Starting phenix.real_space_refine on Sat Mar 16 20:50:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grq_34212/03_2024/8grq_34212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grq_34212/03_2024/8grq_34212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grq_34212/03_2024/8grq_34212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grq_34212/03_2024/8grq_34212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grq_34212/03_2024/8grq_34212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8grq_34212/03_2024/8grq_34212.pdb" } resolution = 3.87 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1168 atoms to isotropic. 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 4 6.06 5 P 294 5.49 5 S 36 5.16 5 C 8230 2.51 5 N 2706 2.21 5 O 3293 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14563 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 849 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 722 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 87} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 602 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "N" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1174 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12208 SG CYS K 24 62.105 63.367 34.776 1.00172.74 S ATOM 12229 SG CYS K 27 58.255 63.031 33.350 1.00177.83 S ATOM 12365 SG CYS K 44 59.781 65.988 34.198 1.00172.35 S ATOM 12391 SG CYS K 47 58.931 63.740 37.112 1.00176.07 S ATOM 12322 SG CYS K 39 70.895 59.640 45.120 1.00151.18 S ATOM 12495 SG CYS K 61 67.586 57.821 45.169 1.00176.74 S ATOM 12513 SG CYS K 64 70.913 55.890 45.707 1.00187.38 S ATOM 12906 SG CYS M 50 87.356 78.652 40.369 1.00315.19 S ATOM 12929 SG CYS M 53 91.231 78.160 41.005 1.00349.31 S ATOM 13066 SG CYS M 71 88.943 75.205 40.394 1.00330.74 S ATOM 13086 SG CYS M 74 88.955 77.314 43.618 1.00335.17 S ATOM 13022 SG CYS M 66 77.403 77.457 48.921 1.00288.65 S ATOM 13142 SG CYS M 83 79.789 79.735 50.921 1.00333.44 S ATOM 13162 SG CYS M 86 76.503 81.265 49.555 1.00326.82 S Time building chain proxies: 7.48, per 1000 atoms: 0.51 Number of scatterers: 14563 At special positions: 0 Unit cell: (120.288, 124.584, 121.362, 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 4 29.99 S 36 16.00 P 294 15.00 O 3293 8.00 N 2706 7.00 C 8230 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 - 3.50 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=0, symmetry=0 Time building additional restraints: 8.49 Conformation dependent library (CDL) restraints added in 1.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 101 " pdb="ZN ZN K 101 " - pdb=" SG CYS K 44 " pdb="ZN ZN K 101 " - pdb=" SG CYS K 27 " pdb="ZN ZN K 101 " - pdb=" SG CYS K 47 " pdb="ZN ZN K 101 " - pdb=" SG CYS K 24 " pdb=" ZN K 102 " pdb="ZN ZN K 102 " - pdb=" NE2 HIS K 41 " pdb="ZN ZN K 102 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 102 " - pdb=" SG CYS K 61 " pdb="ZN ZN K 102 " - pdb=" SG CYS K 64 " pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 74 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 53 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 71 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 50 " pdb=" ZN M 202 " pdb="ZN ZN M 202 " - pdb=" ND1 HIS M 68 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 83 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 86 " pdb="ZN ZN M 202 " - pdb=" SG CYS M 66 " Number of angles added : 18 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 63.5% alpha, 3.9% beta 145 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 6.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.692A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.609A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.596A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.368A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.636A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.761A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.585A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.727A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.569A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.657A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.667A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.650A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.818A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.321A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 7 through 22 Processing helix chain 'K' and resid 46 through 54 Processing helix chain 'K' and resid 79 through 97 removed outlier: 4.404A pdb=" N GLU K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU K 85 " --> pdb=" O GLN K 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 49 removed outlier: 4.329A pdb=" N ALA M 39 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 77 removed outlier: 3.532A pdb=" N VAL M 75 " --> pdb=" O CYS M 71 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP M 77 " --> pdb=" O ASN M 73 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 116 Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.743A pdb=" N LEU N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 90 Processing helix chain 'N' and resid 98 through 112 removed outlier: 3.537A pdb=" N LEU N 104 " --> pdb=" O SER N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 130 Processing helix chain 'N' and resid 130 through 146 removed outlier: 3.501A pdb=" N TYR N 134 " --> pdb=" O ASP N 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.889A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.963A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.941A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.533A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.705A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 35 through 36 removed outlier: 3.725A pdb=" N VAL K 35 " --> pdb=" O PHE K 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 22 through 25 501 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 371 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 8.