Starting phenix.real_space_refine on Mon Feb 19 03:56:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/02_2024/7e9c_31029_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/02_2024/7e9c_31029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/02_2024/7e9c_31029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/02_2024/7e9c_31029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/02_2024/7e9c_31029_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/02_2024/7e9c_31029_updated.pdb" } resolution = 3.5 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= 0.008 sd= 0.079 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 11439 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: 5 Type Number sf(0) Gaussians P 260 5.49 5 S 3 5.16 5 C 6945 2.51 5 N 2302 2.21 5 O 2828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "K GLU 182": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12338 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 781 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2652 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Chain: "J" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2678 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Chain: "K" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1204 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'AYA:plan-2': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 6.51, per 1000 atoms: 0.53 Number of scatterers: 12338 At special positions: 0 Unit cell: (116, 117, 111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 P 260 15.00 O 2828 8.00 N 2302 7.00 C 6945 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: 6.92 Conformation dependent library (CDL) restraints added in 1.4 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 3 sheets defined 54.6% alpha, 4.1% beta 116 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 5.80 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 54 through 75 removed outlier: 3.656A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 Processing helix chain 'C' and resid 18 through 22 removed outlier: 3.661A pdb=" N ALA C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 18 through 22' Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 47 through 74 removed outlier: 3.533A pdb=" N ASP C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.522A pdb=" N LYS C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 97' Processing helix chain 'D' and resid 41 through 51 removed outlier: 4.037A pdb=" N THR D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 87 removed outlier: 3.673A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 125 removed outlier: 3.853A pdb=" N ARG D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 removed outlier: 4.130A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.506A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.662A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.918A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 62 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.383A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 94 through 97 No H-bonds generated for 'chain 'G' and resid 94 through 97' Processing helix chain 'H' and resid 41 through 51 removed outlier: 3.881A pdb=" N THR H 51 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 86 Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 124 removed outlier: 4.152A pdb=" N ARG H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 198 removed outlier: 4.219A pdb=" N ALA K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 211 Processing sheet with id= A, first strand: chain 'K' and resid 14 through 16 Processing sheet with id= B, first strand: chain 'K' and resid 146 through 149 removed outlier: 4.059A pdb=" N ILE K 147 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL K 57 " --> pdb=" O ILE K 147 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL K 149 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N SER K 55 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP K 86 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU K 74 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU K 85 " --> pdb=" O LEU K 141 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 131 through 134 removed outlier: 6.938A pdb=" N THR K 172 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU K 134 " --> pdb=" O THR K 172 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ARG K 174 " --> pdb=" O LEU K 134 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 340 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 301 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 3.98 Time building geometry restraints manager: 7.