: 0.8128 (p) REVERT: B 4312 VAL cc_start: 0.8534 (t) cc_final: 0.8016 (t) REVERT: C 37 MET cc_start: 0.7618 (mtm) cc_final: 0.7129 (mtt) REVERT: C 49 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6458 (mt) REVERT: D 25 ASP cc_start: 0.7884 (t0) cc_final: 0.7627 (t70) REVERT: D 37 MET cc_start: 0.7194 (mmm) cc_final: 0.6889 (tpp) REVERT: D 49 LEU cc_start: 0.7222 (OUTLIER) cc_final: 0.7010 (mt) REVERT: F 328 LEU cc_start: 0.7644 (mt) cc_final: 0.7295 (mp) outliers start: 73 outliers final: 10 residues processed: 616 average time/residue: 0.2231 time to fit residues: 211.6734 Evaluate side-chains 299 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 287 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3532 CYS Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain B residue 3535 CYS Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 4129 LEU Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 49 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 8.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3265 GLN A3291 GLN A3400 ASN A4011 ASN A4127 ASN A4534 ASN A4602 ASN B3265 GLN B3291 GLN B3400 ASN B4011 ASN B4602 ASN B4643 ASN B4651 HIS C 98 ASN D 42 GLN D 61 ASN D 108 HIS D 112 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.180490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.127519 restraints weight = 67108.869| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.42 r_work: 0.3668 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 29775 Z= 0.170 Angle : 0.782 40.123 40223 Z= 0.345 Chirality : 0.041 0.189 4636 Planarity : 0.005 0.055 5141 Dihedral : 4.586 49.614 3999 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.50 % Allowed : 14.10 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.14), residues: 3656 helix: 1.33 (0.10), residues: 2418 sheet: 0.85 (0.42), residues: 143 loop : -0.22 (0.19), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B3825 TYR 0.020 0.002 TYR B3750 PHE 0.033 0.002 PHE A3193 TRP 0.021 0.002 TRP A4128 HIS 0.010 0.001 HIS B3685 Details of bonding type rmsd covalent geometry : bond 0.00377 (29751) covalent geometry : angle 0.66365 (40187) hydrogen bonds : bond 0.04667 ( 1868) hydrogen bonds : angle 4.72551 ( 5553) metal coordination : bond 0.01918 ( 24) metal coordination : angle 13.84607 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 329 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3059 LEU cc_start: 0.7670 (mt) cc_final: 0.7328 (mt) REVERT: A 3063 MET cc_start: 0.6821 (mmt) cc_final: 0.6139 (mmt) REVERT: A 4035 LYS cc_start: 0.7200 (mttt) cc_final: 0.6991 (tmmt) REVERT: A 4312 VAL cc_start: 0.8897 (t) cc_final: 0.8681 (t) REVERT: A 4316 THR cc_start: 0.9226 (m) cc_final: 0.8947 (p) REVERT: A 4327 THR cc_start: 0.8203 (m) cc_final: 0.7838 (p) REVERT: A 4383 MET cc_start: 0.0045 (mpp) cc_final: -0.1042 (mmt) REVERT: A 4503 HIS cc_start: 0.7751 (t70) cc_final: 0.7525 (p-80) REVERT: A 4540 LEU cc_start: 0.8678 (tp) cc_final: 0.8352 (mt) REVERT: B 3000 MET cc_start: 0.7225 (ppp) cc_final: 0.6259 (mpp) REVERT: B 3059 LEU cc_start: 0.7682 (mt) cc_final: 0.7348 (mt) REVERT: B 3063 MET cc_start: 0.6823 (mmt) cc_final: 0.6153 (mmt) REVERT: B 3551 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8288 (ptmt) REVERT: B 3633 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8230 (mm) REVERT: B 3956 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7970 (mptt) REVERT: B 4327 THR cc_start: 0.8252 (m) cc_final: 0.7893 (p) REVERT: B 4383 MET cc_start: 0.0049 (mpp) cc_final: -0.1093 (mmt) REVERT: B 4503 HIS cc_start: 0.7766 (t70) cc_final: 0.7484 (p-80) REVERT: C 14 LYS cc_start: 0.8705 (tptt) cc_final: 0.8504 (tptp) REVERT: C 37 MET cc_start: 0.8067 (mtm) cc_final: 0.7218 (tpt) REVERT: C 40 LEU cc_start: 0.8174 (mt) cc_final: 0.7771 (mt) REVERT: C 49 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7020 (mt) REVERT: C 51 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8239 (t0) REVERT: C 86 ILE cc_start: 0.6666 (OUTLIER) cc_final: 0.6462 (mp) REVERT: C 100 TYR cc_start: 0.8113 (m-80) cc_final: 0.7373 (m-80) REVERT: C 107 ARG cc_start: 0.6724 (ttp80) cc_final: 0.6416 (ttp80) REVERT: C 117 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6915 (mt) REVERT: C 138 ASN cc_start: 0.7991 (t0) cc_final: 0.7556 (t0) REVERT: D 20 PHE cc_start: 0.7388 (m-80) cc_final: 0.7095 (m-80) REVERT: D 65 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6473 (p0) REVERT: D 73 MET cc_start: 0.7352 (ptm) cc_final: 0.6933 (ptm) REVERT: D 86 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5802 (mp) REVERT: D 100 TYR cc_start: 0.8250 (m-80) cc_final: 0.7633 (m-80) REVERT: D 127 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7577 (tpm170) REVERT: D 146 MET cc_start: 0.6936 (OUTLIER) cc_final: 0.6356 (tpp) REVERT: E 295 ARG cc_start: 0.8476 (mtp-110) cc_final: 0.8084 (mtp-110) REVERT: E 301 MET cc_start: 0.8151 (ttm) cc_final: 0.7879 (tpp) REVERT: E 311 SER cc_start: 0.8568 (OUTLIER) cc_final: 0.8345 (m) REVERT: F 295 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.8114 (mtp-110) outliers start: 82 outliers final: 33 residues processed: 384 average time/residue: 0.2122 time to fit residues: 128.0208 Evaluate side-chains 311 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 267 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3446 LEU Chi-restraints excluded: chain A residue 3488 GLU Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3625 THR Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4520 VAL Chi-restraints excluded: chain A residue 4597 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3323 LEU Chi-restraints excluded: chain B residue 3419 SER Chi-restraints excluded: chain B residue 3446 LEU Chi-restraints excluded: chain B residue 3543 CYS Chi-restraints excluded: chain B residue 3551 LYS Chi-restraints excluded: chain B residue 3625 THR Chi-restraints excluded: chain B residue 3633 LEU Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 3940 THR Chi-restraints excluded: chain B residue 3956 LYS Chi-restraints excluded: chain B residue 4001 VAL Chi-restraints excluded: chain B residue 4110 SER Chi-restraints excluded: chain B residue 4119 LEU Chi-restraints excluded: chain B residue 4129 LEU Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4318 LYS Chi-restraints excluded: chain B residue 4520 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 311 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 307 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 277 