Starting phenix.real_space_refine on Sat Mar 16 18:08:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/03_2024/7eg4_31105_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/03_2024/7eg4_31105.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/03_2024/7eg4_31105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/03_2024/7eg4_31105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/03_2024/7eg4_31105_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg4_31105/03_2024/7eg4_31105_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Zn 2 6.06 5 Mg 4 5.21 5 S 98 5.16 5 C 9770 2.51 5 N 2582 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 675": "OE1" <-> "OE2" Residue "C GLU 687": "OE1" <-> "OE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C ARG 705": "NH1" <-> "NH2" Residue "C ARG 709": "NH1" <-> "NH2" Residue "C ARG 717": "NH1" <-> "NH2" Residue "C GLU 726": "OE1" <-> "OE2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C GLU 734": "OE1" <-> "OE2" Residue "C GLU 743": "OE1" <-> "OE2" Residue "C GLU 935": "OE1" <-> "OE2" Residue "C ARG 938": "NH1" <-> "NH2" Residue "D ARG 20": "NH1" <-> "NH2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 46": "NH1" <-> "NH2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ARG 217": "NH1" <-> "NH2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D GLU 308": "OE1" <-> "OE2" Residue "D GLU 318": "OE1" <-> "OE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D ARG 378": "NH1" <-> "NH2" Residue "D GLU 412": "OE1" <-> "OE2" Residue "D ARG 426": "NH1" <-> "NH2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A ARG 705": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A GLU 935": "OE1" <-> "OE2" Residue "A ARG 938": "NH1" <-> "NH2" Residue "B ARG 20": "NH1" <-> "NH2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B GLU 353": "OE1" <-> "OE2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B ARG 527": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15258 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "D" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 3004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 3004 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain breaks: 2 Chain: "B" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4600 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 550} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 2, 'J36': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 2, 'J36': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5222 SG CYS D 277 24.703 60.259 74.608 1.00 63.56 S ATOM 5495 SG CYS D 311 25.288 59.169 77.864 1.00 50.53 S ATOM 5501 SG CYS D 312 28.122 61.185 76.154 1.00 45.94 S ATOM 12826 SG CYS B 277 74.874 74.149 74.614 1.00 63.56 S ATOM 13099 SG CYS B 311 74.289 75.238 77.871 1.00 50.53 S ATOM 13105 SG CYS B 312 71.455 73.223 76.160 1.00 45.94 S Time building chain proxies: 8.35, per 1000 atoms: 0.55 Number of scatterers: 15258 At special positions: 0 Unit cell: (100.672, 135.312, 128.817, 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 2 29.99 S 98 16.00 Mg 4 11.99 O 2802 8.00 N 2582 7.00 C 9770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 381 " - pdb=" SG CYS D 411 " distance=2.03 Simple disulfide: pdb=" SG CYS B 381 " - pdb=" SG CYS B 411 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.93 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 275 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 312 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 277 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 311 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 275 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 312 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 277 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 311 " Number of angles added : 6 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 8 sheets defined 41.