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2508 1.33 - 1.45: 4019 1.45 - 1.57: 6024 1.57 - 1.69: 518 1.69 - 1.81: 5 Bond restraints: 13074 Sorted by residual: bond pdb=" N AYA K 2 " pdb=" CT AYA K 2 " ideal model delta sigma weight residual 1.340 1.387 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" N AYA K 2 " pdb=" CA AYA K 2 " ideal model delta sigma weight residual 1.458 1.437 0.021 1.90e-02 2.77e+03 1.23e+00 bond pdb=" CA ILE C 80 " pdb=" CB ILE C 80 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 9.91e-01 bond pdb=" CT AYA K 2 " pdb=" OT AYA K 2 " ideal model delta sigma weight residual 1.226 1.246 -0.020 2.00e-02 2.50e+03 9.76e-01 ... (remaining 13069 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.25: 1104 105.25 - 112.43: 7290 112.43 - 119.61: 3902 119.61 - 126.79: 5732 126.79 - 133.97: 756 Bond angle restraints: 18784 Sorted by residual: angle pdb=" C ALA K 204 " pdb=" N GLN K 205 " pdb=" CA GLN K 205 " ideal model delta sigma weight residual 120.31 114.85 5.46 1.52e+00 4.33e-01 1.29e+01 angle pdb=" CB ARG A 52 " pdb=" CG ARG A 52 " pdb=" CD ARG A 52 " ideal model delta sigma weight residual 111.30 119.52 -8.22 2.30e+00 1.89e-01 1.28e+01 angle pdb=" N GLN K 205 " pdb=" CA GLN K 205 " pdb=" CB GLN K 205 " ideal model delta sigma weight residual 110.28 115.34 -5.06 1.55e+00 4.16e-01 1.06e+01 angle pdb=" CB ARG A 53 " pdb=" CG ARG A 53 " pdb=" CD ARG A 53 " ideal model delta sigma weight residual 111.30 118.79 -7.49 2.30e+00 1.89e-01 1.06e+01 angle pdb=" N GLU K 206 " pdb=" CA GLU K 206 " pdb=" CB GLU K 206 " ideal model delta sigma weight residual 110.12 114.67 -4.55 1.47e+00 4.63e-01 9.56e+00 ... (remaining 18779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 5644 29.14 - 58.29: 1366 58.29 - 87.43: 144 87.43 - 116.57: 3 116.57 - 145.72: 2 Dihedral angle restraints: 7159 sinusoidal: 4551 harmonic: 2608 Sorted by residual: dihedral pdb=" C4' DC I 24 " pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sinusoidal sigma weight residual 220.00 74.28 145.72 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" C4' DG I 63 " pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " pdb=" P DC I 64 " ideal model delta sinusoidal sigma weight residual 220.00 75.24 144.76 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 7156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1878 0.047 - 0.094: 223 0.094 - 0.141: 59 0.141 - 0.189: 3 0.189 - 0.236: 1 Chirality restraints: 2164 Sorted by residual: chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU A 48 " pdb=" CB LEU A 48 " pdb=" CD1 LEU A 48 " pdb=" CD2 LEU A 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA GLN K 205 " pdb=" N GLN K 205 " pdb=" C GLN K 205 " pdb=" CB GLN K 205 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 2161 not shown) Planarity restraints: 1475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 136 " -0.005 2.00e-02 2.50e+03 1.17e-02 4.10e+00 pdb=" N9 DG J 136 " 0.004 2.00e-02 2.50e+03 pdb=" C8 DG J 136 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 136 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J 136 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG J 136 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG J 136 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG J 136 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG J 136 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG J 136 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG J 136 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 136 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO B 32 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 105 " -0.020 2.00e-02 2.50e+03 1.03e-02 2.63e+00 pdb=" N1 DT I 