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 230 optimal weight: 0.6980 chunk 357 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3265 GLN ** A3913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A4534 ASN B3265 GLN B3387 GLN B3438 ASN ** B3913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 ASN D 42 GLN D 108 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.178399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.128553 restraints weight = 66485.099| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 3.47 r_work: 0.3639 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29775 Z= 0.156 Angle : 0.628 20.045 40223 Z= 0.302 Chirality : 0.040 0.234 4636 Planarity : 0.004 0.054 5141 Dihedral : 4.276 46.548 3992 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.72 % Allowed : 13.43 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.14), residues: 3656 helix: 1.60 (0.10), residues: 2416 sheet: 0.79 (0.43), residues: 137 loop : -0.16 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B4319 TYR 0.014 0.001 TYR D 139 PHE 0.033 0.002 PHE D 13 TRP 0.018 0.001 TRP A3959 HIS 0.009 0.001 HIS A3958 Details of bonding type rmsd covalent geometry : bond 0.00351 (29751) covalent geometry : angle 0.59403 (40187) hydrogen bonds : bond 0.04301 ( 1868) hydrogen bonds : angle 4.41795 ( 5553) metal coordination : bond 0.00762 ( 24) metal coordination : angle 6.81178 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 304 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3063 MET cc_start: 0.6705 (mmt) cc_final: 0.6143 (mmt) REVERT: A 3641 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7130 (ptt) REVERT: A 4316 THR cc_start: 0.9317 (m) cc_final: 0.9040 (p) REVERT: A 4383 MET cc_start: 0.0121 (mpp) cc_final: -0.0466 (ppp) REVERT: A 4503 HIS cc_start: 0.7784 (t70) cc_final: 0.7529 (p-80) REVERT: A 4566 MET cc_start: 0.6074 (mtt) cc_final: 0.5775 (mtp) REVERT: B 3000 MET cc_start: 0.7140 (ppp) cc_final: 0.6187 (mpp) REVERT: B 3059 LEU cc_start: 0.7619 (mt) cc_final: 0.7283 (mt) REVERT: B 3063 MET cc_start: 0.6780 (mmt) cc_final: 0.6216 (mmt) REVERT: B 3641 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7097 (ptt) REVERT: B 3956 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8090 (mptt) REVERT: B 3972 MET cc_start: 0.8825 (mmm) cc_final: 0.8600 (mmm) REVERT: B 4383 MET cc_start: 0.0250 (mpp) cc_final: -0.0414 (ppp) REVERT: B 4503 HIS cc_start: 0.7777 (t70) cc_final: 0.7468 (p-80) REVERT: C 32 GLU cc_start: 0.5481 (mm-30) cc_final: 0.5039 (mm-30) REVERT: C 37 MET cc_start: 0.8095 (mtm) cc_final: 0.7494 (mtm) REVERT: C 49 LEU cc_start: 0.7325 (tm) cc_final: 0.7023 (mt) REVERT: C 87 ARG cc_start: 0.7611 (ttp80) cc_final: 0.7331 (mmp80) REVERT: C 100 TYR cc_start: 0.8063 (m-80) cc_final: 0.7557 (m-80) REVERT: C 107 ARG cc_start: 0.6758 (ttp80) cc_final: 0.6471 (ttp80) REVERT: C 139 TYR cc_start: 0.7240 (m-80) cc_final: 0.6891 (m-10) REVERT: D 20 PHE cc_start: 0.7098 (m-80) cc_final: 0.6831 (m-80) REVERT: D 73 MET cc_start: 0.7678 (ptm) cc_final: 0.6868 (ptm) REVERT: D 100 TYR cc_start: 0.8336 (m-80) cc_final: 0.7889 (m-80) REVERT: D 146 MET cc_start: 0.6879 (tmm) cc_final: 0.6449 (tpp) REVERT: E 311 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8402 (m) outliers start: 89 outliers final: 54 residues processed: 371 average time/residue: 0.1860 time to fit residues: 111.2779 Evaluate side-chains 324 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3108 TYR Chi-restraints excluded: chain A residue 3272 LEU Chi-restraints excluded: chain A residue 3307 VAL Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3331 LYS Chi-restraints excluded: chain A residue 3411 PHE Chi-restraints excluded: chain A residue 3419 SER Chi-restraints excluded: chain A residue 3446 LEU Chi-restraints excluded: chain A residue 3495 GLU Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3640 LEU Chi-restraints excluded: chain A residue 3641 MET Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 4037 VAL Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4173 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4520 VAL Chi-restraints excluded: chain A residue 4552 ASP Chi-restraints excluded: chain A residue 4597 LEU Chi-restraints excluded: chain B residue 3108 TYR Chi-restraints excluded: chain B residue 3198 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3323 LEU Chi-restraints excluded: chain B residue 3331 LYS Chi-restraints excluded: chain B residue 3411 PHE Chi-restraints excluded: chain B residue 3419 SER Chi-restraints excluded: chain B residue 3446 LEU Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3543 CYS Chi-restraints excluded: chain B residue 3626 GLU Chi-restraints excluded: chain B residue 3640 LEU Chi-restraints excluded: chain B residue 3641 MET Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 3940 THR Chi-restraints excluded: chain B residue 3956 LYS Chi-restraints excluded: chain B residue 4001 VAL Chi-restraints excluded: chain B residue 4051 GLU Chi-restraints excluded: chain B residue 4129 LEU Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4478 VAL Chi-restraints excluded: chain B residue 4520 VAL Chi-restraints excluded: chain B residue 4552 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 311 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 30.0000 chunk 169 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 260 optimal weight: 0.4980 chunk 128 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 339 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3265 GLN A3387 GLN ** A3398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3438 ASN ** A3913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3265 GLN ** B3913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4602 ASN ** B4651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 112 ASN D 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.177399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.125571 restraints weight = 65823.104| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 3.52 r_work: 0.3588 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29775 Z= 0.177 Angle : 0.625 16.002 40223 Z= 0.304 Chirality : 0.040 0.222 4636 Planarity : 0.004 0.070 5141 Dihedral : 4.192 43.162 3990 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.08 % Allowed : 13.92 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.14), residues: 3656 helix: 1.67 (0.10), residues: 2422 sheet: 0.59 (0.44), residues: 132 loop : -0.23 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 107 TYR 