Starting phenix.real_space_refine on Sat Mar 16 13:31:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/03_2024/7e8d_31015_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/03_2024/7e8d_31015.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/03_2024/7e8d_31015_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/03_2024/7e8d_31015_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/03_2024/7e8d_31015_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/03_2024/7e8d_31015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/03_2024/7e8d_31015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/03_2024/7e8d_31015_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/03_2024/7e8d_31015_updated.pdb" } resolution = 2.8 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 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 3 6.06 5 P 344 5.49 5 S 36 5.16 5 C 8248 2.51 5 N 2766 2.21 5 O 3455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 133": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D GLU 113": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "K TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1012": "OE1" <-> "OE2" Residue "K ARG 1060": "NH1" <-> "NH2" Residue "K GLU 1064": "OE1" <-> "OE2" Residue "K GLU 1095": "OE1" <-> "OE2" Residue "K TYR 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1138": "NH1" <-> "NH2" Residue "K ARG 1160": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14852 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" 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: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 833 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 845 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 3504 Classifications: {'DNA': 172} Link IDs: {'rna3p': 171} Chain: "J" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 3548 Classifications: {'DNA': 172} Link IDs: {'rna3p': 171} Chain: "K" Number of atoms: 1744 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 222, 1739 Unusual residues: {' ZN': 3} Classifications: {'peptide': 219, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 204, None: 4} Not linked: pdbres="GLY K1203 " pdbres=" ZN K1301 " Not linked: pdbres=" ZN K1301 " pdbres=" ZN K1302 " Not linked: pdbres=" ZN K1302 " pdbres=" ZN K1303 " Not linked: pdbres=" ZN K1303 " pdbres="SFG K1304 " Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 222, 1739 Unusual residues: {' ZN': 3} Classifications: {'peptide': 219, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 204, None: 4} Not linked: pdbres="GLY K1203 " pdbres=" ZN K1301 " Not linked: pdbres=" ZN K1301 " pdbres=" ZN K1302 " Not linked: pdbres=" ZN K1302 " pdbres=" ZN K1303 " Not linked: pdbres=" ZN K1303 " pdbres="SFG K1304 " Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1772 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14390 SG CYS K1144 42.120 51.544 56.429 1.00114.62 S ATOM 14749 SG CYS K1191 42.466 50.214 52.961 1.00118.29 S ATOM 14760 SG CYS K1193 45.111 49.280 55.494 1.00118.84 S ATOM 14789 SG CYS K1198 41.809 47.729 55.847 1.00118.80 S ATOM 13361 SG CYS K1016 58.936 85.318 59.757 1.00 85.99 S ATOM 13375 SG CYS K1018 60.570 83.394 62.687 1.00 92.56 S ATOM 13436 SG CYS K1026 61.418 82.746 59.075 1.00 89.86 S ATOM 13480 SG CYS K1032 58.078 81.605 60.455 1.00 81.97 S ATOM 13436 SG CYS K1026 61.418 82.746 59.075 1.00 89.86 S ATOM 13557 SG CYS K1041 58.478 83.005 56.585 1.00 88.34 S ATOM 13596 SG CYS K1046 61.568 85.205 56.581 1.00 92.31 S ATOM 13638 SG CYS K1052 61.850 81.503 55.483 1.00 93.46 S Time building chain proxies: 8.48, per 1000 atoms: 0.57 Number of scatterers: 14852 At special positions: 0 Unit cell: (87.15, 168.49, 142.76, 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 3 29.99 S 36 16.00 P 344 15.00 O 3455 8.00 N 2766 7.00 C 8248 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: 7.33 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K1301 " pdb="ZN ZN K1301 " - pdb=" SG CYS K1193 " pdb="ZN ZN K1301 " - pdb=" SG CYS K1191 " pdb="ZN ZN K1301 " - pdb=" SG CYS K1198 " pdb="ZN ZN K1301 " - pdb=" SG CYS K1144 " pdb=" ZN K1302 " pdb="ZN ZN K1302 " - pdb=" SG CYS K1026 " pdb="ZN ZN K1302 " - pdb=" SG CYS K1016 " pdb="ZN ZN K1302 " - pdb=" SG CYS K1018 " pdb="ZN ZN K1302 " - pdb=" SG CYS K1032 " pdb=" ZN K1303 " pdb="ZN ZN K1303 " - pdb=" SG CYS K1026 " pdb="ZN ZN K1303 " - pdb=" SG CYS K1046 " pdb="ZN ZN K1303 " - pdb=" SG CYS K1041 " pdb="ZN ZN K1303 " - pdb=" SG CYS K1052 " Number of angles added : 18 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 3 sheets defined 51.6% alpha, 3.6% beta 172 base pairs and 318 stacking pairs defined. Time for finding SS restraints: 8.25 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.243A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 84 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 105 through 122 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.106A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.368A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 