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3605 1.34 - 1.46: 4658 1.46 - 1.58: 6518 1.58 - 1.70: 586 1.70 - 1.82: 53 Bond restraints: 15420 Sorted by residual: bond pdb=" CG GLU M 45 " pdb=" CD GLU M 45 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.66e+00 bond pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" CB ASP F 24 " pdb=" CG ASP F 24 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.43e-02 4.89e+03 1.43e+00 bond pdb=" CB CYS K 61 " pdb=" SG CYS K 61 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.37e+00 ... (remaining 15415 not shown) Histogram of bond angle deviations from ideal: 98.81 - 105.86: 1666 105.86 - 112.91: 8406 112.91 - 119.96: 5814 119.96 - 127.01: 5484 127.01 - 134.06: 726 Bond angle restraints: 22096 Sorted by residual: angle pdb=" N SER A 96 " pdb=" CA SER A 96 " pdb=" C SER A 96 " ideal model delta sigma weight residual 110.97 115.40 -4.43 1.09e+00 8.42e-01 1.65e+01 angle pdb=" N GLU M 45 " pdb=" CA GLU M 45 " pdb=" CB GLU M 45 " ideal model delta sigma weight residual 110.28 116.43 -6.15 1.55e+00 4.16e-01 1.57e+01 angle pdb=" C LEU B 62 " pdb=" N GLU B 63 " pdb=" CA GLU B 63 " ideal model delta sigma weight residual 121.18 114.05 7.13 1.98e+00 2.55e-01 1.30e+01 angle pdb=" C LYS K 45 " pdb=" N PHE K 46 " pdb=" CA PHE K 46 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 angle pdb=" CB LYS N 63 " pdb=" CG LYS N 63 " pdb=" CD LYS N 63 " ideal model delta sigma weight residual 111.30 119.12 -7.82 2.30e+00 1.89e-01 1.16e+01 ... (remaining 22091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 7210 34.16 - 68.31: 1338 68.31 - 102.47: 20 102.47 - 136.63: 2 136.63 - 170.79: 2 Dihedral angle restraints: 8572 sinusoidal: 5417 harmonic: 3155 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 49.21 170.79 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA GLU A 50 " pdb=" C GLU A 50 " pdb=" N ILE A 51 " pdb=" CA ILE A 51 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 69.51 150.49 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 8569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1788 0.034 - 0.068: 543 0.068 - 0.103: 137 0.103 - 0.137: 46 0.137 - 0.171: 5 Chirality restraints: 2519 Sorted by residual: chirality pdb=" CA GLU F 63 " pdb=" N GLU F 63 " pdb=" C GLU F 63 " pdb=" CB GLU F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA GLU B 63 " pdb=" N GLU B 63 " pdb=" C GLU B 63 " pdb=" CB GLU B 63 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.86e-01 ... (remaining 2516 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 109 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LEU A 109 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU A 109 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 110 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 45 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C LYS K 45 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS K 45 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE K 46 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE K 46 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C PHE K 46 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE K 46 " 0.011 2.00e-02 2.50e+03 pdb=" N CYS K 47 " 0.010 2.00e-02 2.50e+03 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 512 2.68 - 3.24: 13853 3.24 - 3.79: 28007 3.79 - 4.35: 34420 4.35 - 4.90: 49151 Nonbonded interactions: 125943 Sorted by model distance: nonbonded pdb=" N2 DG I -10 " pdb=" O2 DC J 10 " model vdw 2.125 2.496 nonbonded pdb=" O GLN M 106 " pdb=" OG SER M 109 " model vdw 2.199 2.440 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE2 GLU H 76 " model vdw 2.205 2.520 nonbonded pdb=" OH TYR C 57 " pdb=" NH1 ARG K 71 " model vdw 2.209 2.520 nonbonded pdb=" O ARG N 139 " pdb=" OG1 THR N 142 " model vdw 2.210 2.440 ... (remaining 125938 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 117 or (resid 118 and (name N or name CA or nam \ e C or name O or name CB )))) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 4.530 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 47.580 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15420 Z= 0.211 Angle : 0.669 9.309 22096 Z= 0.407 Chirality : 0.037 0.171 2519 Planarity : 0.004 0.040 1788 Dihedral : 25.399 170.786 6526 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.22 % Allowed : 0.33 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.64 (0.25), residues: 1062 helix: 1.19 (0.21), residues: 656 sheet: 0.77 (1.20), residues: 18 loop : -0.87 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 93 HIS 0.005 0.001 HIS C 82 PHE 0.013 0.001 PHE K 79 TYR 0.020 0.002 TYR B 88 ARG 0.007 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 527 time to evaluate : 1.310 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 48 LEU cc_start: 0.9766 (mp) cc_final: 0.9174 (mp) REVERT: A 70 LEU cc_start: 0.9664 (tp) cc_final: 0.9310 (tt) REVERT: A 99 TYR cc_start: 0.9195 (t80) cc_final: 0.8919 (t80) REVERT: A 108 ASN cc_start: 0.9285 (t0) cc_final: 0.8983 (t0) REVERT: A 112 ILE cc_start: 0.9420 (pt) cc_final: 0.9080 (mt) REVERT: A 120 MET cc_start: 0.8940 (mmm) cc_final: 0.8626 (mmm) REVERT: B 24 ASP cc_start: 0.7033 (t0) cc_final: 0.6808 (t0) REVERT: B 29 ILE cc_start: 0.9564 (mm) cc_final: 0.9317 (mp) REVERT: B 34 ILE cc_start: 0.9766 (mt) cc_final: 0.9554 (mm) REVERT: B 49 LEU cc_start: 0.9020 (mm) cc_final: 0.8592 (mt) REVERT: B 53 GLU cc_start: 0.8288 (pm20) cc_final: 0.7659 (pm20) REVERT: B 79 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8750 (ptpp) REVERT: C 38 ASN cc_start: 0.8806 (m-40) cc_final: 0.8501 (p0) REVERT: C 68 ASN cc_start: 0.9307 (m-40) cc_final: 0.8786 (m110) REVERT: C 100 VAL cc_start: 0.9689 (m) cc_final: 0.9467 (t) REVERT: C 101 THR cc_start: 0.9167 (m) cc_final: 0.8758 (p) REVERT: D 59 MET cc_start: 0.9381 (tpp) cc_final: 0.9066 (tpt) REVERT: D 68 ASP cc_start: 0.9103 (t0) cc_final: 0.8705 (t0) REVERT: D 88 THR cc_start: 0.9310 (m) cc_final: 0.9092 (p) REVERT: D 101 LEU cc_start: 0.9583 (mt) cc_final: 0.9304 (mp) REVERT: E 48 LEU cc_start: 0.9695 (mt) cc_final: 0.9267 (mm) REVERT: E 50 GLU cc_start: 0.9062 (pt0) cc_final: 0.8524 (pt0) REVERT: E 60 LEU cc_start: 0.9103 (mt) cc_final: 0.8153 (mt) REVERT: E 97 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8288 (mt-10) REVERT: E 108 ASN cc_start: 0.9331 (t0) cc_final: 0.9103 (t0) REVERT: E 112 ILE cc_start: 0.9026 (mp) cc_final: 0.8810 (mp) REVERT: E 119 ILE cc_start: 0.9494 (mm) cc_final: 0.9049 (mm) REVERT: F 35 ARG cc_start: 0.9221 (mtp-110) cc_final: 0.8978 (ttm-80) REVERT: F 39 ARG cc_start: 0.9116 (mmt90) cc_final: 0.8385 (mmt90) REVERT: F 44 LYS cc_start: 0.9291 (tptm) cc_final: 0.8915 (tttm) REVERT: F 49 LEU cc_start: 0.9349 (mt) cc_final: 0.8977 (mt) REVERT: F 88 TYR cc_start: 0.8981 (m-10) cc_final: 0.8417 (m-10) REVERT: G 32 ARG cc_start: 0.9137 (ttp80) cc_final: 0.8608 (tmm-80) REVERT: G 35 ARG cc_start: 0.8344 (mtm110) cc_final: 0.7473 (ptm-80) REVERT: G 36 LYS cc_start: 0.8588 (mmtm) cc_final: 0.7762 (mmtm) REVERT: G 38 ASN cc_start: 0.9048 (m-40) cc_final: 0.8826 (m-40) REVERT: G 39 TYR cc_start: 0.9373 (m-80) cc_final: 0.9028 (m-80) REVERT: G 75 LYS cc_start: 0.9335 (mttm) cc_final: 0.8898 (mmmm) REVERT: H 68 ASP cc_start: 0.9155 (t0) cc_final: 0.8950 (t0) REVERT: H 70 PHE cc_start: 0.9371 (t80) cc_final: 0.8942 (t80) REVERT: H 83 TYR cc_start: 0.8665 (m-10) cc_final: 0.8348 (m-10) REVERT: H 86 ARG cc_start: 0.9190 (tpp80) cc_final: 0.8793 (tpp80) REVERT: H 101 LEU cc_start: 0.9258 (mp) cc_final: 0.8840 (mp) REVERT: H 105 GLU cc_start: 0.8289 (tp30) cc_final: 0.7945 (tp30) REVERT: N 38 MET cc_start: 0.3018 (ppp) cc_final: 0.2749 (ppp) REVERT: N 79 ASN cc_start: 0.6534 (p0) cc_final: 0.6268 (p0) outliers start: 2 outliers final: 1 residues processed: 529 average time/residue: 0.3312 time to fit residues: 232.8798 Evaluate side-chains 413 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 412 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 102 optimal weight: 0.0670 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 118 optimal weight: 50.0000 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 109 HIS E 68 GLN G 31 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15420 Z= 0.314 Angle : 0.690 8.793 22096 Z= 0.391 Chirality : 0.041 0.218 2519 Planarity : 0.005 0.041 1788 Dihedral : 29.096 170.304 4404 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 4.82 % Allowed : 20.04 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.66 (0.25), residues: 1062 helix: 1.15 (0.20), residues: 667 sheet: 0.83 (1.21), residues: 24 loop : -0.85 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 33 HIS 0.009 0.002 HIS F 75 PHE 0.030 0.002 PHE F 61 TYR 0.034 0.003 TYR D 83 ARG 0.008 0.001 ARG N 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 449 time to evaluate : 1.219 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: A 80 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9173 (p) REVERT: A 94 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8665 (mm-30) REVERT: A 105 GLU cc_start: 0.8602 (tp30) cc_final: 0.8385 (tp30) REVERT: B 24 ASP cc_start: 0.7366 (t0) cc_final: 0.7160 (t0) REVERT: B 34 ILE cc_start: 0.9769 (mt) cc_final: 0.9565 (mm) REVERT: B 49 LEU cc_start: 0.8911 (mm) cc_final: 0.8610 (mt) REVERT: B 52 GLU cc_start: 0.8288 (pm20) cc_final: 0.7606 (pm20) REVERT: B 53 GLU cc_start: 0.8094 (pm20) cc_final: 0.7834 (pm20) REVERT: C 38 ASN cc_start: 0.8842 (m-40) cc_final: 0.8544 (p0) REVERT: C 54 VAL cc_start: 0.9700 (t) cc_final: 0.9417 (p) REVERT: C 68 ASN cc_start: 0.9168 (m-40) cc_final: 0.8950 (m110) REVERT: C 101 THR cc_start: 0.9269 (m) cc_final: 0.8854 (p) REVERT: D 68 ASP cc_start: 0.9145 (t0) cc_final: 0.8883 (t0) REVERT: D 88 THR cc_start: 0.9460 (m) cc_final: 0.9100 (p) REVERT: D 96 THR cc_start: 0.9562 (m) cc_final: 0.9333 (p) REVERT: D 105 GLU cc_start: 0.8097 (pm20) cc_final: 0.7685 (pm20) REVERT: E 50 GLU cc_start: 0.8992 (pt0) cc_final: 0.8426 (pt0) REVERT: E 125 GLN cc_start: 0.9305 (mt0) cc_final: 0.8943 (mp10) REVERT: F 39 ARG cc_start: 0.9041 (mmt90) cc_final: 0.8454 (mmt90) REVERT: F 49 LEU cc_start: 0.9358 (mt) cc_final: 0.9089 (mm) REVERT: F 79 LYS cc_start: 0.9103 (mtpp) cc_final: 0.8743 (mtmm) REVERT: F 88 TYR cc_start: 0.9178 (m-10) cc_final: 0.8627 (m-80) REVERT: F 95 ARG cc_start: 0.8758 (mtp85) cc_final: 0.8477 (mtt90) REVERT: G 32 ARG cc_start: 0.9150 (ttp80) cc_final: 0.8747 (ttp80) REVERT: G 36 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8347 (mmtm) REVERT: G 38 ASN cc_start: 0.9219 (m-40) cc_final: 0.9011 (m-40) REVERT: G 39 TYR cc_start: 0.9431 (m-80) cc_final: 0.9130 (m-80) REVERT: G 75 LYS cc_start: 0.9400 (mttm) cc_final: 0.8965 (mmmm) REVERT: H 47 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8574 (tm-30) REVERT: H 86 ARG cc_start: 0.9277 (tpp80) cc_final: 0.8928 (tpp80) REVERT: K 50 LYS cc_start: 0.9178 (mptt) cc_final: 0.8949 (mmtt) REVERT: M 77 ASP cc_start: 0.8278 (m-30) cc_final: 0.7644 (p0) REVERT: M 104 MET cc_start: 0.8891 (mmm) cc_final: 0.8584 (mmm) REVERT: N 38 MET cc_start: 0.3620 (ppp) cc_final: 0.3282 (ppp) REVERT: N 79 ASN cc_start: 0.6723 (p0) cc_final: 0.6353 (p0) REVERT: N 140 GLU cc_start: 0.9388 (pt0) cc_final: 0.9150 (pt0) outliers start: 44 outliers final: 31 residues processed: 463 average time/residue: 0.3119 time to fit residues: 195.6876 Evaluate side-chains 441 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 409 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain N residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15420 Z= 0.285 Angle : 0.667 8.742 22096 Z= 0.377 Chirality : 0.040 0.291 2519 Planarity : 0.004 0.042 1788 Dihedral : 29.330 170.844 4404 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 6.02 % Allowed : 22.23 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.74 (0.26), residues: 1062 helix: 1.26 (0.20), residues: 666 sheet: 0.84 (1.23), residues: 24 loop : -0.89 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 141 HIS 0.004 0.001 HIS F 75 PHE 0.030 0.002 PHE F 61 TYR 0.028 0.002 TYR D 83 ARG 0.007 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 452 time to evaluate : 1.225 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 93 GLN cc_start: 0.8975 (tp40) cc_final: 0.8442 (tp40) REVERT: A 120 MET cc_start: 0.8519 (mmm) cc_final: 0.8062 (mtp) REVERT: B 49 LEU cc_start: 0.8958 (mm) cc_final: 0.8609 (mt) REVERT: B 52 GLU cc_start: 0.8334 (pm20) cc_final: 0.7763 (pm20) REVERT: B 53 GLU cc_start: 0.8155 (pm20) cc_final: 0.7903 (pm20) REVERT: B 88 TYR cc_start: 0.8948 (m-80) cc_final: 0.8246 (m-80) REVERT: C 38 ASN cc_start: 0.8876 (m-40) cc_final: 0.8618 (p0) REVERT: C 54 VAL cc_start: 0.9676 (t) cc_final: 0.9450 (p) REVERT: C 95 LYS cc_start: 0.9353 (tttm) cc_final: 0.9118 (tptp) REVERT: C 101 THR cc_start: 0.9169 (m) cc_final: 0.8809 (p) REVERT: D 68 ASP cc_start: 0.9183 (t0) cc_final: 0.8884 (t0) REVERT: D 71 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8370 (tm-30) REVERT: D 80 LEU cc_start: 0.9687 (tp) cc_final: 0.9478 (tp) REVERT: D 83 TYR cc_start: 0.7267 (m-80) cc_final: 0.5841 (m-10) REVERT: D 88 THR cc_start: 0.9469 (m) cc_final: 0.9148 (p) REVERT: D 96 THR cc_start: 0.9566 (m) cc_final: 0.9309 (p) REVERT: E 50 GLU cc_start: 0.9029 (pt0) cc_final: 0.8669 (pt0) REVERT: E 60 LEU cc_start: 0.9194 (mm) cc_final: 0.8993 (mm) REVERT: E 90 MET cc_start: 0.8743 (mmp) cc_final: 0.8470 (mmm) REVERT: E 120 MET cc_start: 0.8384 (mmm) cc_final: 0.8157 (mmm) REVERT: E 122 LYS cc_start: 0.9169 (ptmt) cc_final: 0.8824 (ptmt) REVERT: E 125 GLN cc_start: 0.9355 (mt0) cc_final: 0.9066 (mp10) REVERT: F 35 ARG cc_start: 0.9214 (ttm-80) cc_final: 0.8713 (ttm-80) REVERT: F 39 ARG cc_start: 0.9191 (mmt90) cc_final: 0.8756 (mmt90) REVERT: F 44 LYS cc_start: 0.9404 (tptm) cc_final: 0.8973 (mmmt) REVERT: F 49 LEU cc_start: 0.9308 (mt) cc_final: 0.9041 (mm) REVERT: F 79 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8740 (mtmm) REVERT: F 88 TYR cc_start: 0.9217 (m-10) cc_final: 0.8179 (m-10) REVERT: F 95 ARG cc_start: 0.8807 (mtp85) cc_final: 0.8517 (mtt90) REVERT: G 24 GLN cc_start: 0.8889 (mp10) cc_final: 0.8530 (mp10) REVERT: G 32 ARG cc_start: 0.9221 (ttp80) cc_final: 0.8939 (ttp80) REVERT: G 38 ASN cc_start: 0.9222 (m-40) cc_final: 0.9019 (m-40) REVERT: G 39 TYR cc_start: 0.9384 (m-80) cc_final: 0.9093 (m-80) REVERT: G 42 ARG cc_start: 0.8769 (ptp-110) cc_final: 0.8054 (ptm160) REVERT: G 75 LYS cc_start: 0.9487 (mttm) cc_final: 0.9026 (mmmm) REVERT: G 81 ARG cc_start: 0.9193 (tpt90) cc_final: 0.8907 (tpt170) REVERT: H 37 TYR cc_start: 0.9046 (m-80) cc_final: 0.8761 (m-80) REVERT: H 70 PHE cc_start: 0.9450 (t80) cc_final: 0.9141 (t80) REVERT: H 83 TYR cc_start: 0.8873 (m-10) cc_final: 0.8328 (m-80) REVERT: H 86 ARG cc_start: 0.9266 (tpp80) cc_final: 0.8811 (tpp80) REVERT: K 43 PHE cc_start: 0.7433 (m-10) cc_final: 0.7112 (m-80) REVERT: M 77 ASP cc_start: 0.8244 (m-30) cc_final: 0.7633 (p0) REVERT: M 104 MET cc_start: 0.9001 (mmm) cc_final: 0.8765 (mmm) REVERT: N 38 MET cc_start: 0.3867 (ppp) cc_final: 0.3404 (ppp) REVERT: N 79 ASN cc_start: 0.6938 (p0) cc_final: 0.6561 (p0) outliers start: 55 outliers final: 44 residues processed: 469 average time/residue: 0.3128 time to fit residues: 201.1496 Evaluate side-chains 472 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 427 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 63 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 132 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 119 optimal weight: 0.0770 chunk 126 optimal weight: 0.1980 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 82 HIS E 68 GLN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15420 Z= 0.203 Angle : 0.663 9.469 22096 Z= 0.367 Chirality : 0.038 0.246 2519 Planarity : 0.004 0.039 1788 Dihedral : 29.312 172.139 4404 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.27 % Allowed : 27.05 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.76 (0.25), residues: 1062 helix: 1.26 (0.20), residues: 666 sheet: 0.72 (1.21), residues: 24 loop : -0.84 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 141 HIS 0.004 0.001 HIS G 31 PHE 0.025 0.002 PHE F 61 TYR 0.016 0.002 TYR N 60 ARG 0.007 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 458 time to evaluate : 1.315 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 80 THR cc_start: 0.9404 (p) cc_final: 0.9177 (t) REVERT: A 120 MET cc_start: 0.8428 (mmm) cc_final: 0.7858 (mtp) REVERT: B 49 LEU cc_start: 0.8878 (mm) cc_final: 0.8460 (tp) REVERT: B 52 GLU cc_start: 0.8330 (pm20) cc_final: 0.7895 (pm20) REVERT: C 75 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8398 (mmmm) REVERT: C 95 LYS cc_start: 0.9312 (tttm) cc_final: 0.9091 (tptp) REVERT: C 101 THR cc_start: 0.9073 (m) cc_final: 0.8644 (p) REVERT: D 47 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8844 (tm-30) REVERT: D 80 LEU cc_start: 0.9662 (tp) cc_final: 0.9443 (tp) REVERT: D 88 THR cc_start: 0.9301 (m) cc_final: 0.9044 (p) REVERT: D 96 THR cc_start: 0.9534 (m) cc_final: 0.9291 (p) REVERT: D 120 LYS cc_start: 0.9308 (tmmt) cc_final: 0.9078 (tttp) REVERT: E 119 ILE cc_start: 0.9344 (mm) cc_final: 0.9080 (mt) REVERT: E 120 MET cc_start: 0.8426 (mmm) cc_final: 0.8135 (mmm) REVERT: E 125 GLN cc_start: 0.9336 (mt0) cc_final: 0.9031 (mp10) REVERT: F 44 LYS cc_start: 0.9393 (tptm) cc_final: 0.9120 (tppp) REVERT: F 59 LYS cc_start: 0.9556 (ptmm) cc_final: 0.9135 (ptmm) REVERT: F 63 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: F 79 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8724 (mtmm) REVERT: F 92 ARG cc_start: 0.9158 (mtp-110) cc_final: 0.8910 (ttt-90) REVERT: F 95 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8359 (mtt90) REVERT: G 24 GLN cc_start: 0.8920 (mp10) cc_final: 0.8506 (mp10) REVERT: G 32 ARG cc_start: 0.9267 (ttp80) cc_final: 0.8884 (ttp80) REVERT: G 38 ASN cc_start: 0.9176 (m-40) cc_final: 0.8948 (m-40) REVERT: G 39 TYR cc_start: 0.9337 (m-80) cc_final: 0.8807 (m-80) REVERT: G 42 ARG cc_start: 0.8738 (ptp-110) cc_final: 0.8155 (ptm-80) REVERT: G 75 LYS cc_start: 0.9472 (mttm) cc_final: 0.9016 (mmmm) REVERT: H 33 ARG cc_start: 0.8470 (tpp80) cc_final: 0.8177 (tpt170) REVERT: H 37 TYR cc_start: 0.8963 (m-80) cc_final: 0.8705 (m-80) REVERT: H 42 TYR cc_start: 0.8542 (t80) cc_final: 0.8290 (t80) REVERT: H 86 ARG cc_start: 0.9234 (tpp80) cc_final: 0.8774 (tpp80) REVERT: H 92 ARG cc_start: 0.8696 (mtp-110) cc_final: 0.8194 (ttp80) REVERT: K 43 PHE cc_start: 0.7305 (m-10) cc_final: 0.6928 (m-80) REVERT: K 50 LYS cc_start: 0.9180 (mptt) cc_final: 0.8954 (mptt) REVERT: K 66 ASN cc_start: 0.9158 (t0) cc_final: 0.8799 (m-40) REVERT: M 104 MET cc_start: 0.9026 (mmm) cc_final: 0.8727 (mmm) REVERT: N 29 ASP cc_start: 0.6190 (t70) cc_final: 0.5798 (p0) REVERT: N 38 MET cc_start: 0.4023 (ppp) cc_final: 0.3556 (ppp) REVERT: N 56 PHE cc_start: 0.7419 (m-80) cc_final: 0.7058 (m-80) REVERT: N 79 ASN cc_start: 0.6576 (p0) cc_final: 0.6129 (p0) outliers start: 39 outliers final: 23 residues processed: 470 average time/residue: 0.3053 time to fit residues: 196.2068 Evaluate side-chains 441 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 417 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 116 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 0.0060 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 113 optimal weight: 30.0000 chunk 31 optimal weight: 0.9980 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS ** N 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15420 Z= 0.326 Angle : 0.696 11.421 22096 Z= 0.391 Chirality : 0.041 0.263 2519 Planarity : 0.005 0.042 1788 Dihedral : 29.550 171.778 4404 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 7.34 % Allowed : 27.16 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.61 (0.25), residues: 1062 helix: 1.10 (0.20), residues: 667 sheet: 0.89 (1.24), residues: 24 loop : -0.84 (0.31), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 141 HIS 0.005 0.001 HIS G 31 PHE 0.027 0.002 PHE F 61 TYR 0.033 0.003 TYR D 83 ARG 0.009 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 414 time to evaluate : 1.394 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 94 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8541 (mm-30) REVERT: B 49 LEU cc_start: 0.8992 (mm) cc_final: 0.8663 (tp) REVERT: B 52 GLU cc_start: 0.8434 (pm20) cc_final: 0.8194 (pm20) REVERT: B 53 GLU cc_start: 0.8291 (pm20) cc_final: 0.7858 (pm20) REVERT: B 79 LYS cc_start: 0.9200 (mtmt) cc_final: 0.8683 (ptpt) REVERT: B 88 TYR cc_start: 0.8981 (m-80) cc_final: 0.8618 (m-80) REVERT: C 38 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8393 (t0) REVERT: C 95 LYS cc_start: 0.9322 (tttm) cc_final: 0.9091 (tptp) REVERT: C 101 THR cc_start: 0.9068 (m) cc_final: 0.8701 (p) REVERT: D 47 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8839 (tm-30) REVERT: D 88 THR cc_start: 0.9491 (m) cc_final: 0.9143 (p) REVERT: D 96 THR cc_start: 0.9588 (m) cc_final: 0.9360 (p) REVERT: D 120 LYS cc_start: 0.9303 (tmmt) cc_final: 0.9087 (tttp) REVERT: E 120 MET cc_start: 0.8453 (mmm) cc_final: 0.8122 (mmm) REVERT: E 125 GLN cc_start: 0.9386 (mt0) cc_final: 0.9117 (mp10) REVERT: F 35 ARG cc_start: 0.9153 (ttm-80) cc_final: 0.8879 (ttm-80) REVERT: F 44 LYS cc_start: 0.9387 (tptm) cc_final: 0.9050 (mmmm) REVERT: F 79 LYS cc_start: 0.9082 (mtpp) cc_final: 0.8650 (mtmm) REVERT: F 84 MET cc_start: 0.8686 (mmm) cc_final: 0.8468 (mmm) REVERT: F 88 TYR cc_start: 0.9127 (m-80) cc_final: 0.8768 (m-80) REVERT: F 92 ARG cc_start: 0.9214 (mtp-110) cc_final: 0.8814 (ttt-90) REVERT: F 95 ARG cc_start: 0.8774 (mtp85) cc_final: 0.8449 (mtt90) REVERT: G 24 GLN cc_start: 0.8995 (mp10) cc_final: 0.8548 (mp10) REVERT: G 38 ASN cc_start: 0.9289 (m-40) cc_final: 0.9070 (m-40) REVERT: G 56 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8688 (mt-10) REVERT: G 75 LYS cc_start: 0.9449 (mttm) cc_final: 0.8894 (mtpp) REVERT: H 37 TYR cc_start: 0.9136 (m-80) cc_final: 0.8856 (m-80) REVERT: H 70 PHE cc_start: 0.9433 (t80) cc_final: 0.9190 (t80) REVERT: H 86 ARG cc_start: 0.9275 (tpp80) cc_final: 0.8847 (tpp80) REVERT: M 104 MET cc_start: 0.9064 (mmm) cc_final: 0.8769 (mmm) REVERT: N 29 ASP cc_start: 0.6426 (t70) cc_final: 0.5950 (p0) REVERT: N 31 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7899 (t80) REVERT: N 38 MET cc_start: 0.3773 (ppp) cc_final: 0.3333 (ppp) REVERT: N 79 ASN cc_start: 0.6849 (p0) cc_final: 0.6436 (p0) outliers start: 67 outliers final: 44 residues processed: 440 average time/residue: 0.3055 time to fit residues: 184.9683 Evaluate side-chains 442 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 396 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 94 ILE Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain N residue 31 PHE Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 40.0000 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 105 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 0.0570 chunk 66 optimal weight: 0.7980 overall best weight: 0.