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 696 through 702 Processing helix chain 'C' and resid 710 through 722 Processing helix chain 'C' and resid 724 through 727 No H-bonds generated for 'chain 'C' and resid 724 through 727' Processing helix chain 'C' and resid 732 through 745 Processing helix chain 'C' and resid 754 through 768 Processing helix chain 'C' and resid 817 through 820 No H-bonds generated for 'chain 'C' and resid 817 through 820' Processing helix chain 'C' and resid 823 through 834 Processing helix chain 'C' and resid 845 through 850 Processing helix chain 'C' and resid 854 through 857 No H-bonds generated for 'chain 'C' and resid 854 through 857' Processing helix chain 'C' and resid 864 through 879 Processing helix chain 'C' and resid 891 through 908 removed outlier: 3.837A pdb=" N THR C 908 " --> pdb=" O ALA C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 924 removed outlier: 4.957A pdb=" N PHE C 914 " --> pdb=" O LYS C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 935 through 950 Processing helix chain 'C' and resid 953 through 955 No H-bonds generated for 'chain 'C' and resid 953 through 955' Processing helix chain 'C' and resid 958 through 980 Processing helix chain 'C' and resid 997 through 1007 Processing helix chain 'C' and resid 1009 through 1018 Processing helix chain 'C' and resid 1074 through 1101 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 34 through 53 Processing helix chain 'D' and resid 78 through 86 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 215 through 231 Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 257 through 269 Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'D' and resid 351 through 358 Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 404 through 413 removed outlier: 4.312A pdb=" N GLN D 408 " --> pdb=" O GLU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 431 No H-bonds generated for 'chain 'D' and resid 428 through 431' Processing helix chain 'D' and resid 467 through 483 Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 520 through 523 removed outlier: 3.915A pdb=" N TYR D 523 " --> pdb=" O GLU D 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 523' Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 553 through 558 removed outlier: 3.629A pdb=" N ILE D 557 " --> pdb=" O ASN D 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 689 No H-bonds generated for 'chain 'A' and resid 687 through 689' Processing helix chain 'A' and resid 696 through 702 Processing helix chain 'A' and resid 710 through 722 Processing helix chain 'A' and resid 724 through 727 No H-bonds generated for 'chain 'A' and resid 724 through 727' Processing helix chain 'A' and resid 732 through 745 Processing helix chain 'A' and resid 754 through 768 Processing helix chain 'A' and resid 817 through 820 No H-bonds generated for 'chain 'A' and resid 817 through 820' Processing helix chain 'A' and resid 823 through 834 Processing helix chain 'A' and resid 845 through 850 Processing helix chain 'A' and resid 854 through 857 No H-bonds generated for 'chain 'A' and resid 854 through 857' Processing helix chain 'A' and resid 864 through 879 Processing helix chain 'A' and resid 891 through 908 removed outlier: 3.837A pdb=" N THR A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 924 removed outlier: 4.958A pdb=" N PHE A 914 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 950 Processing helix chain 'A' and resid 953 through 955 No H-bonds generated for 'chain 'A' and resid 953 through 955' Processing helix chain 'A' and resid 958 through 980 Processing helix chain 'A' and resid 997 through 1007 Processing helix chain 'A' and resid 1009 through 1018 Processing helix chain 'A' and resid 1074 through 1101 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 34 through 53 Processing helix chain 'B' and resid 78 through 86 Processing helix chain 'B' and resid 139 through 151 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 215 through 231 Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 257 through 269 Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 351 through 358 Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 404 through 413 removed outlier: 4.312A pdb=" N GLN B 408 " --> pdb=" O GLU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 431 No H-bonds generated for 'chain 'B' and resid 428 through 431' Processing helix chain 'B' and resid 467 through 483 Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 520 through 523 removed outlier: 3.914A pdb=" N TYR B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 529 through 540 Processing helix chain 'B' and resid 553 through 558 removed outlier: 3.629A pdb=" N ILE B 557 " --> pdb=" O ASN B 553 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 15 through 17 removed outlier: 6.520A pdb=" N VAL D 58 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 127 through 129 Processing sheet with id= C, first strand: chain 'D' and resid 204 through 