Starting phenix.real_space_refine on Thu Nov 16 08:06:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/11_2023/7e8d_31015_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/11_2023/7e8d_31015.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/11_2023/7e8d_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_31015/11_2023/7e8d_31015_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/11_2023/7e8d_31015_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/11_2023/7e8d_31015.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/11_2023/7e8d_31015.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/11_2023/7e8d_31015_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e8d_31015/11_2023/7e8d_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-1.21rc1-5144/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: 9.06, per 1000 atoms: 0.61 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: 7.97 Conformation dependent library (CDL) restraints added in 2.0 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: 9.36 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: 7.46 Time building geometry restraints manager: 8.17 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: 6598 35.23 - 70.46: 1697 70.46 - 105.68: 20 105.68 - 140.91: 1 140.91 - 176.14: 7 Dihedral angle restraints: 8323 sinusoidal: 5477 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 8320 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.880 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 54.900 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.880 ------------------------------------------------------------------------------- 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 : 28.836 176.140 6491 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 *********************** 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 : 1.181 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 196 average time/residue: 1.6932 time to fit residues: 356.1652 Evaluate side-chains 175 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 168 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.1789 time to fit residues: 2.3420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.8326 moved from start: 0.0957 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= 0.217 Angle : 0.594 9.459 22861 Z= 0.351 Chirality : 0.037 0.215 2580 Planarity : 0.004 0.041 1709 Dihedral : 32.431 175.762 4552 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.07 % Allowed : 13.75 % Favored : 84.18 % 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: 0.36 (0.26), residues: 966 helix: 1.47 (0.21), residues: 561 sheet: -2.20 (0.68), residues: 38 loop : -1.46 (0.29), residues: 367 *********************** 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 196 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.253 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 188 average time/residue: 1.6752 time to fit residues: 338.4482 Evaluate side-chains 185 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 4 average time/residue: 0.4906 time to fit residues: 3.6908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.8373 moved from start: 0.0921 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= 0.417 Angle : 0.647 11.009 22861 Z= 0.378 Chirality : 0.042 0.229 2580 Planarity : 0.005 0.041 1709 Dihedral : 32.403 174.290 4552 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.35 % Favored : 95.54 % Rotamer: Outliers : 2.19 % Allowed : 14.72 % Favored : 83.09 % 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: 0.45 (0.26), residues: 966 helix: 1.58 (0.21), residues: 561 sheet: -2.21 (0.68), residues: 38 loop : -1.48 (0.29), residues: 367 *********************** 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 193 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 176 time to evaluate : 1.168 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 183 average time/residue: 1.7150 time to fit residues: 336.4416 Evaluate side-chains 184 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 174 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 5 average time/residue: 0.4836 time to fit residues: 4.3068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 9.9990 chunk 86 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.8340 moved from start: 0.1076 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= 0.206 Angle : 0.613 11.272 22861 Z= 0.360 Chirality : 0.037 0.237 2580 Planarity : 0.005 0.074 1709 Dihedral : 32.444 175.497 4552 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % 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: 0.76 (0.27), residues: 966 helix: 1.84 (0.22), residues: 560 sheet: -2.22 (0.69), residues: 38 loop : -1.34 (0.30), residues: 368 *********************** 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 192 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 179 time to evaluate : 1.286 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 185 average time/residue: 1.7099 time to fit residues: 339.5322 Evaluate side-chains 187 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 178 time to evaluate : 1.090 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 4 average time/residue: 0.6333 time to fit residues: 4.2807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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** ** K1053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 15830 Z= 0.258 Angle : 0.603 10.779 22861 Z= 0.354 Chirality : 0.038 0.240 2580 Planarity : 0.004 0.039 1709 Dihedral : 32.335 175.000 4552 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.82 % Allowed : 16.42 % 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: 0.84 (0.27), residues: 966 helix: 1.90 (0.22), residues: 560 sheet: -2.28 (0.68), residues: 38 loop : -1.30 (0.30), residues: 368 *********************** 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: 14 poor density : 177 time to evaluate : 1.222 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 183 average time/residue: 1.7384 time to fit residues: 341.9088 Evaluate side-chains 182 