0.017 0.001 TYR A3192 PHE 0.065 0.002 PHE D 93 TRP 0.010 0.001 TRP B3190 HIS 0.006 0.001 HIS B3958 Details of bonding type rmsd covalent geometry : bond 0.00400 (29751) covalent geometry : angle 0.60323 (40187) hydrogen bonds : bond 0.04251 ( 1868) hydrogen bonds : angle 4.32251 ( 5553) metal coordination : bond 0.00888 ( 24) metal coordination : angle 5.52688 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 275 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3063 MET cc_start: 0.6935 (mmt) cc_final: 0.6462 (mmt) REVERT: A 3225 ARG cc_start: 0.7416 (tpp80) cc_final: 0.7068 (mmm160) REVERT: A 3642 ILE cc_start: 0.8965 (mp) cc_final: 0.8603 (tp) REVERT: A 4244 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8386 (mp) REVERT: A 4316 THR cc_start: 0.9320 (m) cc_final: 0.9109 (p) REVERT: B 3642 ILE cc_start: 0.8995 (mp) cc_final: 0.8640 (tp) REVERT: B 3956 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8028 (mmtm) REVERT: B 4244 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8399 (mp) REVERT: B 4316 THR cc_start: 0.8798 (m) cc_final: 0.8597 (p) REVERT: B 4507 VAL cc_start: 0.8848 (t) cc_final: 0.8542 (p) REVERT: C 32 GLU cc_start: 0.5941 (mm-30) cc_final: 0.5562 (mm-30) REVERT: C 37 MET cc_start: 0.8115 (mtm) cc_final: 0.7565 (mtm) REVERT: C 49 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7055 (mt) REVERT: C 87 ARG cc_start: 0.7577 (ttp80) cc_final: 0.7250 (mmp80) REVERT: C 100 TYR cc_start: 0.8042 (m-80) cc_final: 0.6969 (m-80) REVERT: C 107 ARG cc_start: 0.6974 (ttp80) cc_final: 0.6681 (ttp80) REVERT: C 139 TYR cc_start: 0.7444 (m-80) cc_final: 0.7141 (m-10) REVERT: D 65 ASP cc_start: 0.6959 (OUTLIER) cc_final: 0.6489 (p0) REVERT: D 73 MET cc_start: 0.8074 (ptm) cc_final: 0.6960 (ptm) REVERT: D 93 PHE cc_start: 0.6094 (p90) cc_final: 0.5759 (p90) REVERT: D 100 TYR cc_start: 0.8427 (m-80) cc_final: 0.7811 (m-80) REVERT: D 127 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.7798 (tpm170) REVERT: D 144 GLN cc_start: 0.8256 (tp40) cc_final: 0.7876 (mt0) REVERT: E 295 ARG cc_start: 0.8478 (mtp-110) cc_final: 0.8164 (mtp-110) REVERT: E 311 SER cc_start: 0.8679 (OUTLIER) cc_final: 0.8449 (m) REVERT: F 295 ARG cc_start: 0.8480 (mtp-110) cc_final: 0.8114 (mtp-110) outliers start: 101 outliers final: 61 residues processed: 356 average time/residue: 0.1886 time to fit residues: 108.3574 Evaluate side-chains 312 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 245 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3108 TYR Chi-restraints excluded: chain A residue 3213 LEU Chi-restraints excluded: chain A residue 3227 LEU Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3272 LEU Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3331 LYS Chi-restraints excluded: chain A residue 3411 PHE Chi-restraints excluded: chain A residue 3419 SER Chi-restraints excluded: chain A residue 3482 THR Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3495 GLU Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3640 LEU Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 4037 VAL Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4312 VAL Chi-restraints excluded: chain A residue 4520 VAL Chi-restraints excluded: chain A residue 4597 LEU Chi-restraints excluded: chain B residue 3108 TYR Chi-restraints excluded: chain B residue 3198 LEU Chi-restraints excluded: chain B residue 3213 LEU Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3323 LEU Chi-restraints excluded: chain B residue 3331 LYS Chi-restraints excluded: chain B residue 3411 PHE Chi-restraints excluded: chain B residue 3419 SER Chi-restraints excluded: chain B residue 3446 LEU Chi-restraints excluded: chain B residue 3482 THR Chi-restraints excluded: chain B residue 3488 GLU Chi-restraints excluded: chain B residue 3495 GLU Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3543 CYS Chi-restraints excluded: chain B residue 3633 LEU Chi-restraints excluded: chain B residue 3640 LEU Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 3869 SER Chi-restraints excluded: chain B residue 3870 THR Chi-restraints excluded: chain B residue 3956 LYS Chi-restraints excluded: chain B residue 4001 VAL Chi-restraints excluded: chain B residue 4051 GLU Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain B residue 4244 LEU Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4520 VAL Chi-restraints excluded: chain B residue 4552 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain E residue 300 LYS Chi-restraints excluded: chain E residue 311 SER Chi-restraints excluded: chain E residue 317 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 88 optimal weight: 0.6980 chunk 283 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 193 optimal weight: 0.5980 chunk 39 optimal weight: 0.0170 chunk 258 optimal weight: 0.9980 chunk 324 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3265 GLN A3291 GLN A3913 ASN B3113 GLN B3265 GLN ** B3913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.178032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.122475 restraints weight = 65858.801| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.37 r_work: 0.3619 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29775 Z= 0.127 Angle : 0.580 15.139 40223 Z= 0.283 Chirality : 0.039 0.289 4636 Planarity : 0.004 0.059 5141 Dihedral : 4.052 41.977 3988 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.56 % Allowed : 14.93 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.14), residues: 3656 helix: 1.83 (0.10), residues: 2404 sheet: 0.62 (0.47), residues: 115 loop : -0.20 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 107 TYR 0.015 0.001 TYR C 100 PHE 0.035 0.001 PHE D 93 TRP 0.014 0.001 TRP A3959 HIS 0.006 0.001 HIS A4195 Details of bonding type rmsd covalent geometry : bond 0.00277 (29751) covalent geometry : angle 0.56308 (40187) hydrogen bonds : bond 0.03890 ( 1868) hydrogen bonds : angle 4.20159 ( 5553) metal coordination : bond 0.00574 ( 24) metal coordination : angle 4.63541 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 280 time to evaluate : 1.