121 Processing helix chain 'K' and resid 1010 through 1012 No H-bonds generated for 'chain 'K' and resid 1010 through 1012' Processing helix chain 'K' and resid 1099 through 1112 Processing helix chain 'K' and resid 1136 through 1139 Processing sheet with id= A, first strand: chain 'K' and resid 1065 through 1069 Processing sheet with id= B, first strand: chain 'K' and resid 1095 through 1097 removed outlier: 6.311A pdb=" N ILE K1128 " --> pdb=" O THR K1121 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N THR K1121 " --> pdb=" O ILE K1128 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 1148 through 1155 removed outlier: 4.613A pdb=" N VAL K1161 " --> pdb=" O TYR K1092 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA K1165 " --> pdb=" O PHE K1088 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE K1088 " --> pdb=" O ALA K1165 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 444 hydrogen bonds 884 hydrogen bond angles 0 basepair planarities 172 basepair parallelities 318 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 7.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2521 1.33 - 1.45: 5349 1.45 - 1.57: 7222 1.57 - 1.69: 686 1.69 - 1.81: 52 Bond restraints: 15830 Sorted by residual: bond pdb=" C1' SFG K1304 " pdb=" C2' SFG K1304 " ideal model delta sigma weight residual 1.292 1.510 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C1' SFG K1304 " pdb=" O4' SFG K1304 " ideal model delta sigma weight residual 1.609 1.417 0.192 2.00e-02 2.50e+03 9.17e+01 bond pdb=" C4 SFG K1304 " pdb=" C5 SFG K1304 " ideal model delta sigma weight residual 1.340 1.465 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C4' SFG K1304 " pdb=" O4' SFG K1304 " ideal model delta sigma weight residual 1.301 1.424 -0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" C6 SFG K1304 " pdb=" N6 SFG K1304 " ideal model delta sigma weight residual 1.461 1.351 0.110 2.00e-02 2.50e+03 3.04e+01 ... (remaining 15825 not shown) Histogram of bond angle deviations from ideal: 97.54 - 105.21: 1562 105.21 - 112.88: 9126 112.88 - 120.55: 6986 120.55 - 128.22: 4746 128.22 - 135.89: 441 Bond angle restraints: 22861 Sorted by residual: angle pdb=" N1 SFG K1304 " pdb=" C6 SFG K1304 " pdb=" N6 SFG K1304 " ideal model delta sigma weight residual 102.77 121.18 -18.41 3.00e+00 1.11e-01 3.77e+01 angle pdb=" C5 SFG K1304 " pdb=" C6 SFG K1304 " pdb=" N6 SFG K1304 " ideal model delta sigma weight residual 136.73 121.23 15.50 3.00e+00 1.11e-01 2.67e+01 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 119.72 -6.54 2.37e+00 1.78e-01 7.61e+00 angle pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " pdb=" C1' DG I 21 " ideal model delta sigma weight residual 101.60 97.54 4.06 1.50e+00 4.44e-01 7.34e+00 angle pdb=" C4' DA I 41 " pdb=" C3' DA I 41 " pdb=" C2' DA I 41 " ideal model delta sigma weight residual 102.40 106.11 -3.71 1.50e+00 4.44e-01 6.10e+00 ... (remaining 22856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 6839 35.23 - 70.46: 1744 70.46 - 105.68: 20 105.68 - 140.91: 1 140.91 - 176.14: 7 Dihedral angle restraints: 8611 sinusoidal: 5765 harmonic: 2846 Sorted by residual: dihedral pdb=" CA LYS C 15 " pdb=" C LYS C 15 " pdb=" N THR C 16 " pdb=" CA THR C 16 " ideal model delta harmonic sigma weight residual 180.00 148.55 31.45 0 5.00e+00 4.00e-02 3.96e+01 dihedral pdb=" CA ASN K1186 " pdb=" C ASN K1186 " pdb=" N GLU K1187 " pdb=" CA GLU K1187 " ideal model delta harmonic sigma weight residual -180.00 -159.13 -20.87 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASN K1180 " pdb=" C ASN K1180 " pdb=" N LEU K1181 " pdb=" CA LEU K1181 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1914 0.050 - 0.101: 575 0.101 - 0.151: 87 0.151 - 0.201: 3 0.201 - 0.251: 1 Chirality restraints: 2580 Sorted by residual: chirality pdb=" C2' SFG K1304 " pdb=" C1' SFG K1304 " pdb=" C3' SFG K1304 " pdb=" O2' SFG K1304 " both_signs ideal model delta sigma weight residual False -2.39 -2.64 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA THR C 16 " pdb=" N THR C 16 " pdb=" C THR C 16 " pdb=" CB THR C 16 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA SFG K1304 " pdb=" N SFG K1304 " pdb=" C SFG K1304 " pdb=" CB SFG K1304 " both_signs ideal model delta sigma weight residual False 2.63 2.45 0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 2577 not shown) Planarity restraints: 1709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 20 " -0.030 2.00e-02 2.50e+03 1.34e-02 4.90e+00 pdb=" N9 DA I 20 " 0.031 2.00e-02 2.50e+03 pdb=" C8 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 20 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 20 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 20 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 20 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I 20 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 20 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 20 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 