207 removed outlier: 6.534A pdb=" N TYR D 236 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LYS D 207 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE D 238 " --> pdb=" O LYS D 207 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 440 through 443 removed outlier: 7.042A pdb=" N PHE D 458 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 15 through 17 removed outlier: 6.521A pdb=" N VAL B 58 " --> pdb=" O LEU B 16 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 127 through 129 Processing sheet with id= G, first strand: chain 'B' and resid 204 through 207 removed outlier: 6.534A pdb=" N TYR B 236 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LYS B 207 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N PHE B 238 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 440 through 443 removed outlier: 7.043A pdb=" N PHE B 458 " --> pdb=" O LEU B 441 " (cutoff:3.500A) 542 hydrogen bonds defined for protein. 1548 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.82 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4903 1.34 - 1.46: 2841 1.46 - 1.57: 7704 1.57 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 15598 Sorted by residual: bond pdb=" N GLU D 345 " pdb=" CA GLU D 345 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.56e-02 4.11e+03 7.45e+00 bond pdb=" N GLU B 345 " pdb=" CA GLU B 345 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.56e-02 4.11e+03 7.45e+00 bond pdb=" C GLU B 393 " pdb=" N ASN B 394 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" C GLU D 393 " pdb=" N ASN D 394 " ideal model delta sigma weight residual 1.332 1.301 0.031 1.40e-02 5.10e+03 4.93e+00 bond pdb=" C10 J36 C1201 " pdb=" C8 J36 C1201 " ideal model delta sigma weight residual 1.418 1.461 -0.043 2.00e-02 2.50e+03 4.62e+00 ... (remaining 15593 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.08: 295 106.08 - 113.22: 8545 113.22 - 120.37: 6183 120.37 - 127.51: 5881 127.51 - 134.65: 160 Bond angle restraints: 21064 Sorted by residual: angle pdb=" C PRO B 502 " pdb=" N GLU B 503 " pdb=" CA GLU B 503 " ideal model delta sigma weight residual 122.35 128.23 -5.88 1.46e+00 4.69e-01 1.62e+01 angle pdb=" C PRO D 502 " pdb=" N GLU D 503 " pdb=" CA GLU D 503 " ideal model delta sigma weight residual 122.35 128.21 -5.86 1.46e+00 4.69e-01 1.61e+01 angle pdb=" N ASP B 546 " pdb=" CA ASP B 546 " pdb=" C ASP B 546 " ideal model delta sigma weight residual 114.56 110.28 4.28 1.27e+00 6.20e-01 1.14e+01 angle pdb=" N ASP D 546 " pdb=" CA ASP D 546 " pdb=" C ASP D 546 " ideal model delta sigma weight residual 114.56 110.31 4.25 1.27e+00 6.20e-01 1.12e+01 angle pdb=" C TYR C 807 " pdb=" N ASN C 808 " pdb=" CA ASN C 808 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 ... (remaining 21059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8466 17.99 - 35.97: 806 35.97 - 53.96: 120 53.96 - 71.95: 20 71.95 - 89.93: 16 Dihedral angle restraints: 9428 sinusoidal: 3912 harmonic: 5516 Sorted by residual: dihedral pdb=" CB CYS B 381 " pdb=" SG CYS B 381 " pdb=" SG CYS B 411 " pdb=" CB CYS B 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.11 -70.11 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS D 381 " pdb=" SG CYS D 381 " pdb=" SG CYS D 411 " pdb=" CB CYS D 411 " ideal model delta sinusoidal sigma weight residual 93.00 163.10 -70.10 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CA TYR B 390 " pdb=" C TYR B 390 " pdb=" N THR B 391 " pdb=" CA THR B 391 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 9425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1407 0.037 - 0.074: 667 0.074 - 0.111: 159 0.111 - 0.148: 43 0.148 - 0.185: 10 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CA PRO D 382 " pdb=" N PRO D 382 " pdb=" C PRO D 382 " pdb=" CB PRO D 382 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA PRO B 382 " pdb=" N PRO B 382 " pdb=" C PRO B 382 " pdb=" CB PRO B 382 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.40e-01 chirality pdb=" CA PHE D 550 " pdb=" N PHE D 550 " pdb=" C PHE D 550 " pdb=" CB PHE D 550 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 2283 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 344 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C ALA D 344 " 0.072 2.00e-02 2.50e+03 pdb=" O ALA D 344 " -0.027 2.00e-02 2.50e+03 pdb=" N GLU D 345 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1087 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C LYS C1087 