105 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT I 105 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 105 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 105 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 105 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 105 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 105 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 105 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 105 " 0.000 2.00e-02 2.50e+03 ... (remaining 1472 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1616 2.76 - 3.29: 11748 3.29 - 3.83: 23869 3.83 - 4.36: 25926 4.36 - 4.90: 38626 Nonbonded interactions: 101785 Sorted by model distance: nonbonded pdb=" OD1 ASN K 21 " pdb=" OH TYR K 40 " model vdw 2.221 2.440 nonbonded pdb=" O ILE E 62 " pdb=" NE2 GLN E 93 " model vdw 2.225 2.520 nonbonded pdb=" OG1 THR K 78 " pdb=" O ASN K 81 " model vdw 2.232 2.440 nonbonded pdb=" N4 DC I 64 " pdb=" N6 DA I 65 " model vdw 2.236 3.200 nonbonded pdb=" O ILE A 119 " pdb=" OG SER B 47 " model vdw 2.280 2.440 ... (remaining 101780 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 46 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 132)) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 116)) selection = (chain 'G' and (resid 16 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 116)) } ncs_group { reference = (chain 'D' and (resid 35 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 127)) selection = (chain 'H' and (resid 35 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 127)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.140 Construct map_model_manager: 0.010 Extract box with map and model: 2.160 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 38.790 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13074 Z= 0.169 Angle : 0.583 8.215 18784 Z= 0.349 Chirality : 0.035 0.236 2164 Planarity : 0.003 0.043 1475 Dihedral : 26.936 145.718 5471 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.28), residues: 875 helix: 1.26 (0.23), residues: 518 sheet: -0.56 (0.99), residues: 29 loop : -1.76 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 86 HIS 0.007 0.001 HIS G 113 PHE 0.025 0.001 PHE H 73 TYR 0.016 0.001 TYR D 45 ARG 0.019 0.001 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 GLN cc_start: 0.7910 (pm20) cc_final: 0.7513 (pm20) REVERT: B 83 SER cc_start: 0.8215 (t) cc_final: 0.7960 (t) REVERT: B 98 TYR cc_start: 0.7617 (m-10) cc_final: 0.7384 (m-10) REVERT: C 34 LEU cc_start: 0.8841 (tp) cc_final: 0.8631 (tp) REVERT: C 82 ARG cc_start: 0.8508 (tpt90) cc_final: 0.7864 (tpt90) REVERT: D 46 LYS cc_start: 0.8399 (mtpp) cc_final: 0.8013 (mtpt) REVERT: D 71 ASP cc_start: 0.8258 (t70) cc_final: 0.7830 (t0) REVERT: E 130 LEU cc_start: 0.8284 (tp) cc_final: 0.7943 (tp) REVERT: F 52 GLU cc_start: 0.7666 (tp30) cc_final: 0.7423 (mm-30) REVERT: G 37 ARG cc_start: 0.7496 (mmp80) cc_final: 0.6440 (mtm-85) REVERT: G 57 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7529 (tm-30) REVERT: G 65 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7389 (tm-30) REVERT: H 71 ASP cc_start: 0.7979 (t70) cc_final: 0.7486 (t0) REVERT: H 79 GLU cc_start: 0.8357 (tp30) cc_final: 0.7946 (tp30) REVERT: H 111 LYS cc_start: 0.8181 (tmmt) cc_final: 0.7913 (tmtt) REVERT: K 13 ILE cc_start: 0.4961 (mt) cc_final: 0.4726 (pt) REVERT: K 52 ARG cc_start: 0.7312 (ttp-170) cc_final: 0.6795 (ttp-170) REVERT: K 75 ARG cc_start: 0.7257 (ttp-170) cc_final: 0.6642 (mtm180) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2899 time to fit residues: 78.9207 Evaluate side-chains 160 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.0050 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 20.0000 overall best weight: 1.5798 ------------------------------------------------------------------------------- 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 113 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 115 ASN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13074 Z= 0.198 Angle : 0.547 6.383 18784 Z= 0.321 Chirality : 0.035 0.194 2164 Planarity : 0.005 0.048 1475 Dihedral : 30.368 147.125 3811 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.04 % Allowed : 15.08 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.28), residues: 875 helix: 1.29 (0.23), residues: 521 sheet: -0.54 (0.90), residues: 33 loop : -1.75 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 11 HIS 0.008 0.001 HIS F 75 PHE 0.011 0.002 PHE A 54 TYR 0.016 0.002 TYR D 45 ARG 0.006 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 189 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8368 (tm-30) REVERT: B 27 GLN cc_start: 0.7991 (pm20) cc_final: 0.7569 (pm20) REVERT: B 52 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8146 (tm-30) REVERT: B 83 SER cc_start: 0.8596 (t) cc_final: 0.8371 (t) REVERT: B 98 TYR cc_start: 0.8564 (m-10) cc_final: 0.8108 (m-10) REVERT: C 34 LEU cc_start: 0.8968 (tp) cc_final: 0.8690 (tp) REVERT: C 82 ARG cc_start: 0.8582 (tpt90) cc_final: 0.7714 (tpt90) REVERT: C 90 ASN cc_start: 0.8986 (m-40) cc_final: 0.8721 (m-40) REVERT: D 71 ASP cc_start: 0.8250 (t70) cc_final: 0.7792 (t0) REVERT: E 130 LEU cc_start: 0.8765 (tp) cc_final: 0.8560 (tp) REVERT: F 52 GLU cc_start: 0.7588 (tp30) cc_final: 0.7164 (tp30) REVERT: G 37 ARG cc_start: 0.7602 (mmp80) cc_final: 0.7001 (mtm-85) REVERT: G 57 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7581 (tm-30) REVERT: G 65 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7415 (tm-30) REVERT: H 40 TYR cc_start: 0.7684 (m-80) cc_final: 0.7317 (m-80) REVERT: H 71 ASP cc_start: 0.8081 (t70) cc_final: 0.7355 (t0) REVERT: H 79 GLU cc_start: 0.8359 (tp30) cc_final: 0.7962 (tp30) REVERT: K 52 ARG cc_start: 0.7478 (ttp-170) cc_final: 0.6835 (ttp-170) REVERT: K 75 ARG cc_start: 0.7335 (ttp-170) cc_final: 0.7022 (ttm170) REVERT: K 205 GLN cc_start: 0.8429 (pm20) cc_final: 0.8179 (pm20) outliers start: 22 outliers final: 13 residues processed: 202 average time/residue: 0.3038 time to fit residues: 81.8707 Evaluate side-chains 187 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 174 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 65 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.0670 chunk 111 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13074 Z= 0.160 Angle : 0.520 6.280 18784 Z= 0.305 Chirality : 0.034 0.151 2164 Planarity : 0.004 0.040 1475 Dihedral : 30.275 146.193 3811 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.73 % Allowed : 19.23 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 875 helix: 1.28 (0.23), residues: 525 sheet: -0.47 (0.83), residues: 33 loop : -1.65 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 11 HIS 0.010 0.001 HIS F 75 PHE 0.010 0.001 PHE K 144 TYR 0.025 0.001 TYR H 86 ARG 0.005 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8135 (ptt-90) cc_final: 0.7772 (ptt90) REVERT: A 50 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8375 (tm-30) REVERT: A 52 ARG cc_start: 0.8269 (mpp-170) cc_final: 0.7866 (mtm180) REVERT: A 128 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7295 (mmm-85) REVERT: B 27 GLN cc_start: 0.8011 (pm20) cc_final: 0.7549 (pm20) REVERT: B 52 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8105 (tm-30) REVERT: B 83 SER cc_start: 0.8708 (t) cc_final: 0.8453 (t) REVERT: C 34 LEU cc_start: 0.8892 (tp) cc_final: 0.8655 (tp) REVERT: C 82 ARG cc_start: 0.8513 (tpt90) cc_final: 0.7774 (tpt90) REVERT: C 90 ASN cc_start: 0.8968 (m-40) cc_final: 0.8673 (m110) REVERT: D 46 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8488 (mtmt) REVERT: D 71 ASP cc_start: 0.8262 (t70) cc_final: 0.7805 (t0) REVERT: E 95 SER cc_start: 0.8631 (t) cc_final: 0.8072 (p) REVERT: F 74 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8767 (mm-30) REVERT: G 37 ARG cc_start: 0.7689 (mmp80) cc_final: 0.7068 (mtm180) REVERT: G 57 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7484 (tm-30) REVERT: G 65 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7487 (tm-30) REVERT: H 79 GLU cc_start: 0.8390 (tp30) cc_final: 0.8013 (tp30) REVERT: K 52 ARG cc_start: 0.7436 (ttp-170) cc_final: 0.6864 (ttp-170) REVERT: K 75 ARG cc_start: 0.7322 (ttp-170) cc_final: 0.7027 (mtm180) REVERT: K 205 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.8097 (pm20) outliers start: 27 outliers final: 17 residues processed: 200 average time/residue: 0.3219 time