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3225 ARG cc_start: 0.7353 (tpp80) cc_final: 0.7060 (mmm160) REVERT: A 3642 ILE cc_start: 0.8906 (mp) cc_final: 0.8583 (tp) REVERT: A 4286 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: A 4316 THR cc_start: 0.9307 (m) cc_final: 0.9087 (p) REVERT: B 3642 ILE cc_start: 0.8912 (mp) cc_final: 0.8561 (tp) REVERT: B 3956 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8195 (mmtm) REVERT: B 4129 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8604 (tp) REVERT: B 4286 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: B 4316 THR cc_start: 0.8719 (m) cc_final: 0.8472 (p) REVERT: B 4507 VAL cc_start: 0.8888 (t) cc_final: 0.8576 (p) REVERT: C 32 GLU cc_start: 0.5718 (mm-30) cc_final: 0.5429 (mm-30) REVERT: C 37 MET cc_start: 0.8104 (mtm) cc_final: 0.7621 (mtm) REVERT: C 49 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7031 (mt) REVERT: C 100 TYR cc_start: 0.7926 (m-80) cc_final: 0.7546 (m-80) REVERT: C 107 ARG cc_start: 0.6916 (ttp80) cc_final: 0.6631 (ttp80) REVERT: C 125 MET cc_start: 0.8427 (tpt) cc_final: 0.8187 (mmm) REVERT: D 65 ASP cc_start: 0.6659 (OUTLIER) cc_final: 0.6271 (p0) REVERT: D 100 TYR cc_start: 0.8475 (m-80) cc_final: 0.7752 (m-80) REVERT: D 112 ASN cc_start: 0.8412 (t0) cc_final: 0.8113 (t0) REVERT: D 127 ARG cc_start: 0.8518 (mtm-85) cc_final: 0.7750 (tpm170) REVERT: D 146 MET cc_start: 0.6958 (OUTLIER) cc_final: 0.6632 (tpt) REVERT: E 295 ARG cc_start: 0.8359 (mtp-110) cc_final: 0.7947 (mtp-110) REVERT: F 295 ARG cc_start: 0.8414 (mtp-110) cc_final: 0.8038 (mtp-110) outliers start: 84 outliers final: 62 residues processed: 342 average time/residue: 0.1672 time to fit residues: 92.7276 Evaluate side-chains 324 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 255 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3108 TYR Chi-restraints excluded: chain A residue 3198 LEU Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3269 LEU Chi-restraints excluded: chain A residue 3272 LEU Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3331 LYS Chi-restraints excluded: chain A residue 3411 PHE Chi-restraints excluded: chain A residue 3412 LEU Chi-restraints excluded: chain A residue 3419 SER Chi-restraints excluded: chain A residue 3488 GLU Chi-restraints excluded: chain A residue 3495 GLU Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3640 LEU Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 3931 LEU Chi-restraints excluded: chain A residue 4037 VAL Chi-restraints excluded: chain A residue 4119 LEU Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4135 THR Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4173 LEU Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4286 GLU Chi-restraints excluded: chain A residue 4312 VAL Chi-restraints excluded: chain A residue 4520 VAL Chi-restraints excluded: chain A residue 4597 LEU Chi-restraints excluded: chain B residue 3108 TYR Chi-restraints excluded: chain B residue 3198 LEU Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3323 LEU Chi-restraints excluded: chain B residue 3331 LYS Chi-restraints excluded: chain B residue 3411 PHE Chi-restraints excluded: chain B residue 3419 SER Chi-restraints excluded: chain B residue 3488 GLU Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3495 GLU Chi-restraints excluded: chain B residue 3633 LEU Chi-restraints excluded: chain B residue 3640 LEU Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 3869 SER Chi-restraints excluded: chain B residue 3931 LEU Chi-restraints excluded: chain B residue 3956 LYS Chi-restraints excluded: chain B residue 4001 VAL Chi-restraints excluded: chain B residue 4051 GLU Chi-restraints excluded: chain B residue 4129 LEU Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4173 LEU Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4286 GLU Chi-restraints excluded: chain B residue 4300 THR Chi-restraints excluded: chain B residue 4520 VAL Chi-restraints excluded: chain B residue 4552 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain E residue 317 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 361 optimal weight: 4.9990 chunk 292 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 259 optimal weight: 0.6980 chunk 313 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 362 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3113 GLN A4614 GLN B3291 GLN ** B3913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.175185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.122289 restraints weight = 65337.716| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.43 r_work: 0.3533 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 29775 Z= 0.224 Angle : 0.648 15.838 40223 Z= 0.317 Chirality : 0.041 0.168 4636 Planarity : 0.004 0.060 5141 Dihedral : 4.154 41.192 3988 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.87 % Allowed : 15.32 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.14), residues: 3656 helix: 1.68 (0.10), residues: 2414 sheet: 0.66 (0.47), residues: 115 loop : -0.28 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 107 TYR 0.017 0.002 TYR A4101 PHE 0.018 0.002 PHE C 93 TRP 0.012 0.002 TRP A3959 HIS 0.006 0.001 HIS A4195 Details of bonding type rmsd covalent geometry : bond 0.00522 (29751) covalent geometry : angle 0.63586 (40187) hydrogen bonds : bond 0.04406 ( 1868) hydrogen bonds : angle 4.30497 ( 5553) metal coordination : bond 0.00913 ( 24) metal coordination : angle 4.27785 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 272 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3225 ARG cc_start: 0.7501 (tpp80) cc_final: 0.7119 (mmm160) REVERT: A 4244 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8448 (mp) REVERT: A 4316 THR cc_start: 0.9298 (m) cc_final: 0.9086 (p) REVERT: A 4383 MET cc_start: -0.0082 (mpp) cc_final: -0.0854 (ppp) REVERT: B 3642 ILE cc_start: 0.8916 (mp) cc_final: 0.8602 (tp) REVERT: B 4129 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8668 (tp) REVERT: B 4244 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8432 (mp) REVERT: B 4507 VAL cc_start: 0.8819 (t) cc_final: 0.8508 (p) REVERT: C 32 GLU cc_start: 0.5879 (mm-30) cc_final: 0.5654 (mm-30) REVERT: C 37 MET cc_start: 0.8275 (mtm) cc_final: 0.7627 (mtm) REVERT: C 49 LEU cc_start: 0.7333 (tm) cc_final: 0.7116 (mt) REVERT: C 87 ARG cc_start: 0.7473 (ttp80) cc_final: 0.7271 (mmp80) REVERT: C 100 TYR cc_start: 0.8198 (m-80) cc_final: 0.7607 (m-80) REVERT: C 107 ARG cc_start: 0.6783 (ttp80) cc_final: 0.6524 (ttp80) REVERT: C 136 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7597 (mm110) REVERT: C 139 TYR cc_start: 0.7257 (m-80) cc_final: 0.6766 (m-10) REVERT: D 9 GLN cc_start: 0.9043 (mt0) cc_final: 0.8515 (tp-100) REVERT: D 65 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6312 (p0) REVERT: D 72 MET cc_start: 0.7756 (mtt) cc_final: 0.7479 (ttm) REVERT: D 100 TYR cc_start: 0.8824 (m-80) cc_final: 0.8354 (m-80) REVERT: D 112 ASN cc_start: 0.8507 (t0) cc_final: 0.8269 (t0) REVERT: D 144 GLN cc_start: 0.8205 (tp40) cc_final: 0.7843 (mt0) REVERT: D 146 MET cc_start: 0.7023 (tmm) cc_final: 0.6683 (tpt) REVERT: E 295 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8073 (mtp-110) outliers start: 94 outliers final: 67 residues processed: 346 average time/residue: 0.1957 time to fit residues: 109.2297 Evaluate side-chains 322 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 251 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3198 LEU Chi-restraints excluded: chain A residue 3213 LEU Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3272 LEU Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3331 LYS Chi-restraints excluded: chain A residue 3411 PHE Chi-restraints excluded: chain A residue 3412 LEU Chi-restraints excluded: chain A residue 3419 SER Chi-restraints excluded: chain A residue 3482 THR Chi-restraints excluded: chain A residue 3488 GLU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3495 GLU Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3640 LEU Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 3931 LEU Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 4037 VAL Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4135 THR Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4244 LEU Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4302 THR Chi-restraints excluded: chain A residue 4312 VAL Chi-restraints excluded: chain A residue 4520 VAL Chi-restraints excluded: chain A residue 4597 LEU Chi-restraints excluded: chain B residue 3198 LEU Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3323 LEU Chi-restraints excluded: chain B residue 3331 LYS Chi-restraints excluded: chain B residue 3411 PHE Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3419 SER Chi-restraints excluded: chain B residue 3482 THR Chi-restraints excluded: chain B residue 3488 GLU Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3495 GLU Chi-restraints excluded: chain B residue 3540 VAL Chi-restraints excluded: chain B residue 3543 CYS Chi-restraints excluded: chain B residue 3633 LEU Chi-restraints excluded: chain B residue 3640 LEU Chi-restraints excluded: chain B residue 3807 CYS Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 3869 SER Chi-restraints excluded: chain B residue 3870 THR Chi-restraints excluded: chain B residue 3931 LEU Chi-restraints excluded: chain B residue 4001 VAL Chi-restraints excluded: chain B residue 4051 GLU Chi-restraints excluded: chain B residue 4129 LEU Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain B residue 4244 LEU Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4300 THR Chi-restraints excluded: chain B residue 4520 VAL Chi-restraints excluded: chain B residue 4552 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 MET Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 317 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 205 optimal weight: 0.5980 chunk 231 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 171 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3913 ASN B4651 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.176998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.121727 restraints weight = 67132.546| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.75 r_work: 0.3562 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29775 Z= 0.134 Angle : 0.596 11.726 40223 Z= 0.287 Chirality : 0.039 0.303 4636 Planarity : 0.004 0.059 5141 Dihedral : 4.058 41.541 3988 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.59 % Allowed : 15.81 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.14), residues: 3656 helix: 1.81 (0.10), residues: 2416 sheet: 0.69 (0.47), residues: 115 loop : -0.28 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 107 TYR 0.016 0.001 TYR C 100 PHE 0.019 0.001 PHE D 66 TRP 0.017 0.001 TRP A3959 HIS 0.006 0.001 HIS B4195 Details of bonding type rmsd covalent geometry : bond 0.00298 (29751) covalent geometry : angle 0.58527 (40187) hydrogen bonds : bond 0.03872 ( 1868) hydrogen bonds : angle 4.16982 ( 5553) metal coordination : bond 0.00523 ( 24) metal coordination : angle 3.81032 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 279 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3641 MET cc_start: 0.7715 (ptt) cc_final: 0.7195 (ptt) REVERT: A 3714 MET cc_start: 0.7745 (tpp) cc_final: 0.7501 (tpp) REVERT: A 3792 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7690 (p) REVERT: A 4310 MET cc_start: 0.8177 (mtm) cc_final: 0.7699 (mmm) REVERT: A 4316 THR cc_start: 0.9289 (m) cc_final: 0.9074 (p) REVERT: A 4383 MET cc_start: -0.0091 (mpp) cc_final: -0.0842 (ppp) REVERT: A 4507 VAL cc_start: 0.8976 (t) cc_final: 0.8660 (p) REVERT: B 3642 ILE cc_start: 0.8892 (mp) cc_final: 0.8578 (tp) REVERT: B 3972 MET cc_start: 0.8924 (mmm) cc_final: 0.8660 (mmm) REVERT: B 4129 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8606 (tp) REVERT: B 4507 VAL cc_start: 0.8922 (t) cc_final: 0.8606 (p) REVERT: C 37 MET cc_start: 0.8184 (mtm) cc_final: 0.7662 (mtm) REVERT: C 49 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7343 (mt) REVERT: C 87 ARG cc_start: 0.7481 (ttp80) cc_final: 0.7242 (mmp80) REVERT: C 100 TYR cc_start: 0.8168 (m-80) cc_final: 0.7897 (m-80) REVERT: C 107 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6678 (ttp80) REVERT: C 136 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7583 (mm110) REVERT: D 9 GLN cc_start: 0.9038 (mt0) cc_final: 0.8511 (tp-100) REVERT: D 100 TYR cc_start: 0.8727 (m-80) cc_final: 0.8241 (m-80) REVERT: D 112 ASN cc_start: 0.8523 (t0) cc_final: 0.8289 (t0) REVERT: D 127 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.7687 (tpm170) REVERT: D 144 GLN cc_start: 0.8182 (tp40) cc_final: 0.7775 (mt0) REVERT: D 146 MET cc_start: 0.7098 (tmm) cc_final: 0.6785 (tpt) REVERT: E 295 ARG cc_start: 0.8366 (mtp-110) cc_final: 0.7941 (mtp-110) REVERT: E 305 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8848 (pm20) REVERT: F 295 ARG cc_start: 0.8335 (mtp-110) cc_final: 0.8051 (mtp-110) outliers start: 85 outliers final: 67 residues processed: 343 average time/residue: 0.1987 time to fit residues: 110.2292 Evaluate side-chains 326 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 255 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3108 TYR Chi-restraints excluded: chain A residue 3198 LEU Chi-restraints excluded: chain A residue 3213 LEU Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3272 LEU Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3331 LYS Chi-restraints excluded: chain A residue 