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS C1087 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS C1088 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A1087 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C LYS A1087 " 0.072 2.00e-02 2.50e+03 pdb=" O LYS A1087 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS A1088 " -0.024 2.00e-02 2.50e+03 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 110 2.52 - 3.11: 12189 3.11 - 3.71: 22046 3.71 - 4.30: 32593 4.30 - 4.90: 55472 Nonbonded interactions: 122410 Sorted by model distance: nonbonded pdb=" OD2 ASP C 837 " pdb="MG MG C1202 " model vdw 1.920 2.170 nonbonded pdb=" OD2 ASP A 837 " pdb="MG MG A1202 " model vdw 1.921 2.170 nonbonded pdb=" OG1 THR B 152 " pdb=" O GLY B 154 " model vdw 2.101 2.440 nonbonded pdb=" OG1 THR D 152 " pdb=" O GLY D 154 " model vdw 2.101 2.440 nonbonded pdb=" NE2 HIS C 836 " pdb="MG MG C1202 " model vdw 2.111 2.250 ... (remaining 122405 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.380 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.600 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 43.710 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.008 0.052 15598 Z= 0.542 Angle : 0.699 6.365 21064 Z= 0.400 Chirality : 0.045 0.185 2286 Planarity : 0.005 0.048 2694 Dihedral : 14.251 89.934 5854 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 0.12 % Allowed : 5.50 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.17), residues: 1862 helix: -0.69 (0.16), residues: 854 sheet: -2.53 (0.35), residues: 166 loop : -3.54 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 110 HIS 0.004 0.001 HIS D 380 PHE 0.030 0.002 PHE D 550 TYR 0.022 0.002 TYR D 70 ARG 0.007 0.001 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 1.910 Fit side-chains revert: symmetry clash REVERT: C 923 LYS cc_start: 0.7435 (ttmt) cc_final: 0.7231 (ttmm) REVERT: C 1022 MET cc_start: 0.8710 (tpp) cc_final: 0.8146 (mmt) REVERT: D 48 MET cc_start: 0.8793 (ttt) cc_final: 0.8405 (ttt) REVERT: D 137 MET cc_start: 0.8948 (mtt) cc_final: 0.8668 (mtt) REVERT: D 221 ILE cc_start: 0.8439 (tp) cc_final: 0.7994 (pt) REVERT: D 377 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8212 (tp-100) REVERT: A 878 MET cc_start: 0.8331 (mtt) cc_final: 0.7933 (mtt) REVERT: A 923 LYS cc_start: 0.7475 (ttmt) cc_final: 0.7233 (ttmm) REVERT: A 1022 MET cc_start: 0.8401 (tpp) cc_final: 0.8049 (mmt) REVERT: B 48 MET cc_start: 0.8825 (ttt) cc_final: 0.8561 (ttt) REVERT: B 216 GLN cc_start: 0.6429 (tm-30) cc_final: 0.5410 (tt0) REVERT: B 265 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8052 (tp30) REVERT: B 341 MET cc_start: 0.8587 (mmm) cc_final: 0.8377 (mmt) REVERT: B 352 TYR cc_start: 0.7950 (t80) cc_final: 0.7743 (t80) REVERT: B 369 TRP cc_start: 0.8154 (m-90) cc_final: 0.7908 (m-90) REVERT: B 494 MET cc_start: 0.8451 (mmt) cc_final: 0.8210 (mmt) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.3290 time to fit residues: 107.0846 Evaluate side-chains 153 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 0.0980 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 168 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 713 GLN C 936 ASN C1081 GLN C1094 GLN D 172 GLN D 284 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 509 GLN D 553 ASN A 713 GLN A 936 ASN A1081 GLN B 172 GLN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 377 GLN B 509 GLN B 553 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15598 Z= 0.186 Angle : 0.547 9.680 21064 Z= 0.286 Chirality : 0.041 0.189 2286 Planarity : 0.004 0.051 2694 Dihedral : 4.449 26.150 2074 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 1.50 % Allowed : 9.81 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.19), residues: 1862 helix: 0.76 (0.17), residues: 858 sheet: -2.16 (0.36), residues: 180 loop : -2.99 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 369 HIS 0.003 0.001 HIS B 380 PHE 0.030 0.001 PHE D 550 TYR 0.028 0.001 TYR D 301 ARG 0.012 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.751 Fit side-chains REVERT: C 923 LYS cc_start: 0.7317 (ttmt) cc_final: 0.7020 (ttmm) REVERT: C 1022 MET cc_start: 0.8668 (tpp) cc_final: 0.8177 (mmt) REVERT: C 1094 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8479 (mm-40) REVERT: D 39 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7970 (mtpt) REVERT: D 48 MET cc_start: 0.8575 (ttt) cc_final: 0.8254 (ttt) REVERT: D 137 MET cc_start: 0.8919 (mtt) cc_final: 