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.195 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 3 average time/residue: 0.1784 time to fit residues: 2.2754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15830 Z= 0.219 Angle : 0.600 10.855 22861 Z= 0.353 Chirality : 0.037 0.257 2580 Planarity : 0.004 0.040 1709 Dihedral : 32.328 175.529 4552 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.22 % Allowed : 17.03 % 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: 0.91 (0.27), residues: 966 helix: 1.96 (0.22), residues: 561 sheet: -2.23 (0.68), residues: 38 loop : -1.28 (0.30), residues: 367 *********************** 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 186 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 177 time to evaluate : 1.135 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 184 average time/residue: 1.6854 time to fit residues: 332.8215 Evaluate side-chains 184 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 177 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.1963 time to fit residues: 2.0006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 69 optimal weight: 0.4980 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15830 Z= 0.244 Angle : 0.588 11.581 22861 Z= 0.347 Chirality : 0.037 0.205 2580 Planarity : 0.004 0.038 1709 Dihedral : 32.145 176.260 4552 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % 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: 1.03 (0.27), residues: 966 helix: 2.07 (0.22), residues: 561 sheet: -2.18 (0.67), residues: 38 loop : -1.25 (0.30), residues: 367 *********************** 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 191 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 1.180 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 183 average time/residue: 1.7228 time to fit residues: 338.4944 Evaluate side-chains 181 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 1.212 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 3 average time/residue: 0.2635 time to fit residues: 2.5424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 110 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: 0.8330 moved from start: 0.1394 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= 0.270 Angle : 0.597 11.860 22861 Z= 0.350 Chirality : 0.038 0.282 2580 Planarity : 0.004 0.039 1709 Dihedral : 32.119 175.493 4552 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.46 % Allowed : 17.27 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.27), residues: 966 helix: 2.04 (0.22), residues: 561 sheet: -2.09 (0.67), residues: 38 loop : -1.24 (0.30), residues: 367 *********************** 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 190 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.365 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 185 average time/residue: 1.7847 time to fit residues: 354.4073 Evaluate side-chains 182 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 173 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.1875 time to fit residues: 2.2807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 106 optimal weight: 0.0170 chunk 114 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 113 optimal weight: 0.6980 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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: 0.8315 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15830 Z= 0.190 Angle : 0.597 11.837 22861 Z= 0.349 Chirality : 0.036 0.273 2580 Planarity : 0.004 0.039 1709 Dihedral : 32.132 175.991 4552 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.34 % Allowed : 17.88 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 966 helix: 2.17 (0.22), residues: 561 sheet: -2.10 (0.67), residues: 38 loop : -1.20 (0.30), residues: 367 *********************** 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 186 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 176 time to evaluate : 1.253 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 182 average time/residue: 1.7095 time to fit residues: 334.3718 Evaluate side-chains 181 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 173 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 2 average time/residue: 0.1930 time to fit residues: 1.8537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 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 K1004 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: 0.8359 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15830 Z= 0.391 Angle : 0.644 12.538 22861 Z= 0.372 Chirality : 0.041 0.304 2580 Planarity : 0.005 0.040 1709 Dihedral : 32.188 174.320 4552 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 1.22 % Allowed : 18.00 % Favored : 80.78 % 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: -2.10 (0.67), residues: 38 loop : -1.35 (0.29), residues: 367 ********************** 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: 9 poor density : 173 time to evaluate : 1.220 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 180 average time/residue: 1.7421 time to fit residues: 336.6409 Evaluate side-chains 179 residues out of total 825 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 1 average time/residue: 0.3348 time to fit residues: 1.9305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 110 ASN ** 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 = 0.4049 r_free = 0.4049 target = 0.141065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095406 restraints weight = 33063.384| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.54 r_work: 0.3169 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15830 Z= 0.219 Angle : 0.610 12.549 22861 Z= 0.355 Chirality : 0.037 0.301 2580 Planarity : 0.004 0.063 1709 Dihedral : 32.223 175.234 4552 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.34 % Allowed : 18.00 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 966 helix: 2.01 (0.22), residues: 562 sheet: -2.13 (0.67), residues: 38 loop : -1.27 (0.30), residues: 366 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5799.83 seconds wall clock time: 103 minutes 26.05 seconds (6206.05 seconds total)