to fit residues: 84.5819 Evaluate side-chains 188 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain K residue 43 ARG Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 50.0000 chunk 109 optimal weight: 10.0000 chunk 97 optimal weight: 30.0000 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 13074 Z= 0.449 Angle : 0.746 13.135 18784 Z= 0.423 Chirality : 0.043 0.199 2164 Planarity : 0.006 0.055 1475 Dihedral : 31.571 150.148 3811 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 6.64 % Allowed : 20.89 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.26), residues: 875 helix: 0.32 (0.22), residues: 530 sheet: -0.33 (0.81), residues: 31 loop : -2.05 (0.30), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 86 HIS 0.010 0.002 HIS F 75 PHE 0.021 0.003 PHE F 100 TYR 0.034 0.003 TYR D 43 ARG 0.009 0.001 ARG E 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 226 time to evaluate : 0.990 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: A 46 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.6958 (p) REVERT: A 50 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8161 (tm-30) REVERT: A 54 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8177 (m-10) REVERT: B 39 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8158 (mmt-90) REVERT: B 88 TYR cc_start: 0.8702 (m-10) cc_final: 0.8465 (m-10) REVERT: C 39 ASN cc_start: 0.7784 (t0) cc_final: 0.7496 (t0) REVERT: C 40 TYR cc_start: 0.7990 (m-80) cc_final: 0.7655 (m-80) REVERT: C 57 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7945 (tm-30) REVERT: C 82 ARG cc_start: 0.8878 (tpt90) cc_final: 0.8100 (tpt90) REVERT: D 116 GLU cc_start: 0.8278 (tp30) cc_final: 0.7304 (tm-30) REVERT: E 79 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7144 (ptmm) REVERT: F 44 LYS cc_start: 0.8067 (mttt) cc_final: 0.7819 (mttp) REVERT: F 74 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8591 (mm-30) REVERT: F 84 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8064 (tp) REVERT: G 40 TYR cc_start: 0.8633 (m-10) cc_final: 0.8212 (m-80) REVERT: G 57 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7546 (tm-30) REVERT: G 65 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7552 (tm-30) REVERT: G 91 ASP cc_start: 0.7336 (t0) cc_final: 0.7086 (t0) REVERT: H 62 MET cc_start: 0.8679 (tpp) cc_final: 0.8430 (tpt) REVERT: H 122 THR cc_start: 0.9134 (m) cc_final: 0.8843 (p) REVERT: K 52 ARG cc_start: 0.7610 (ttp-170) cc_final: 0.7075 (ttp-170) REVERT: K 206 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7356 (mp0) outliers start: 48 outliers final: 24 residues processed: 248 average time/residue: 0.3139 time to fit residues: 102.9654 Evaluate side-chains 217 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 205 GLN Chi-restraints excluded: chain K residue 206 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN E 93 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13074 Z= 0.294 Angle : 0.621 8.604 18784 Z= 0.361 Chirality : 0.038 0.168 2164 Planarity : 0.005 0.054 1475 Dihedral : 31.250 148.412 3811 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.26 % Allowed : 27.11 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.27), residues: 875 helix: 0.81 (0.22), residues: 530 sheet: -0.39 (0.90), residues: 29 loop : -2.03 (0.30), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 11 HIS 0.008 0.001 HIS F 75 PHE 0.017 0.002 PHE F 100 TYR 0.016 0.002 TYR D 86 ARG 0.009 0.001 ARG H 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 214 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7518 (p) REVERT: A 50 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8245 (tm-30) REVERT: B 39 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8261 (mmt-90) REVERT: B 44 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8624 (mmmm) REVERT: B 53 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8180 (tm-30) REVERT: C 39 ASN cc_start: 0.7827 (OUTLIER) cc_final: 0.7545 (t0) REVERT: C 82 ARG cc_start: 0.8872 (tpt90) cc_final: 0.7967 (tpt90) REVERT: D 116 GLU cc_start: 0.8151 (tp30) cc_final: 0.7262 (tm-30) REVERT: E 52 ARG cc_start: 0.9079 (ptp90) cc_final: 0.8752 (mtm-85) REVERT: E 94 GLU cc_start: 0.8361 (tp30) cc_final: 