20 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 100 " -0.024 2.00e-02 2.50e+03 1.12e-02 3.47e+00 pdb=" N9 DA J 100 " 0.027 2.00e-02 2.50e+03 pdb=" C8 DA J 100 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA J 100 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA J 100 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA J 100 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA J 100 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA J 100 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA J 100 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA J 100 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DA J 100 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 48 " 0.024 2.00e-02 2.50e+03 1.15e-02 3.32e+00 pdb=" N1 DT I 48 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DT I 48 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 48 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 48 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 48 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 48 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DT I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 48 " -0.002 2.00e-02 2.50e+03 ... (remaining 1706 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 288 2.64 - 3.20: 12378 3.20 - 3.77: 27719 3.77 - 4.33: 38297 4.33 - 4.90: 53372 Nonbonded interactions: 132054 Sorted by model distance: nonbonded pdb=" NH2 ARG C 11 " pdb=" O2 DT I 117 " model vdw 2.070 2.520 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.161 2.440 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.234 2.440 nonbonded pdb=" OE2 GLU K1101 " pdb=" NE ARG K1105 " model vdw 2.251 2.520 ... (remaining 132049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 11 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 98 or (resid 99 and (name N or nam \ e CA or name C or name O or name CB )) or resid 100 through 119)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 31 through 124) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 5.670 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 51.920 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.110 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:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.011 0.218 15830 Z= 0.627 Angle : 0.730 18.409 22861 Z= 0.429 Chirality : 0.046 0.251 2580 Planarity : 0.004 0.044 1709 Dihedral : 28.754 176.140 6779 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 1.95 % Allowed : 6.20 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.71 (0.25), residues: 966 helix: 0.52 (0.21), residues: 561 sheet: -2.44 (0.68), residues: 38 loop : -1.79 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP K1075 HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE K1088 TYR 0.013 0.002 TYR A 54 ARG 0.004 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 188 time to evaluate : 1.542 Fit side-chains revert: symmetry clash REVERT: C 15 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8247 (ttpp) REVERT: D 71 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7467 (mt-10) REVERT: D 113 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: H 34 LYS cc_start: 0.8575 (mptt) cc_final: 0.8279 (mmtm) REVERT: K 1126 ARG cc_start: 0.7953 (mtm180) cc_final: 0.7658 (mtm110) outliers start: 15 outliers final: 7 residues processed: 196 average time/residue: 1.7009 time to fit residues: 357.5931 Evaluate side-chains 176 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1115 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN K1110 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15830 Z= 0.250 Angle : 0.605 9.284 22861 Z= 0.358 Chirality : 0.038 0.205 2580 Planarity : 0.004 0.050 1709 Dihedral : 32.063 175.710 4851 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.07 % Allowed : 13.87 % Favored : 84.06 % 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: 0.29 (0.26), residues: 966 helix: 1.42 (0.21), residues: 560 sheet: -2.22 (0.68), residues: 38 loop : -1.50 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1075 HIS 0.003 0.001 HIS B 75 PHE 0.017 0.002 PHE K1051 TYR 0.010 0.001 TYR B 51 ARG 0.006 0.000 ARG K1060 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 181 time to evaluate : 1.187 Fit side-chains REVERT: A 53 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7141 (ttp-110) REVERT: D 113 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7770 (tt0) REVERT: E 79 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8884 (tttm) REVERT: G 75 LYS cc_start: 0.8788 (mmtp) cc_final: 0.8447 (mmmt) REVERT: H 34 LYS cc_start: 0.8584 (mptt) cc_final: 0.8310 (mmtm) outliers start: 16 outliers final: 8 residues processed: 188 average time/residue: 1.6737 time to fit residues: 337.7758 Evaluate side-chains 187 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN H 63 ASN K1044 GLN ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 15830 Z= 0.398 Angle : 0.643 11.372 22861 Z= 0.376 Chirality : 0.041 0.222 2580 Planarity : 0.005 0.041 1709 Dihedral : 31.970 174.640 4848 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.68 % Allowed : 14.72 % Favored : 82.60 % 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: 0.46 (0.26), residues: 966 helix: 1.58 (0.21), residues: 560 sheet: -2.22 (0.68), residues: 38 loop : -1.47 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K1075 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.002 PHE K1088 TYR 0.010 0.002 TYR C 57 ARG 0.007 0.001 ARG K1060 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7159 (ttp-110) REVERT: D 113 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7823 (tp30) REVERT: G 75 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8494 (mmmt) outliers start: 21 outliers final: 10 residues processed: 185 average time/residue: 1.6290 time to fit residues: 323.8615 Evaluate side-chains 185 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15830 Z= 0.261 Angle : 0.618 11.143 22861 Z= 0.363 Chirality : 0.038 0.234 2580 Planarity : 0.005 0.072 1709 Dihedral : 31.969 175.208 4848 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.82 % Allowed : 16.79 % Favored : 81.39 % 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: 0.65 (0.26), residues: 966 helix: 1.74 (0.21), residues: 560 sheet: -2.25 (0.69), residues: 38 loop : -1.39 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1075 HIS 0.003 0.001 HIS B 75 PHE 0.024 0.002 PHE K1028 TYR 0.011 0.001 TYR B 51 ARG 0.007 0.000 ARG K1084 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 176 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7149 (ttp-110) REVERT: D 113 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: G 75 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8455 (mmmt) REVERT: H 113 GLU cc_start: 0.7993 (tt0) cc_final: 0.7753 (tt0) outliers start: 14 outliers final: 7 residues processed: 181 average time/residue: 1.6893 time to fit residues: 327.9364 Evaluate side-chains 186 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 177 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 40.0000 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15830 Z= 0.272 Angle : 0.614 11.182 22861 Z= 0.360 Chirality : 0.038 0.249 2580 Planarity : 0.004 0.046 1709 Dihedral : 31.910 175.085 4848 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.70 % Allowed : 16.55 % Favored : 81.75 % 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: 0.75 (0.26), residues: 966 helix: 1.83 (0.21), residues: 560 sheet: -2.27 (0.69), residues: 38 loop : -1.34 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1075 HIS 0.003 0.001 HIS B 75 PHE 0.018 0.002 PHE K1051 TYR 0.011 0.001 TYR B 51 ARG 0.012 0.000 ARG K1060 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7151 (ttp-110) REVERT: D 113 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7828 (tt0) outliers start: 13 outliers final: 7 residues processed: 183 average time/residue: 1.6324 time to fit residues: 320.4641 Evaluate side-chains 185 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1115 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15830 Z= 0.226 Angle : 0.595 10.795 22861 Z= 0.351 Chirality : 0.037 0.197 2580 Planarity : 0.004 0.042 1709 Dihedral : 31.855 175.578 4846 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.70 % Allowed : 16.91 % Favored : 81.39 % 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: 0.85 (0.27), residues: 966 helix: 1.91 (0.22), residues: 562 sheet: -2.30 (0.68), residues: 38 loop : -1.32 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1075 HIS 0.003 0.001 HIS B 75 PHE 0.019 0.002 PHE K1028 TYR 0.011 0.001 TYR B 51 ARG 0.007 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 180 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8471 (mppt) REVERT: C 61 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7333 (tp30) REVERT: D 113 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7816 (tp30) REVERT: G 107 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8947 (m) REVERT: H 71 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7462 (mm-30) outliers start: 13 outliers final: 7 residues processed: 185 average time/residue: 1.6346 time to fit residues: 325.0743 Evaluate side-chains 188 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 1093 VAL Chi-restraints excluded: chain K residue 1115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15830 Z= 0.307 Angle : 0.613 11.704 22861 Z= 0.359 Chirality : 0.039 0.272 2580 Planarity : 0.004 0.040 1709 Dihedral : 31.735 175.193 4846 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.07 % Allowed : 17.03 % Favored : 80.90 % 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: 0.84 (0.27), residues: 966 helix: 1.92 (0.22), residues: 560 sheet: -2.21 (0.67), residues: 38 loop : -1.32 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K1075 HIS 0.003 0.001 HIS F 75 PHE 0.018 0.002 PHE K1028 TYR 0.012 0.001 TYR B 51 ARG 0.008 0.000 ARG K1084 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 