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN E 93 GLN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 GLN ** K 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 143 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15420 Z= 0.207 Angle : 0.696 10.907 22096 Z= 0.382 Chirality : 0.039 0.315 2519 Planarity : 0.004 0.044 1788 Dihedral : 29.504 172.612 4404 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.05 % Allowed : 31.00 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.66 (0.26), residues: 1062 helix: 1.14 (0.20), residues: 664 sheet: 0.91 (1.24), residues: 24 loop : -0.79 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 93 HIS 0.006 0.001 HIS G 31 PHE 0.030 0.002 PHE F 61 TYR 0.023 0.002 TYR B 88 ARG 0.006 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 437 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: A 94 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8539 (mm-30) REVERT: B 49 LEU cc_start: 0.8877 (mm) cc_final: 0.8556 (tp) REVERT: B 52 GLU cc_start: 0.8357 (pm20) cc_final: 0.8085 (pm20) REVERT: B 53 GLU cc_start: 0.8367 (pm20) cc_final: 0.8003 (pm20) REVERT: B 79 LYS cc_start: 0.9185 (mtmt) cc_final: 0.8717 (ptpt) REVERT: B 88 TYR cc_start: 0.8858 (m-80) cc_final: 0.8443 (m-80) REVERT: C 38 ASN cc_start: 0.8672 (m-40) cc_final: 0.8110 (t0) REVERT: C 75 LYS cc_start: 0.8605 (mmmm) cc_final: 0.8123 (mmmm) REVERT: C 95 LYS cc_start: 0.9281 (tttm) cc_final: 0.9050 (tptp) REVERT: C 101 THR cc_start: 0.8991 (m) cc_final: 0.8613 (p) REVERT: D 47 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8885 (tm-30) REVERT: D 68 ASP cc_start: 0.9118 (t0) cc_final: 0.8799 (t0) REVERT: D 80 LEU cc_start: 0.9582 (tp) cc_final: 0.9326 (tp) REVERT: D 88 THR cc_start: 0.9272 (m) cc_final: 0.9049 (p) REVERT: D 96 THR cc_start: 0.9550 (m) cc_final: 0.9273 (p) REVERT: D 105 GLU cc_start: 0.7936 (pm20) cc_final: 0.7329 (pm20) REVERT: D 108 LYS cc_start: 0.9348 (ptpp) cc_final: 0.9100 (pttp) REVERT: D 120 LYS cc_start: 0.9328 (tmmt) cc_final: 0.9067 (tttp) REVERT: E 79 LYS cc_start: 0.8720 (tptp) cc_final: 0.8487 (tptp) REVERT: E 120 MET cc_start: 0.8387 (mmm) cc_final: 0.8015 (mmm) REVERT: E 122 LYS cc_start: 0.9194 (ptmt) cc_final: 0.8640 (ptmt) REVERT: E 125 GLN cc_start: 0.9351 (mt0) cc_final: 0.9039 (mp10) REVERT: F 79 LYS cc_start: 0.9106 (mtpp) cc_final: 0.8699 (mtmm) REVERT: F 92 ARG cc_start: 0.9131 (mtp-110) cc_final: 0.8634 (ttt-90) REVERT: F 95 ARG cc_start: 0.8684 (mtp85) cc_final: 0.8371 (mtt90) REVERT: G 24 GLN cc_start: 0.9129 (mp10) cc_final: 0.8650 (mp10) REVERT: G 38 ASN cc_start: 0.9215 (m-40) cc_final: 0.8385 (m-40) REVERT: G 57 TYR cc_start: 0.9187 (t80) cc_final: 0.8898 (t80) REVERT: G 75 LYS cc_start: 0.9406 (mttm) cc_final: 0.8827 (mtpp) REVERT: G 90 ASP cc_start: 0.8647 (t0) cc_final: 0.8353 (t0) REVERT: H 37 TYR cc_start: 0.9000 (m-80) cc_final: 0.8733 (m-10) REVERT: H 42 TYR cc_start: 0.8564 (t80) cc_final: 0.8273 (t80) REVERT: H 70 PHE cc_start: 0.9413 (t80) cc_final: 0.9146 (t80) REVERT: H 86 ARG cc_start: 0.9242 (tpp80) cc_final: 0.8721 (tpp80) REVERT: H 95 GLN cc_start: 0.9475 (pt0) cc_final: 0.9179 (tt0) REVERT: H 101 LEU cc_start: 0.9196 (mm) cc_final: 0.8872 (mm) REVERT: K 38 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8443 (mmtm) REVERT: K 66 ASN cc_start: 0.9171 (t0) cc_final: 0.8771 (m-40) REVERT: N 38 MET cc_start: 0.4170 (ppp) cc_final: 0.3780 (ppp) REVERT: N 79 ASN cc_start: 0.6764 (p0) cc_final: 0.6347 (p0) REVERT: N 132 ASP cc_start: 0.8828 (m-30) cc_final: 0.8602 (p0) REVERT: N 140 GLU cc_start: 0.9341 (pt0) cc_final: 0.9121 (tp30) outliers start: 37 outliers final: 29 residues processed: 446 average time/residue: 0.3029 time to fit residues: 185.9640 Evaluate side-chains 438 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 409 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 64 ASN Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 106 optimal weight: 0.0270 chunk 70 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 15420 Z= 0.278 Angle : 0.714 11.306 22096 Z= 0.393 Chirality : 0.041 0.294 2519 Planarity : 0.005 0.043 1788 Dihedral : 29.655 172.550 4403 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 5.48 % Allowed : 32.31 % Favored : 62.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.68 (0.26), residues: 1062 helix: 1.12 (0.20), residues: 666 sheet: 0.94 (1.22), residues: 24 loop : -0.73 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 93 HIS 0.007 0.001 HIS F 75 PHE 0.028 0.002 PHE F 61 TYR 0.021 0.002 TYR D 40 ARG 0.009 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 412 time to evaluate : 1.169 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 94 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8684 (mm-30) REVERT: B 49 LEU cc_start: 0.8974 (mm) cc_final: 0.8590 (tp) REVERT: B 52 GLU cc_start: 0.8460 (pm20) cc_final: 0.8167 (pm20) REVERT: B 53 GLU cc_start: 0.8472 (pm20) cc_final: 0.8122 (pm20) REVERT: B 67 ARG cc_start: 0.8862 (ttm110) cc_final: 0.8502 (ttm110) REVERT: B 88 TYR cc_start: 0.8861 (m-80) cc_final: 0.7608 (m-10) REVERT: C 38 ASN cc_start: 0.8747 (m-40) cc_final: 0.8154 (t0) REVERT: C 75 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8328 (mmmm) REVERT: C 95 LYS cc_start: 0.9307 (tttm) cc_final: 0.9076 (tptp) REVERT: C 101 THR cc_start: 0.8928 (m) cc_final: 0.8558 (p) REVERT: D 40 TYR cc_start: 0.8538 (m-80) cc_final: 0.8215 (m-80) REVERT: D 47 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8912 (tm-30) REVERT: D 68 ASP cc_start: 0.9136 (t0) cc_final: 0.8782 (t0) REVERT: D 80 LEU cc_start: 0.9639 (tp) cc_final: 0.9382 (tp) REVERT: D 83 TYR cc_start: 0.7431 (m-10) cc_final: 0.7015 (m-10) REVERT: D 88 THR cc_start: 0.9358 (m) cc_final: 0.9121 (p) REVERT: D 96 THR cc_start: 0.9568 (m) cc_final: 0.9263 (p) REVERT: D 120 LYS cc_start: 0.9355 (tmmt) cc_final: 0.9094 (tttp) REVERT: E 120 MET cc_start: 0.8439 (mmm) cc_final: 0.8079 (mmm) REVERT: E 122 LYS cc_start: 0.9187 (ptmt) cc_final: 0.8622 (ptmt) REVERT: E 125 GLN cc_start: 0.9375 (mt0) cc_final: 0.9107 (mp10) REVERT: F 79 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8696 (mtmm) REVERT: F 88 TYR cc_start: 0.8163 (m-10) cc_final: 0.7680 (m-80) REVERT: F 95 ARG cc_start: 0.8750 (mtp85) cc_final: 0.8407 (mtt90) REVERT: G 24 GLN cc_start: 0.9125 (mp10) cc_final: 0.8660 (mp10) REVERT: G 38 ASN cc_start: 0.9267 (m-40) cc_final: 0.8371 (t0) REVERT: G 75 LYS cc_start: 0.9377 (mttm) cc_final: 0.9175 (mmtm) REVERT: H 37 TYR cc_start: 0.9101 (m-80) cc_final: 0.8874 (m-80) REVERT: H 70 PHE cc_start: 0.9434 (t80) cc_final: 0.9144 (t80) REVERT: H 86 ARG cc_start: 0.9288 (tpp80) cc_final: 0.8814 (tpp80) REVERT: K 38 LYS cc_start: 0.8770 (mmtm) cc_final: 