0.8660 (mtt) REVERT: D 177 MET cc_start: 0.8693 (mtm) cc_final: 0.8307 (mtp) REVERT: A 923 LYS cc_start: 0.7454 (ttmt) cc_final: 0.7139 (ttmm) REVERT: A 1022 MET cc_start: 0.8426 (tpp) cc_final: 0.7974 (mmt) REVERT: B 341 MET cc_start: 0.8587 (mmm) cc_final: 0.8252 (mmt) REVERT: B 352 TYR cc_start: 0.7891 (t80) cc_final: 0.7679 (t80) REVERT: B 369 TRP cc_start: 0.8178 (m-90) cc_final: 0.7967 (m-90) REVERT: B 387 ARG cc_start: 0.5947 (ptt90) cc_final: 0.5606 (ptm160) outliers start: 25 outliers final: 13 residues processed: 195 average time/residue: 0.2889 time to fit residues: 82.1029 Evaluate side-chains 165 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 135 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN D 380 HIS B 41 ASN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15598 Z= 0.359 Angle : 0.588 7.460 21064 Z= 0.309 Chirality : 0.043 0.177 2286 Planarity : 0.005 0.057 2694 Dihedral : 4.606 28.591 2074 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 2.57 % Allowed : 12.86 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.19), residues: 1862 helix: 0.96 (0.18), residues: 854 sheet: -1.88 (0.36), residues: 184 loop : -2.83 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 110 HIS 0.006 0.001 HIS B 323 PHE 0.028 0.002 PHE D 550 TYR 0.013 0.002 TYR A 738 ARG 0.008 0.001 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 2.013 Fit side-chains REVERT: C 923 LYS cc_start: 0.7306 (ttmt) cc_final: 0.7081 (ttmm) REVERT: C 935 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7137 (mt-10) REVERT: D 48 MET cc_start: 0.8800 (ttt) cc_final: 0.8481 (ttt) REVERT: D 137 MET cc_start: 0.8948 (mtt) cc_final: 0.8682 (mtt) REVERT: D 216 GLN cc_start: 0.6789 (tm-30) cc_final: 0.5912 (tt0) REVERT: D 301 TYR cc_start: 0.8486 (m-80) cc_final: 0.8218 (m-10) REVERT: A 923 LYS cc_start: 0.7389 (ttmt) cc_final: 0.7090 (ttmm) REVERT: A 935 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7163 (mt-10) REVERT: B 341 MET cc_start: 0.8555 (mmm) cc_final: 0.8276 (mmt) REVERT: B 352 TYR cc_start: 0.7947 (t80) cc_final: 0.7501 (t80) REVERT: B 369 TRP cc_start: 0.8123 (m-90) cc_final: 0.7868 (m-90) REVERT: B 505 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.4806 (mmp) outliers start: 43 outliers final: 34 residues processed: 195 average time/residue: 0.2699 time to fit residues: 78.2869 Evaluate side-chains 187 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain C residue 1094 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 7.9990 chunk 127 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN B 41 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15598 Z= 0.242 Angle : 0.523 7.176 21064 Z= 0.276 Chirality : 0.041 0.161 2286 Planarity : 0.004 0.058 2694 Dihedral : 4.388 28.700 2074 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 2.45 % Allowed : 14.59 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.20), residues: 1862 helix: 1.25 (0.18), residues: 858 sheet: -1.45 (0.37), residues: 182 loop : -2.65 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1026 HIS 0.003 0.001 HIS B 323 PHE 0.030 0.001 PHE D 550 TYR 0.013 0.001 TYR C 801 ARG 0.008 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.560 Fit side-chains REVERT: C 923 LYS cc_start: 0.7262 (ttmt) cc_final: 0.7014 (ttmm) REVERT: D 48 MET cc_start: 0.8772 (ttt) cc_final: 0.8440 (ttt) REVERT: D 137 MET cc_start: 0.8948 (mtt) cc_final: 0.8686 (mtt) REVERT: D 301 TYR cc_start: 0.8418 (m-80) cc_final: 0.8177 (m-10) REVERT: D 464 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: A 923 LYS cc_start: 0.7374 (ttmt) cc_final: 0.7051 (ttmm) REVERT: A 935 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7067 (mt-10) REVERT: B 341 MET cc_start: 0.8521 (mmm) cc_final: 0.8229 (mmt) REVERT: B 352 TYR cc_start: 0.7873 (t80) cc_final: 0.7535 (t80) REVERT: B 369 TRP cc_start: 0.8105 (m-90) cc_final: 0.7867 (m-90) REVERT: B 464 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7002 (mt-10) REVERT: B 505 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.4562 (mmp) outliers start: 41 outliers final: 26 residues processed: 192 average time/residue: 0.2655 time to fit residues: 76.1977 Evaluate side-chains 184 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 41 ASN Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 ASN D 216 GLN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 553 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15598 Z= 0.315 Angle : 0.549 7.506 21064 Z= 0.289 Chirality : 0.042 0.183 2286 Planarity : 0.004 0.058 2694 Dihedral : 4.473 28.848 2074 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 3.29 % Allowed : 15.07 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1862 helix: 1.32 (0.18), residues: 852 sheet: -1.28 (0.37), residues: 182 loop : -2.60 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1026 HIS 0.006 0.001 HIS D 323 PHE 0.027 0.001 PHE D 550 TYR 0.012 0.001 TYR C 738 ARG 0.006 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 162 time to evaluate : 1.628 Fit side-chains REVERT: C 923 LYS cc_start: 0.7310 (ttmt) cc_final: 0.7061 (ttmm) REVERT: D 48 MET cc_start: 0.8830 (ttt) cc_final: 0.8505 (ttt) REVERT: D 137 MET cc_start: 0.8940 (mtt) cc_final: 0.8689 (mtt) REVERT: D 301 TYR cc_start: 0.8444 (m-80) cc_final: 0.8199 (m-10) REVERT: D 422 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8732 (pt) REVERT: D 464 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7365 (mt-10) REVERT: A 709 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7835 (ttm-80) REVERT: A 923 LYS cc_start: 0.7439 (ttmt) cc_final: 0.7105 (ttmm) REVERT: A 935 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7008 (mt-10) REVERT: B 341 MET cc_start: 0.8472 (mmm) cc_final: 0.8192 (mmt) REVERT: B 369 TRP cc_start: 0.8092 (m-90) cc_final: 0.7866 (m-90) REVERT: B 422 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8748 (pt) REVERT: B 464 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7263 (mt-10) REVERT: B 505 MET cc_start: 0.5747 (OUTLIER) cc_final: 0.4610 (mmp) outliers start: 55 outliers final: 34 residues processed: 199 average time/residue: 0.2709 time to fit residues: 80.9148 Evaluate side-chains 190 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 151 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 179 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 216 GLN D 284 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15598 Z= 0.194 Angle : 0.500 7.674 21064 Z= 0.263 Chirality : 0.040 0.209 2286 Planarity : 0.004 0.058 2694 Dihedral : 4.262 27.391 2074 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.02 % Favored : 90.98 % Rotamer: Outliers : 2.99 % Allowed : 16.15 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1862 helix: 1.49 (0.18), residues: 860 sheet: -0.77 (0.40), residues: 162 loop : -2.40 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1026 HIS 0.003 0.001 HIS D 380 PHE 0.028 0.001 PHE D 550 TYR 0.014 0.001 TYR B 352 ARG 0.005 0.000 ARG D 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 160 time to evaluate : 1.976 Fit side-chains REVERT: C 923 LYS cc_start: 0.7294 (ttmt) cc_final: 0.7023 (ttmm) REVERT: D 48 MET cc_start: 0.8752 (ttt) cc_final: 0.8398 (ttt) REVERT: D 137 MET cc_start: 0.8941 (mtt) cc_final: 0.8682 (mtt) REVERT: D 301 TYR cc_start: 0.8382 (m-80) cc_final: 0.8182 (m-10) REVERT: D 422 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8723 (pt) REVERT: D 464 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: A 709 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7837 (ttm-80) REVERT: A 923 LYS cc_start: 0.7421 (ttmt) cc_final: 0.7080 (ttmm) REVERT: A 935 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7049 (mt-10) REVERT: B 341 MET cc_start: 0.8481 (mmm) cc_final: 0.8193 (mmt) REVERT: B 369 TRP cc_start: 0.8071 (m-90) cc_final: 0.7860 (m-90) REVERT: B 422 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8706 (pt) REVERT: B 464 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: B 505 MET cc_start: 0.5633 (OUTLIER) cc_final: 0.4544 (mmp) outliers start: 50 outliers final: 30 residues processed: 195 average time/residue: 0.2774 time to fit residues: 80.5867 Evaluate side-chains 189 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 818 SER Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain C residue 1025 LYS Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 151 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 216 GLN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15598 Z= 0.146 Angle : 0.478 8.173 21064 Z= 0.250 Chirality : 0.039 0.164 2286 Planarity : 0.004 0.058 2694 Dihedral : 4.032 25.273 2074 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.27 % Allowed : 16.63 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.20), residues: 1862 helix: 1.75 (0.18), residues: 856 sheet: -0.57 (0.41), residues: 164 loop : -2.21 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1026 