178 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7152 (ttp-110) REVERT: B 77 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8506 (mppt) outliers start: 16 outliers final: 9 residues processed: 184 average time/residue: 1.6480 time to fit residues: 325.5669 Evaluate side-chains 185 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 174 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1093 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN K1044 GLN ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15830 Z= 0.247 Angle : 0.610 11.566 22861 Z= 0.357 Chirality : 0.037 0.274 2580 Planarity : 0.004 0.041 1709 Dihedral : 31.743 175.379 4842 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.82 % Allowed : 17.15 % Favored : 81.02 % 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: 0.94 (0.27), residues: 966 helix: 2.00 (0.22), residues: 560 sheet: -2.20 (0.67), residues: 38 loop : -1.29 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1075 HIS 0.003 0.001 HIS B 75 PHE 0.020 0.001 PHE K1028 TYR 0.011 0.001 TYR B 51 ARG 0.006 0.000 ARG K1084 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 172 time to evaluate : 1.178 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7141 (ttp-110) REVERT: B 77 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8496 (mppt) outliers start: 14 outliers final: 9 residues processed: 177 average time/residue: 1.6649 time to fit residues: 316.5228 Evaluate side-chains 184 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 173 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1093 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN K1004 GLN K1044 GLN ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 15830 Z= 0.373 Angle : 0.638 12.356 22861 Z= 0.370 Chirality : 0.041 0.296 2580 Planarity : 0.004 0.039 1709 Dihedral : 31.754 174.303 4842 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.07 % Allowed : 17.40 % Favored : 80.54 % 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: 0.74 (0.26), residues: 966 helix: 1.82 (0.21), residues: 561 sheet: -2.17 (0.66), residues: 38 loop : -1.37 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K1075 HIS 0.004 0.001 HIS B 75 PHE 0.016 0.002 PHE K1051 TYR 0.012 0.002 TYR B 88 ARG 0.007 0.000 ARG K1084 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7151 (ttp-110) REVERT: B 77 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8528 (mppt) outliers start: 16 outliers final: 9 residues processed: 176 average time/residue: 1.6420 time to fit residues: 310.2844 Evaluate side-chains 182 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1093 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 126 optimal weight: 0.0070 chunk 116 optimal weight: 8.9990 chunk 100 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN K1044 GLN ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15830 Z= 0.269 Angle : 0.629 12.362 22861 Z= 0.365 Chirality : 0.038 0.296 2580 Planarity : 0.004 0.040 1709 Dihedral : 31.770 174.718 4842 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.34 % Allowed : 18.37 % Favored : 80.29 % 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 (0.27), residues: 966 helix: 1.91 (0.22), residues: 561 sheet: -2.18 (0.67), residues: 38 loop : -1.34 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K1075 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.002 PHE E 67 TYR 0.013 0.001 TYR B 88 ARG 0.007 0.000 ARG K1084 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 172 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7137 (ttp-110) REVERT: B 77 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8518 (mppt) outliers start: 10 outliers final: 8 residues processed: 176 average time/residue: 1.6759 time to fit residues: 316.5177 Evaluate side-chains 181 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 171 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain K residue 996 VAL Chi-restraints excluded: chain K residue 1093 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN K1044 GLN ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.140306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094443 restraints weight = 31882.208| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.47 r_work: 0.3158 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15830 Z= 0.236 Angle : 0.619 12.321 22861 Z= 0.360 Chirality : 0.037 0.297 2580 Planarity : 0.004 0.069 1709 Dihedral : 31.761 174.959 4842 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.46 % Allowed : 18.25 % Favored : 80.29 % 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: 0.90 (0.27), residues: 966 helix: 1.98 (0.22), residues: 560 sheet: -2.18 (0.67), residues: 38 loop : -1.32 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1075 HIS 0.003 0.001 HIS B 75 PHE 0.012 0.002 PHE K1139 TYR 0.012 0.001 TYR B 88 ARG 0.011 0.000 ARG K1060 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5612.65 seconds wall clock time: 99 minutes 21.72 seconds (5961.72 seconds total)