0.8530 (mmtm) REVERT: K 66 ASN cc_start: 0.9225 (t0) cc_final: 0.8939 (t0) REVERT: M 104 MET cc_start: 0.8863 (mmm) cc_final: 0.8564 (mmm) REVERT: N 38 MET cc_start: 0.3955 (ppp) cc_final: 0.3582 (ppp) REVERT: N 79 ASN cc_start: 0.6817 (p0) cc_final: 0.6407 (p0) outliers start: 50 outliers final: 36 residues processed: 430 average time/residue: 0.3122 time to fit residues: 183.4176 Evaluate side-chains 434 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 398 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15420 Z= 0.265 Angle : 0.738 12.231 22096 Z= 0.403 Chirality : 0.041 0.348 2519 Planarity : 0.005 0.043 1788 Dihedral : 29.738 172.298 4403 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.76 % Rotamer: Outliers : 5.15 % Allowed : 33.08 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.69 (0.26), residues: 1062 helix: 1.12 (0.20), residues: 664 sheet: 0.93 (1.20), residues: 24 loop : -0.70 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 33 HIS 0.005 0.001 HIS G 31 PHE 0.027 0.002 PHE F 61 TYR 0.020 0.002 TYR B 88 ARG 0.006 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 412 time to evaluate : 1.272 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 94 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8627 (mm-30) REVERT: B 49 LEU cc_start: 0.8950 (mm) cc_final: 0.8529 (tp) REVERT: B 52 GLU cc_start: 0.8394 (pm20) cc_final: 0.8075 (pm20) REVERT: B 53 GLU cc_start: 0.8401 (pm20) cc_final: 0.8049 (pm20) REVERT: B 88 TYR cc_start: 0.8892 (m-80) cc_final: 0.8405 (m-10) REVERT: C 36 LYS cc_start: 0.9266 (mmtm) cc_final: 0.9063 (mmmm) REVERT: C 38 ASN cc_start: 0.8695 (m-40) cc_final: 0.8264 (t0) REVERT: C 75 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8397 (mmmm) REVERT: C 95 LYS cc_start: 0.9302 (tttm) cc_final: 0.9061 (tptp) REVERT: C 101 THR cc_start: 0.8878 (m) cc_final: 0.8561 (p) REVERT: C 104 GLN cc_start: 0.8251 (mp-120) cc_final: 0.7987 (mp10) REVERT: D 40 TYR cc_start: 0.8545 (m-80) cc_final: 0.8298 (m-80) REVERT: D 47 GLN cc_start: 0.9200 (tm-30) cc_final: 0.8949 (tm-30) REVERT: D 80 LEU cc_start: 0.9637 (tp) cc_final: 0.9334 (tp) REVERT: D 88 THR cc_start: 0.9386 (m) cc_final: 0.9123 (p) REVERT: D 96 THR cc_start: 0.9572 (m) cc_final: 0.9266 (p) REVERT: D 105 GLU cc_start: 0.8017 (pm20) cc_final: 0.7203 (pm20) REVERT: D 108 LYS cc_start: 0.9354 (ptpp) cc_final: 0.9030 (pttp) REVERT: D 120 LYS cc_start: 0.9374 (tmmt) cc_final: 0.9117 (ttpp) REVERT: E 120 MET cc_start: 0.8445 (mmm) cc_final: 0.8079 (mmm) REVERT: E 122 LYS cc_start: 0.9203 (ptmt) cc_final: 0.8628 (ptmt) REVERT: E 125 GLN cc_start: 0.9374 (mt0) cc_final: 0.9120 (mp10) REVERT: F 88 TYR cc_start: 0.8312 (m-10) cc_final: 0.8070 (m-10) REVERT: F 92 ARG cc_start: 0.9282 (mtp-110) cc_final: 0.8918 (ttt-90) REVERT: G 38 ASN cc_start: 0.9266 (m-40) cc_final: 0.8546 (m-40) REVERT: G 57 TYR cc_start: 0.9121 (t80) cc_final: 0.8499 (t80) REVERT: G 61 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8463 (mt-10) REVERT: G 75 LYS cc_start: 0.9345 (mttm) cc_final: 0.8829 (mtpp) REVERT: H 70 PHE cc_start: 0.9421 (t80) cc_final: 0.9144 (t80) REVERT: H 86 ARG cc_start: 0.9287 (tpp80) cc_final: 0.8976 (tpp80) REVERT: K 38 LYS cc_start: 0.8700 (mmtm) cc_final: 0.8444 (mmtm) REVERT: K 54 GLN cc_start: 0.9272 (pp30) cc_final: 0.8968 (pp30) REVERT: K 66 ASN cc_start: 0.9199 (t0) cc_final: 0.8773 (m-40) REVERT: M 104 MET cc_start: 0.8882 (mmm) cc_final: 0.8630 (mmm) REVERT: N 29 ASP cc_start: 0.6486 (t70) cc_final: 0.5987 (p0) REVERT: N 38 MET cc_start: 0.3872 (ppp) cc_final: 0.3497 (ppp) REVERT: N 79 ASN cc_start: 0.6813 (p0) cc_final: 0.6400 (p0) REVERT: N 132 ASP cc_start: 0.8805 (m-30) cc_final: 0.8578 (p0) outliers start: 47 outliers final: 35 residues processed: 430 average time/residue: 0.3118 time to fit residues: 185.0126 Evaluate side-chains 430 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 395 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 67 ASN Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 106 optimal weight: 0.1980 chunk 111 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 124 optimal weight: 40.0000 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15420 Z= 0.286 Angle : 0.755 11.317 22096 Z= 0.410 Chirality : 0.042 0.355 2519 Planarity : 0.005 0.043 1788 Dihedral : 29.802 172.115 4403 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 20.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 5.15 % Allowed : 32.97 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.64 (0.26), residues: 1062 helix: 1.07 (0.20), residues: 664 sheet: 0.90 (1.23), residues: 24 loop : -0.70 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 93 HIS 0.005 0.001 HIS G 31 PHE 0.029 0.003 PHE A 67 TYR 0.019 0.002 TYR C 39 ARG 0.005 0.001 ARG M 112 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 401 time to evaluate : 1.241 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 94 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8743 (mm-30) REVERT: B 39 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8067 (mmt90) REVERT: B 49 LEU cc_start: 0.9026 (mm) cc_final: 0.8585 (tp) REVERT: B 52 GLU cc_start: 0.8468 (pm20) cc_final: 0.8175 (pm20) REVERT: B 53 GLU cc_start: 0.8422 (pm20) cc_final: 0.8094 (pm20) REVERT: B 88 TYR cc_start: 0.9035 (m-80) cc_final: 0.8546 (m-10) REVERT: C 38 ASN cc_start: 0.8716 (m-40) cc_final: 0.7956 (t0) REVERT: C 75 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8425 (mmmm) REVERT: C 95 LYS cc_start: 0.9299 (tttm) cc_final: 0.9057 (tptp) REVERT: C 101 THR cc_start: 0.8893 (m) cc_final: 0.8527 (p) REVERT: D 47 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8961 (tm-30) REVERT: D 68 ASP cc_start: 0.9172 (t0) cc_final: 0.8933 (t0) REVERT: D 80 LEU cc_start: 0.9659 (tp) cc_final: 0.9356 (tp) REVERT: D 88 THR cc_start: 0.9432 (m) cc_final: 0.9154 (p) REVERT: D 96 THR cc_start: 0.9578 (m) cc_final: 0.9277 (p) REVERT: D 105 GLU cc_start: 0.7921 (pm20) cc_final: 