3412 LEU Chi-restraints excluded: chain A residue 3419 SER Chi-restraints excluded: chain A residue 3482 THR Chi-restraints excluded: chain A residue 3488 GLU Chi-restraints excluded: chain A residue 3495 GLU Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3640 LEU Chi-restraints excluded: chain A residue 3792 VAL Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 3931 LEU Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4037 VAL Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4135 THR Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4286 GLU Chi-restraints excluded: chain A residue 4312 VAL Chi-restraints excluded: chain A residue 4520 VAL Chi-restraints excluded: chain A residue 4597 LEU Chi-restraints excluded: chain B residue 3108 TYR Chi-restraints excluded: chain B residue 3198 LEU Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3323 LEU Chi-restraints excluded: chain B residue 3331 LYS Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3419 SER Chi-restraints excluded: chain B residue 3482 THR Chi-restraints excluded: chain B residue 3488 GLU Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3495 GLU Chi-restraints excluded: chain B residue 3520 VAL Chi-restraints excluded: chain B residue 3633 LEU Chi-restraints excluded: chain B residue 3640 LEU Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 3869 SER Chi-restraints excluded: chain B residue 3870 THR Chi-restraints excluded: chain B residue 3931 LEU Chi-restraints excluded: chain B residue 4001 VAL Chi-restraints excluded: chain B residue 4051 GLU Chi-restraints excluded: chain B residue 4129 LEU Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4286 GLU Chi-restraints excluded: chain B residue 4300 THR Chi-restraints excluded: chain B residue 4520 VAL Chi-restraints excluded: chain B residue 4552 ASP Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 317 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 113 optimal weight: 0.2980 chunk 173 optimal weight: 5.9990 chunk 192 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 220 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 172 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 269 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 236 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B3398 GLN B4651 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.177459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.127181 restraints weight = 65605.049| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.38 r_work: 0.3609 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29775 Z= 0.120 Angle : 0.593 15.136 40223 Z= 0.284 Chirality : 0.038 0.339 4636 Planarity : 0.004 0.059 5141 Dihedral : 3.952 41.009 3988 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.20 % Allowed : 16.45 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.14), residues: 3656 helix: 1.92 (0.10), residues: 2414 sheet: 0.82 (0.50), residues: 107 loop : -0.28 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 306 TYR 0.012 0.001 TYR A3461 PHE 0.019 0.001 PHE D 66 TRP 0.019 0.001 TRP B3959 HIS 0.007 0.001 HIS B4195 Details of bonding type rmsd covalent geometry : bond 0.00264 (29751) covalent geometry : angle 0.58061 (40187) hydrogen bonds : bond 0.03717 ( 1868) hydrogen bonds : angle 4.09796 ( 5553) metal coordination : bond 0.00750 ( 24) metal coordination : angle 4.00808 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 272 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4310 MET cc_start: 0.8095 (mtm) cc_final: 0.7672 (mmm) REVERT: A 4316 THR cc_start: 0.9272 (m) cc_final: 0.9050 (p) REVERT: A 4383 MET cc_start: -0.0117 (mpp) cc_final: -0.0871 (ppp) REVERT: A 4507 VAL cc_start: 0.8844 (t) cc_final: 0.8531 (p) REVERT: A 4596 MET cc_start: 0.5212 (tpt) cc_final: 0.4310 (mtt) REVERT: B 3972 MET cc_start: 0.8949 (mmm) cc_final: 0.8727 (mmm) REVERT: B 4046 LYS cc_start: 0.8445 (tptm) cc_final: 0.7894 (mmmt) REVERT: B 4129 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8598 (tp) REVERT: B 4507 VAL cc_start: 0.8826 (t) cc_final: 0.8525 (p) REVERT: C 37 MET cc_start: 0.8217 (mtm) cc_final: 0.7659 (mtm) REVERT: C 49 LEU cc_start: 0.7492 (tm) cc_final: 0.7169 (mt) REVERT: C 100 TYR cc_start: 0.8311 (m-80) cc_final: 0.7930 (m-80) REVERT: C 107 ARG cc_start: 0.6934 (ttp80) cc_final: 0.6672 (ttp80) REVERT: C 139 TYR cc_start: 0.7386 (m-80) cc_final: 0.7014 (m-10) REVERT: D 9 GLN cc_start: 0.9048 (mt0) cc_final: 0.8542 (tp-100) REVERT: D 100 TYR cc_start: 0.8700 (m-80) cc_final: 0.8229 (m-80) REVERT: D 112 ASN cc_start: 0.8486 (t0) cc_final: 0.8283 (t0) REVERT: D 144 GLN cc_start: 0.8178 (tp40) cc_final: 0.7748 (mt0) REVERT: E 295 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.7981 (mtp-110) REVERT: E 305 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8894 (pm20) REVERT: F 295 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7953 (mtp-110) outliers start: 72 outliers final: 58 residues processed: 333 average time/residue: 0.1863 time to fit residues: 100.7996 Evaluate side-chains 309 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3198 LEU Chi-restraints excluded: chain A residue 3206 VAL Chi-restraints excluded: chain A residue 3213 LEU Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3272 LEU Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3331 LYS Chi-restraints excluded: chain A residue 3412 LEU Chi-restraints excluded: chain A residue 3419 SER Chi-restraints excluded: chain A residue 3488 GLU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3495 GLU Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 3931 LEU Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4037 VAL Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4135 THR Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4286 GLU Chi-restraints excluded: chain A residue 4312 VAL Chi-restraints excluded: chain A residue 4520 VAL Chi-restraints excluded: chain A residue 4597 LEU Chi-restraints excluded: chain B residue 3198 LEU Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3323 LEU Chi-restraints excluded: chain B residue 3331 LYS Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3488 GLU Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3495 GLU Chi-restraints excluded: chain B residue 3520 VAL Chi-restraints excluded: chain B residue 3633 LEU Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 3870 THR Chi-restraints excluded: chain B residue 3931 LEU Chi-restraints excluded: chain B residue 4001 VAL Chi-restraints excluded: chain B residue 4129 LEU