0.8160 (tp30) REVERT: E 95 SER cc_start: 0.8578 (t) cc_final: 0.7930 (p) REVERT: G 40 TYR cc_start: 0.8830 (m-10) cc_final: 0.8545 (m-80) REVERT: G 57 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7524 (tm-30) REVERT: G 65 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7490 (tm-30) REVERT: G 91 ASP cc_start: 0.7247 (t0) cc_final: 0.6833 (t0) REVERT: G 93 GLU cc_start: 0.6523 (pm20) cc_final: 0.6306 (pm20) REVERT: H 62 MET cc_start: 0.8657 (tpp) cc_final: 0.8294 (tpt) REVERT: H 122 THR cc_start: 0.9153 (m) cc_final: 0.8860 (p) REVERT: K 52 ARG cc_start: 0.7538 (ttp-170) cc_final: 0.6991 (ttp-170) outliers start: 38 outliers final: 24 residues processed: 236 average time/residue: 0.2962 time to fit residues: 93.1366 Evaluate side-chains 225 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 39 ASN Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 20.0000 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13074 Z= 0.253 Angle : 0.597 8.229 18784 Z= 0.349 Chirality : 0.037 0.219 2164 Planarity : 0.005 0.043 1475 Dihedral : 31.141 147.572 3811 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.26 % Allowed : 26.83 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.28), residues: 875 helix: 0.99 (0.23), residues: 535 sheet: -0.31 (0.92), residues: 32 loop : -2.00 (0.31), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 11 HIS 0.005 0.001 HIS C 32 PHE 0.025 0.002 PHE F 100 TYR 0.038 0.002 TYR D 86 ARG 0.008 0.001 ARG H 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 212 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 39 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8276 (mmt-90) REVERT: B 53 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 33 ARG cc_start: 0.8180 (ptm-80) cc_final: 0.7303 (ptm-80) REVERT: C 82 ARG cc_start: 0.8853 (tpt90) cc_final: 0.7948 (tpt90) REVERT: C 93 GLU cc_start: 0.7951 (pm20) cc_final: 0.7742 (pm20) REVERT: F 77 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8847 (mmtm) REVERT: G 40 TYR cc_start: 0.8864 (m-10) cc_final: 0.8604 (m-80) REVERT: G 57 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7537 (tm-30) REVERT: G 65 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7405 (tm-30) REVERT: G 91 ASP cc_start: 0.7301 (t0) cc_final: 0.6766 (t0) REVERT: G 93 GLU cc_start: 0.6603 (pm20) cc_final: 0.6341 (pm20) REVERT: H 36 ARG cc_start: 0.7736 (mmm160) cc_final: 0.7158 (mmm160) REVERT: H 62 MET cc_start: 0.8667 (tpp) cc_final: 0.8288 (tpt) REVERT: H 122 THR cc_start: 0.9132 (m) cc_final: 0.8837 (p) REVERT: K 52 ARG cc_start: 0.7579 (ttp-170) cc_final: 0.7040 (ttp-170) REVERT: K 86 TRP cc_start: 0.6356 (m-90) cc_final: 0.5762 (m-90) outliers start: 38 outliers final: 31 residues processed: 231 average time/residue: 0.3065 time to fit residues: 94.8414 Evaluate side-chains 228 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 196 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 39 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.2980 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13074 Z= 0.174 Angle : 0.565 6.865 18784 Z= 0.330 Chirality : 0.035 0.174 2164 Planarity : 0.004 0.050 1475 Dihedral : 30.788 147.277 3811 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.73 % Allowed : 29.32 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.28), residues: 875 helix: 1.40 (0.23), residues: 520 sheet: -0.03 (0.94), residues: 32 loop : -1.91 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 11 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE E 67 TYR 0.029 0.002 TYR D 86 ARG 0.007 0.001 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 215 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8309 (tm-30) REVERT: C 33 ARG cc_start: 0.8028 (ptm-80) cc_final: 0.7350 (ptm-80) REVERT: C 39 ASN cc_start: 0.7636 (t0) cc_final: 0.7403 (t0) REVERT: C 82 ARG cc_start: 0.8729 (tpt90) cc_final: 0.7929 (tpt90) REVERT: C 86 LEU cc_start: 0.9114 (tp) cc_final: 0.8770 (tp) REVERT: C 93 GLU cc_start: 0.7954 (pm20) cc_final: 0.7720 (pm20) REVERT: F 52 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7326 (tm-30) REVERT: F 74 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8569 (mm-30) REVERT: G 33 ARG cc_start: 