0.7320 (pm20) REVERT: D 108 LYS cc_start: 0.9413 (ptpp) cc_final: 0.9130 (pttp) REVERT: D 120 LYS cc_start: 0.9364 (tmmt) cc_final: 0.9094 (ttpp) REVERT: E 50 GLU cc_start: 0.9190 (pt0) cc_final: 0.8520 (pt0) REVERT: E 79 LYS cc_start: 0.9239 (tptp) cc_final: 0.9007 (tptp) REVERT: E 120 MET cc_start: 0.8375 (mmm) cc_final: 0.7997 (mmm) REVERT: E 122 LYS cc_start: 0.9259 (ptmt) cc_final: 0.8775 (ptmt) REVERT: E 125 GLN cc_start: 0.9372 (mt0) cc_final: 0.9129 (mp10) REVERT: F 44 LYS cc_start: 0.9028 (mmtp) cc_final: 0.8826 (mmtp) REVERT: F 92 ARG cc_start: 0.9286 (mtp-110) cc_final: 0.8892 (ttt-90) REVERT: F 95 ARG cc_start: 0.8719 (mtp85) cc_final: 0.8407 (mtt90) REVERT: G 38 ASN cc_start: 0.9271 (m-40) cc_final: 0.8441 (t0) REVERT: G 57 TYR cc_start: 0.9133 (t80) cc_final: 0.8348 (t80) REVERT: G 61 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8340 (mt-10) REVERT: G 75 LYS cc_start: 0.9282 (mttm) cc_final: 0.8752 (mtpp) REVERT: H 33 ARG cc_start: 0.8571 (tpp80) cc_final: 0.7882 (tpp80) REVERT: H 86 ARG cc_start: 0.9276 (tpp80) cc_final: 0.8903 (tpp80) REVERT: K 38 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8461 (mmtm) REVERT: K 66 ASN cc_start: 0.9222 (t0) cc_final: 0.8956 (t0) REVERT: M 104 MET cc_start: 0.8909 (mmm) cc_final: 0.8659 (mmm) REVERT: N 38 MET cc_start: 0.3917 (ppp) cc_final: 0.3536 (ppp) REVERT: N 79 ASN cc_start: 0.6817 (p0) cc_final: 0.6406 (p0) outliers start: 47 outliers final: 38 residues processed: 422 average time/residue: 0.3095 time to fit residues: 178.5526 Evaluate side-chains 438 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 399 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 110 optimal weight: 0.0470 overall best weight: 3.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15420 Z= 0.352 Angle : 0.799 11.103 22096 Z= 0.436 Chirality : 0.043 0.356 2519 Planarity : 0.005 0.044 1788 Dihedral : 29.934 171.603 4403 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 5.15 % Allowed : 33.84 % Favored : 61.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.54 (0.26), residues: 1062 helix: 1.00 (0.20), residues: 661 sheet: 0.83 (1.25), residues: 24 loop : -0.74 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 141 HIS 0.005 0.001 HIS F 75 PHE 0.035 0.003 PHE A 67 TYR 0.053 0.003 TYR F 88 ARG 0.008 0.001 ARG G 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 399 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8779 (mm-30) REVERT: B 49 LEU cc_start: 0.9077 (mm) cc_final: 0.8807 (mt) REVERT: B 52 GLU cc_start: 0.8523 (pm20) cc_final: 0.8248 (pm20) REVERT: B 53 GLU cc_start: 0.8424 (pm20) cc_final: 0.8060 (pm20) REVERT: B 79 LYS cc_start: 0.9286 (mtmt) cc_final: 0.9070 (mtmt) REVERT: B 88 TYR cc_start: 0.9071 (m-80) cc_final: 0.8603 (m-10) REVERT: C 38 ASN cc_start: 0.8807 (m-40) cc_final: 0.8020 (t0) REVERT: C 75 LYS cc_start: 0.8698 (mmmm) cc_final: 0.8467 (mmmm) REVERT: C 95 LYS cc_start: 0.9319 (tttm) cc_final: 0.9067 (tptp) REVERT: C 101 THR cc_start: 0.8913 (m) cc_final: 0.8554 (p) REVERT: D 47 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8968 (tm-30) REVERT: D 68 ASP cc_start: 0.9194 (t0) cc_final: 0.8950 (t0) REVERT: D 80 LEU cc_start: 0.9679 (tp) cc_final: 0.9398 (tp) REVERT: D 88 THR cc_start: 0.9517 (m) cc_final: 0.9201 (p) REVERT: D 96 THR cc_start: 0.9607 (m) cc_final: 0.9327 (p) REVERT: D 105 GLU cc_start: 0.8068 (pm20) cc_final: 0.7542 (pm20) REVERT: D 108 LYS cc_start: 0.9415 (ptpp) cc_final: 0.9151 (pttp) REVERT: D 120 LYS cc_start: 0.9360 (tmmt) cc_final: 0.9095 (ttpp) REVERT: E 120 MET cc_start: 0.8384 (mmm) cc_final: 0.7987 (mmm) REVERT: E 125 GLN cc_start: 0.9378 (mt0) cc_final: 0.9144 (mp10) REVERT: F 84 MET cc_start: 0.8605 (mmm) cc_final: 0.7618 (mmm) REVERT: F 88 TYR cc_start: 0.8907 (m-80) cc_final: 0.7672 (m-80) REVERT: F 95 ARG cc_start: 0.8775 (mtp85) cc_final: 0.8412 (mtt90) REVERT: G 38 ASN cc_start: 0.9315 (m-40) cc_final: 0.8468 (t0) REVERT: G 57 TYR cc_start: 0.9152 (t80) cc_final: 0.8487 (t80) REVERT: G 61 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8448 (mt-10) REVERT: G 75 LYS cc_start: 0.9303 (mttm) cc_final: 0.8837 (mtpp) REVERT: H 33 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8076 (tpp80) REVERT: H 70 PHE cc_start: 0.9426 (t80) cc_final: 0.9169 (t80) REVERT: H 86 ARG cc_start: 0.9267 (tpp80) cc_final: 0.8884 (tpp80) REVERT: K 38 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8517 (mmtm) REVERT: M 104 MET cc_start: 0.8937 (mmm) cc_final: 0.8702 (mmm) REVERT: N 38 MET cc_start: 0.3745 (ppp) cc_final: 0.3414 (ppp) outliers start: 47 outliers final: 39 residues processed: 423 average time/residue: 0.2999 time to fit residues: 174.8276 Evaluate side-chains 427 residues out of total 930 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 388 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 69 PHE Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 108 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.053059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.042613 restraints weight = 93137.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.043841 restraints weight = 43860.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.044685 restraints weight = 26501.326| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15420 Z= 0.228 Angle : 0.784 13.067 22096 Z= 0.417 Chirality : 0.042 0.366 2519 Planarity : 0.005 0.042 1788 Dihedral : 29.754 172.000 4403 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 3.40 % Allowed : 35.71 % Favored : 60.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.53 (0.26), residues: 1062 helix: 0.99 (0.20), residues: 660 sheet: 1.35 (1.24), residues: 23 loop : -0.76 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 33 HIS 0.006 0.001 HIS G 31 PHE 0.039 0.002 PHE A 67 TYR 0.039 0.002 TYR F 88 ARG 0.009 0.001 ARG M 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3596.77 seconds wall clock time: 64 minutes 57.32 seconds (3897.32 seconds total)