Chi-restraints excluded: chain B residue 4135 THR Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4286 GLU Chi-restraints excluded: chain B residue 4300 THR Chi-restraints excluded: chain B residue 4520 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 317 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 282 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 45 optimal weight: 0.0020 chunk 23 optimal weight: 0.6980 chunk 119 optimal weight: 0.5980 chunk 1 optimal weight: 20.0000 chunk 362 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3848 GLN A4011 ASN B3536 ASN B3848 GLN B4651 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.177784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.127604 restraints weight = 65647.447| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 3.49 r_work: 0.3602 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29775 Z= 0.120 Angle : 0.592 14.030 40223 Z= 0.284 Chirality : 0.038 0.346 4636 Planarity : 0.004 0.058 5141 Dihedral : 3.907 40.152 3988 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.14 % Allowed : 16.58 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.14), residues: 3656 helix: 1.98 (0.10), residues: 2413 sheet: 0.90 (0.50), residues: 108 loop : -0.31 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 107 TYR 0.016 0.001 TYR C 100 PHE 0.020 0.001 PHE D 66 TRP 0.020 0.001 TRP B3959 HIS 0.007 0.001 HIS B4195 Details of bonding type rmsd covalent geometry : bond 0.00262 (29751) covalent geometry : angle 0.58334 (40187) hydrogen bonds : bond 0.03647 ( 1868) hydrogen bonds : angle 4.06954 ( 5553) metal coordination : bond 0.00608 ( 24) metal coordination : angle 3.36546 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 262 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3714 MET cc_start: 0.7872 (tpp) cc_final: 0.7401 (tpp) REVERT: A 4310 MET cc_start: 0.8096 (mtm) cc_final: 0.7683 (mmm) REVERT: A 4316 THR cc_start: 0.9268 (m) cc_final: 0.9046 (p) REVERT: A 4507 VAL cc_start: 0.8854 (t) cc_final: 0.8542 (p) REVERT: A 4596 MET cc_start: 0.5209 (tpt) cc_final: 0.4317 (mtt) REVERT: B 3269 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8939 (mp) REVERT: B 3714 MET cc_start: 0.7846 (tpp) cc_final: 0.7489 (tpp) REVERT: B 3972 MET cc_start: 0.8963 (mmm) cc_final: 0.8735 (mmm) REVERT: B 4046 LYS cc_start: 0.8481 (tptm) cc_final: 0.7868 (mmmt) REVERT: B 4129 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8538 (tp) REVERT: B 4507 VAL cc_start: 0.8828 (t) cc_final: 0.8547 (p) REVERT: C 37 MET cc_start: 0.8188 (mtm) cc_final: 0.7704 (mtm) REVERT: C 49 LEU cc_start: 0.7575 (tm) cc_final: 0.7290 (mt) REVERT: C 100 TYR cc_start: 0.8314 (m-80) cc_final: 0.7886 (m-80) REVERT: C 107 ARG cc_start: 0.6871 (ttp80) cc_final: 0.6597 (ttp80) REVERT: D 9 GLN cc_start: 0.9008 (mt0) cc_final: 0.8515 (tp-100) REVERT: D 65 ASP cc_start: 0.6648 (OUTLIER) cc_final: 0.6252 (p0) REVERT: D 100 TYR cc_start: 0.8715 (m-80) cc_final: 0.8232 (m-80) REVERT: D 144 GLN cc_start: 0.8114 (tp40) cc_final: 0.7696 (mt0) REVERT: E 295 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.7914 (mtp-110) REVERT: E 305 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8878 (pm20) REVERT: F 295 ARG cc_start: 0.8234 (mtp-110) cc_final: 0.7856 (mtp-110) outliers start: 70 outliers final: 59 residues processed: 322 average time/residue: 0.1972 time to fit residues: 103.5889 Evaluate side-chains 312 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 249 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3198 LEU Chi-restraints excluded: chain A residue 3206 VAL Chi-restraints excluded: chain A residue 3213 LEU Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3272 LEU Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3331 LYS Chi-restraints excluded: chain A residue 3412 LEU Chi-restraints excluded: chain A residue 3419 SER Chi-restraints excluded: chain A residue 3488 GLU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3495 GLU Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 3931 LEU Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4037 VAL Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4135 THR Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4286 GLU Chi-restraints excluded: chain A residue 4302 THR Chi-restraints excluded: chain A residue 4312 VAL Chi-restraints excluded: chain A residue 4520 VAL Chi-restraints excluded: chain A residue 4597 LEU Chi-restraints excluded: chain B residue 3198 LEU Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3269 LEU Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3323 LEU Chi-restraints excluded: chain B residue 3331 LYS Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3419 SER Chi-restraints excluded: chain B residue 3488 GLU Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3495 GLU Chi-restraints excluded: chain B residue 3520 VAL Chi-restraints excluded: chain B residue 3633 LEU Chi-restraints excluded: chain B residue 3848 GLN Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 4001 VAL Chi-restraints excluded: chain B residue 4129 LEU Chi-restraints excluded: chain B residue 4135 THR Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4173 LEU Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4286 GLU Chi-restraints excluded: chain B residue 4300 THR Chi-restraints excluded: chain B residue 4520 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 317 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 356 optimal weight: 0.8980 chunk 245 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 47 optimal weight: 0.2980 chunk 283 optimal weight: 3.9990 chunk 273 optimal weight: 0.4980 chunk 197 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 362 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3793 ASN A3848 GLN B3848 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 = 0.177730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.122036 restraints weight = 65543.980| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.50 r_work: 0.3598 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29775 Z= 0.124 Angle : 0.595 12.543 40223 Z= 0.287 Chirality : 0.039 0.329 4636 Planarity : 0.004 0.058 5141 Dihedral : 3.873 38.940 3988 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.05 % Allowed : 16.79 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.14), residues: 3656 helix: 2.00 (0.10), residues: 2415 sheet: 1.11 (0.49), residues: 115 loop : -0.33 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 107 TYR 0.027 0.001 TYR C 100 PHE 0.019 0.001 PHE D 66 TRP 0.017 0.001 TRP B3959 HIS 0.007 0.001 HIS B4195 Details of bonding type rmsd covalent geometry : bond 0.00277 (29751) covalent geometry : angle 0.58964 (40187) hydrogen bonds : bond 0.03631 ( 1868) hydrogen bonds : angle 4.05467 ( 5553) metal coordination : bond 0.00541 ( 24) metal coordination : angle 2.80999 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7312 Ramachandran restraints generated. 