0.7508 (tmm-80) cc_final: 0.6985 (tmm-80) REVERT: G 57 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7582 (tm-30) REVERT: G 65 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7428 (tm-30) REVERT: G 91 ASP cc_start: 0.7355 (t0) cc_final: 0.6942 (t0) REVERT: G 93 GLU cc_start: 0.6674 (pm20) cc_final: 0.6426 (pm20) REVERT: H 36 ARG cc_start: 0.7748 (mmm160) cc_final: 0.7256 (mmm160) REVERT: H 49 LYS cc_start: 0.9069 (mmtp) cc_final: 0.8840 (mmtp) REVERT: H 122 THR cc_start: 0.9119 (m) cc_final: 0.8865 (p) REVERT: K 52 ARG cc_start: 0.7507 (ttp-170) cc_final: 0.6949 (ttp-170) outliers start: 27 outliers final: 19 residues processed: 229 average time/residue: 0.2868 time to fit residues: 88.8644 Evaluate side-chains 222 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 203 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 95 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13074 Z= 0.182 Angle : 0.573 8.505 18784 Z= 0.329 Chirality : 0.035 0.162 2164 Planarity : 0.004 0.049 1475 Dihedral : 30.755 147.436 3811 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.46 % Allowed : 30.43 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.29), residues: 875 helix: 1.37 (0.23), residues: 519 sheet: -0.25 (0.90), residues: 32 loop : -1.80 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 86 HIS 0.007 0.001 HIS F 75 PHE 0.009 0.001 PHE F 100 TYR 0.030 0.002 TYR H 86 ARG 0.007 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8276 (tm-30) REVERT: B 53 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8307 (tm-30) REVERT: B 74 GLU cc_start: 0.8854 (tt0) cc_final: 0.8625 (tp30) REVERT: C 33 ARG cc_start: 0.8086 (ptm-80) cc_final: 0.7391 (ptm-80) REVERT: C 39 ASN cc_start: 0.7810 (t0) cc_final: 0.7585 (t0) REVERT: C 82 ARG cc_start: 0.8733 (tpt90) cc_final: 0.8100 (tpt90) REVERT: C 93 GLU cc_start: 0.7983 (pm20) cc_final: 0.7737 (pm20) REVERT: D 116 GLU cc_start: 0.8065 (tp30) cc_final: 0.7275 (tm-30) REVERT: F 74 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8473 (mm-30) REVERT: G 33 ARG cc_start: 0.7549 (tmm-80) cc_final: 0.7035 (tmm-80) REVERT: G 57 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7507 (tm-30) REVERT: G 65 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7372 (tm-30) REVERT: G 91 ASP cc_start: 0.7339 (t0) cc_final: 0.6922 (t0) REVERT: G 93 GLU cc_start: 0.6610 (pm20) cc_final: 0.6301 (pm20) REVERT: H 36 ARG cc_start: 0.7793 (mmm160) cc_final: 0.7425 (mmm160) REVERT: H 122 THR cc_start: 0.9122 (m) cc_final: 0.8883 (p) REVERT: K 52 ARG cc_start: 0.7513 (ttp-170) cc_final: 0.7044 (ttp-170) outliers start: 25 outliers final: 22 residues processed: 220 average time/residue: 0.2934 time to fit residues: 87.4210 Evaluate side-chains 217 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 205 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 40.0000 chunk 65 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13074 Z= 0.218 Angle : 0.582 7.406 18784 Z= 0.334 Chirality : 0.036 0.179 2164 Planarity : 0.004 0.045 1475 Dihedral : 30.791 147.653 3811 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.15 % Allowed : 30.15 % Favored : 65.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.29), residues: 875 helix: 1.26 (0.23), residues: 532 sheet: -0.52 (0.92), residues: 31 loop : -1.75 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 86 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE K 144 TYR 0.026 0.002 TYR B 88 ARG 0.007 0.001 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 203 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8269 (tm-30) REVERT: B 53 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8194 (tm-30) REVERT: C 33 ARG cc_start: 0.8133 (ptm-80) cc_final: 0.7808 (ptm-80) REVERT: C 39 ASN cc_start: 0.7829 (t0) cc_final: 0.7573 (t0) REVERT: C 82 ARG cc_start: 0.8815 (tpt90) cc_final: 0.7687 (tpt90) REVERT: C 86 LEU cc_start: 0.9095 (tp) cc_final: 0.8788 (tp) REVERT: C 93 GLU cc_start: 0.7965 (pm20) cc_final: 0.7552 (pm20) REVERT: D 116 GLU cc_start: 0.8041 (tp30) cc_final: 0.7253 (tm-30) REVERT: F 74 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8451 (mm-30) REVERT: F 77 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8737 (mmtt) REVERT: G 33 ARG cc_start: 0.7565 (tmm-80) cc_final: 0.6998 (tmm-80) REVERT: G 40 TYR cc_start: 0.8424 (m-80) cc_final: 0.8079 (m-10) REVERT: G 57 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7464 (tm-30) REVERT: G 65 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7373 (tm-30) REVERT: G 91 ASP cc_start: 0.7298 (t0) cc_final: 0.6845 (t0) REVERT: G 93 GLU cc_start: 0.6663 (pm20) cc_final: 0.6346 (pm20) REVERT: H 36 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7509 (mmm160) REVERT: H 122 THR cc_start: 0.9124 (m) cc_final: 0.8857 (p) REVERT: K 43 ARG cc_start: 0.8252 (ptp-170) cc_final: 0.7759 (ptp-110) REVERT: K 52 ARG cc_start: 0.7522 (ttp-170) cc_final: 0.7038 (ttp-170) outliers start: 30 outliers final: 26 residues processed: 221 average time/residue: 0.2962 time to fit residues: 88.1230 Evaluate side-chains 221 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 50.0000 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 71 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13074 Z= 0.247 Angle : 0.624 11.279 18784 Z= 0.355 Chirality : 0.036 0.189 2164 Planarity : 0.004 0.044 1475 Dihedral : 30.903 148.242 3811 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.73 % Allowed : 30.98 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.29), residues: 875 helix: 1.16 (0.23), residues: 532 sheet: -0.20 (1.00), residues: 31 loop : -1.84 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 86 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE F 100 TYR 0.023 0.002 TYR D 86 ARG 0.007 0.001 ARG A 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 205 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8275 (tm-30) REVERT: B 53 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8187 (tm-30) REVERT: C 33 ARG cc_start: 0.8174 (ptm-80) cc_final: 0.7883 (ptm-80) REVERT: C 82 ARG cc_start: 0.8852 (tpt90) cc_final: 0.7897 (tpt90) REVERT: C 93 GLU cc_start: 0.7927 (pm20) cc_final: 0.7460 (pm20) REVERT: D 116 GLU cc_start: 0.8054 (tp30) cc_final: 0.7253 (tm-30) REVERT: G 33 ARG cc_start: 0.7581 (tmm-80) cc_final: 0.7040 (tmm-80) REVERT: G 40 TYR cc_start: 0.8447 (m-80) cc_final: 0.8150 (m-10) REVERT: G 57 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7466 (tm-30) REVERT: G 65 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7398 (tm-30) REVERT: G 91 ASP cc_start: 0.7307 (t0) cc_final: 0.6859 (t0) REVERT: G 93 GLU cc_start: 0.6733 (pm20) cc_final: 0.6418 (pm20) REVERT: H 36 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7603 (mmm160) REVERT: H 122 THR cc_start: 0.9134 (m) cc_final: 0.8874 (p) REVERT: K 43 ARG cc_start: 0.8307 (ptp-170) cc_final: 0.7873 (ptp-110) REVERT: K 52 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7034 (ttp-170) REVERT: K 55 SER cc_start: 0.6209 (p) cc_final: 0.5843 (p) outliers start: 27 outliers final: 26 residues processed: 220 average time/residue: 0.3202 time to fit residues: 94.8701 Evaluate side-chains 221 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 195 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 152 VAL Chi-restraints excluded: chain K residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.0470 chunk 92 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.119702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.081509 restraints weight = 35645.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.084010 restraints weight = 18274.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085532 restraints weight = 12765.323| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13074 Z= 0.191 Angle : 0.599 10.843 18784 Z= 0.341 Chirality : 0.036 0.175 2164 Planarity : 0.004 0.051 1475 Dihedral : 30.762 148.278 3811 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.60 % Allowed : 31.12 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 875 helix: 1.26 (0.23), residues: 528 sheet: -0.38 (0.95), residues: 31 loop : -1.76 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 11 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE F 100 TYR 0.020 0.002 TYR B 88 ARG 0.006 0.001 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2455.96 seconds wall clock time: 45 minutes 26.20 seconds (2726.20 seconds total)