HIS 0.003 0.001 HIS D 380 PHE 0.027 0.001 PHE B 145 TYR 0.011 0.001 TYR D 70 ARG 0.006 0.000 ARG B 526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 166 time to evaluate : 1.764 Fit side-chains REVERT: C 812 ASP cc_start: 0.8027 (m-30) cc_final: 0.7726 (m-30) REVERT: C 923 LYS cc_start: 0.7339 (ttmt) cc_final: 0.7056 (ttmm) REVERT: D 48 MET cc_start: 0.8679 (ttt) cc_final: 0.8339 (ttt) REVERT: D 195 LYS cc_start: 0.8588 (tptt) cc_final: 0.8379 (mmtm) REVERT: D 301 TYR cc_start: 0.8361 (m-80) cc_final: 0.8120 (m-10) REVERT: D 422 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8683 (pt) REVERT: D 464 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7023 (mt-10) REVERT: A 923 LYS cc_start: 0.7361 (ttmt) cc_final: 0.7015 (ttmm) REVERT: B 301 TYR cc_start: 0.8367 (m-80) cc_final: 0.8121 (m-10) REVERT: B 341 MET cc_start: 0.8441 (mmm) cc_final: 0.8096 (mmt) REVERT: B 464 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.6954 (mt-10) REVERT: B 505 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.4837 (mmp) outliers start: 38 outliers final: 21 residues processed: 193 average time/residue: 0.2684 time to fit residues: 77.6693 Evaluate side-chains 179 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.2980 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 88 optimal weight: 0.2980 chunk 16 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 216 GLN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15598 Z= 0.144 Angle : 0.478 7.935 21064 Z= 0.250 Chirality : 0.039 0.236 2286 Planarity : 0.004 0.059 2694 Dihedral : 3.937 24.049 2074 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 1.50 % Allowed : 17.34 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1862 helix: 1.85 (0.18), residues: 856 sheet: -0.47 (0.41), residues: 164 loop : -2.15 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1026 HIS 0.003 0.001 HIS D 380 PHE 0.028 0.001 PHE B 145 TYR 0.010 0.001 TYR B 70 ARG 0.005 0.000 ARG B 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 1.780 Fit side-chains REVERT: C 812 ASP cc_start: 0.8051 (m-30) cc_final: 0.7737 (m-30) REVERT: C 923 LYS cc_start: 0.7366 (ttmt) cc_final: 0.7036 (ttmm) REVERT: D 48 MET cc_start: 0.8692 (ttt) cc_final: 0.8396 (ttt) REVERT: D 195 LYS cc_start: 0.8569 (tptt) cc_final: 0.8274 (mmtm) REVERT: D 464 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6932 (mt-10) REVERT: A 923 LYS cc_start: 0.7383 (ttmt) cc_final: 0.7032 (ttmm) REVERT: B 301 TYR cc_start: 0.8351 (m-80) cc_final: 0.8070 (m-10) REVERT: B 341 MET cc_start: 0.8350 (mmm) cc_final: 0.8038 (mmt) REVERT: B 464 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6861 (mt-10) REVERT: B 505 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.4764 (mmp) outliers start: 25 outliers final: 16 residues processed: 181 average time/residue: 0.2533 time to fit residues: 68.9632 Evaluate side-chains 171 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 156 optimal weight: 0.9980 chunk 167 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 ASN D 216 GLN D 274 HIS ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15598 Z= 0.173 Angle : 0.487 8.091 21064 Z= 0.255 Chirality : 0.039 0.158 2286 Planarity : 0.004 0.059 2694 Dihedral : 3.939 24.438 2074 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.08 % Favored : 90.92 % Rotamer: Outliers : 2.21 % Allowed : 16.93 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.20), residues: 1862 helix: 1.82 (0.18), residues: 856 sheet: -0.37 (0.41), residues: 164 loop : -2.14 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1026 HIS 0.003 0.001 HIS D 380 PHE 0.024 0.001 PHE B 550 TYR 0.010 0.001 TYR B 70 ARG 0.006 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 1.890 Fit side-chains REVERT: C 812 ASP cc_start: 0.8045 (m-30) cc_final: 0.7742 (m-30) REVERT: C 923 LYS cc_start: 0.7380 (ttmt) cc_final: 0.7044 (ttmm) REVERT: D 48 MET cc_start: 0.8712 (ttt) cc_final: 0.8413 (ttt) REVERT: D 195 LYS cc_start: 0.8580 (tptt) cc_final: 0.8287 (mmtm) REVERT: D 301 TYR cc_start: 0.8363 (m-80) cc_final: 0.8105 (m-10) REVERT: D 464 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6948 (mt-10) REVERT: D 505 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.4779 (mmp) REVERT: A 923 LYS cc_start: 0.7413 (ttmt) cc_final: 0.7076 (ttmm) REVERT: B 301 TYR cc_start: 0.8350 (m-80) cc_final: 0.8088 (m-10) REVERT: B 341 MET cc_start: 0.8366 (mmm) cc_final: 0.8051 (mmt) REVERT: B 455 