3656 Oldfield, 0 Emsley, 3656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 258 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4310 MET cc_start: 0.8112 (mtm) cc_final: 0.7690 (mmm) REVERT: A 4316 THR cc_start: 0.9269 (m) cc_final: 0.9054 (p) REVERT: A 4479 MET cc_start: 0.6225 (pmm) cc_final: 0.6008 (pmm) REVERT: A 4596 MET cc_start: 0.5206 (tpt) cc_final: 0.4316 (mtt) REVERT: B 3269 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8945 (mp) REVERT: B 3972 MET cc_start: 0.8942 (mmm) cc_final: 0.8724 (mmm) REVERT: B 4046 LYS cc_start: 0.8476 (tptm) cc_final: 0.7860 (mmmt) REVERT: B 4129 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8531 (tp) REVERT: B 4507 VAL cc_start: 0.8916 (t) cc_final: 0.8630 (p) REVERT: B 4596 MET cc_start: 0.5020 (tpt) cc_final: 0.4173 (mtt) REVERT: C 37 MET cc_start: 0.8211 (mtm) cc_final: 0.7706 (mtm) REVERT: C 49 LEU cc_start: 0.7652 (tm) cc_final: 0.7327 (mt) REVERT: C 107 ARG cc_start: 0.6842 (ttp80) cc_final: 0.6591 (ttp80) REVERT: D 9 GLN cc_start: 0.8970 (mt0) cc_final: 0.8471 (tp-100) REVERT: D 65 ASP cc_start: 0.6372 (OUTLIER) cc_final: 0.5992 (p0) REVERT: D 100 TYR cc_start: 0.8738 (m-80) cc_final: 0.8257 (m-80) REVERT: D 144 GLN cc_start: 0.8063 (tp40) cc_final: 0.7629 (mt0) REVERT: E 295 ARG cc_start: 0.8253 (mtp-110) cc_final: 0.7819 (mtp-110) REVERT: F 295 ARG cc_start: 0.8176 (mtp-110) cc_final: 0.7823 (mtp-110) outliers start: 67 outliers final: 60 residues processed: 318 average time/residue: 0.1967 time to fit residues: 101.7211 Evaluate side-chains 313 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 250 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3198 LEU Chi-restraints excluded: chain A residue 3206 VAL Chi-restraints excluded: chain A residue 3213 LEU Chi-restraints excluded: chain A residue 3237 VAL Chi-restraints excluded: chain A residue 3272 LEU Chi-restraints excluded: chain A residue 3323 LEU Chi-restraints excluded: chain A residue 3331 LYS Chi-restraints excluded: chain A residue 3412 LEU Chi-restraints excluded: chain A residue 3419 SER Chi-restraints excluded: chain A residue 3488 GLU Chi-restraints excluded: chain A residue 3490 SER Chi-restraints excluded: chain A residue 3495 GLU Chi-restraints excluded: chain A residue 3522 PHE Chi-restraints excluded: chain A residue 3540 VAL Chi-restraints excluded: chain A residue 3793 ASN Chi-restraints excluded: chain A residue 3848 GLN Chi-restraints excluded: chain A residue 3866 HIS Chi-restraints excluded: chain A residue 3931 LEU Chi-restraints excluded: chain A residue 3940 THR Chi-restraints excluded: chain A residue 3958 HIS Chi-restraints excluded: chain A residue 3979 ILE Chi-restraints excluded: chain A residue 4037 VAL Chi-restraints excluded: chain A residue 4129 LEU Chi-restraints excluded: chain A residue 4135 THR Chi-restraints excluded: chain A residue 4167 THR Chi-restraints excluded: chain A residue 4230 THR Chi-restraints excluded: chain A residue 4261 ARG Chi-restraints excluded: chain A residue 4263 VAL Chi-restraints excluded: chain A residue 4286 GLU Chi-restraints excluded: chain A residue 4302 THR Chi-restraints excluded: chain A residue 4312 VAL Chi-restraints excluded: chain A residue 4597 LEU Chi-restraints excluded: chain B residue 3198 LEU Chi-restraints excluded: chain B residue 3227 LEU Chi-restraints excluded: chain B residue 3237 VAL Chi-restraints excluded: chain B residue 3269 LEU Chi-restraints excluded: chain B residue 3272 LEU Chi-restraints excluded: chain B residue 3323 LEU Chi-restraints excluded: chain B residue 3331 LYS Chi-restraints excluded: chain B residue 3412 LEU Chi-restraints excluded: chain B residue 3419 SER Chi-restraints excluded: chain B residue 3488 GLU Chi-restraints excluded: chain B residue 3490 SER Chi-restraints excluded: chain B residue 3495 GLU Chi-restraints excluded: chain B residue 3633 LEU Chi-restraints excluded: chain B residue 3866 HIS Chi-restraints excluded: chain B residue 3931 LEU Chi-restraints excluded: chain B residue 4001 VAL Chi-restraints excluded: chain B residue 4129 LEU Chi-restraints excluded: chain B residue 4135 THR Chi-restraints excluded: chain B residue 4167 THR Chi-restraints excluded: chain B residue 4173 LEU Chi-restraints excluded: chain B residue 4230 THR Chi-restraints excluded: chain B residue 4263 VAL Chi-restraints excluded: chain B residue 4286 GLU Chi-restraints excluded: chain B residue 4300 THR Chi-restraints excluded: chain B residue 4520 VAL Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 317 SER Chi-restraints excluded: chain F residue 317 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 235 optimal weight: 0.4980 chunk 145 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 170 optimal weight: 20.0000 chunk 245 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 330 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3793 ASN A3848 GLN ** C 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.176992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.125635 restraints weight = 65780.966| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 3.52 r_work: 0.3570 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29775 Z= 0.142 Angle : 0.600 11.681 40223 Z= 0.290 Chirality : 0.039 0.298 4636 Planarity : 0.004 0.058 5141 Dihedral : 3.895 38.234 3988 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.98 % Allowed : 16.94 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.14), residues: 3656 helix: 1.96 (0.10), residues: 2420 sheet: 1.10 (0.49), residues: 115 loop : -0.35 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A3794 TYR 0.013 0.001 TYR A3461 PHE 0.018 0.001 PHE D 66 TRP 0.019 0.001 TRP B3959 HIS 0.007 0.001 HIS B4195 Details of bonding type rmsd covalent geometry : bond 0.00324 (29751) covalent geometry : angle 0.59490 (40187) hydrogen bonds : bond 0.03723 ( 1868) hydrogen bonds : angle 4.06090 ( 5553) metal coordination : bond 0.00585 ( 24) metal coordination : angle 2.67747 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12006.59 seconds wall clock time: 205 minutes 17.70 seconds (12317.70 seconds total)