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8522 (tp) REVERT: B 464 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.6885 (mt-10) REVERT: B 505 MET cc_start: 0.5693 (OUTLIER) cc_final: 0.4669 (mmp) outliers start: 37 outliers final: 22 residues processed: 188 average time/residue: 0.2569 time to fit residues: 73.7197 Evaluate side-chains 181 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 809 VAL Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 0.3980 chunk 185 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 999 ASN D 274 HIS D 284 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15598 Z= 0.163 Angle : 0.487 9.141 21064 Z= 0.254 Chirality : 0.039 0.156 2286 Planarity : 0.004 0.059 2694 Dihedral : 3.924 24.162 2074 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.85 % Allowed : 17.17 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1862 helix: 1.83 (0.18), residues: 858 sheet: -0.30 (0.41), residues: 164 loop : -2.09 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C1026 HIS 0.003 0.001 HIS D 380 PHE 0.025 0.001 PHE B 550 TYR 0.010 0.001 TYR B 70 ARG 0.005 0.000 ARG B 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3724 Ramachandran restraints generated. 1862 Oldfield, 0 Emsley, 1862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 1.883 Fit side-chains REVERT: C 812 ASP cc_start: 0.8018 (m-30) cc_final: 0.7724 (m-30) REVERT: C 923 LYS cc_start: 0.7366 (ttmt) cc_final: 0.7023 (ttmm) REVERT: D 48 MET cc_start: 0.8691 (ttt) cc_final: 0.8408 (ttt) REVERT: D 195 LYS cc_start: 0.8582 (tptt) cc_final: 0.8282 (mmtm) REVERT: D 376 ARG cc_start: 0.6211 (ttm170) cc_final: 0.5845 (ttm-80) REVERT: D 455 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8537 (tp) REVERT: D 464 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6939 (mt-10) REVERT: D 505 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.4726 (mmp) REVERT: A 923 LYS cc_start: 0.7429 (ttmt) cc_final: 0.7059 (ttmm) REVERT: B 301 TYR cc_start: 0.8358 (m-80) cc_final: 0.8033 (m-10) REVERT: B 341 MET cc_start: 0.8367 (mmm) cc_final: 0.8054 (mmt) REVERT: B 376 ARG cc_start: 0.6067 (ttm110) cc_final: 0.5595 (ttm-80) REVERT: B 464 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6882 (mt-10) REVERT: B 505 MET cc_start: 0.5621 (OUTLIER) cc_final: 0.4575 (mmp) outliers start: 31 outliers final: 22 residues processed: 185 average time/residue: 0.2642 time to fit residues: 74.1521 Evaluate side-chains 181 residues out of total 1676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 861 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 373 GLU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 411 CYS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 460 MET Chi-restraints excluded: chain D residue 464 GLU Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 505 MET Chi-restraints excluded: chain A residue 861 ASP Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 1090 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 411 CYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 464 GLU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 505 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.0870 chunk 157 optimal weight: 0.7980 chunk 45 optimal weight: 0.0970 chunk 136 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 147 optimal weight: 0.0070 chunk 61 optimal weight: 0.7980 chunk 151 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 943 GLN C 999 ASN D 284 ASN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN A 943 GLN B 284 ASN ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 553 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108056 restraints weight = 21471.242| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.28 r_work: 0.3129 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15598 Z= 0.121 Angle : 0.468 8.907 21064 Z= 0.245 Chirality : 0.038 0.155 2286 Planarity : 0.004 0.060 2694 Dihedral : 3.716 21.278 2074 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 1.32 % Allowed : 17.82 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1862 helix: 2.00 (0.18), residues: 856 sheet: -0.20 (0.41), residues: 164 loop : -2.01 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 874 HIS 0.003 0.000 HIS D 380 PHE 0.022 0.001 PHE B 550 TYR 0.010 0.001 TYR B 70 ARG 0.009 0.000 ARG A 717 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3116.40 seconds wall clock time: 57 minutes 9.96 seconds (3429.96 seconds total)