Starting phenix.real_space_refine on Sat Feb 17 03:32:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvo_27011/02_2024/8cvo_27011_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvo_27011/02_2024/8cvo_27011.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvo_27011/02_2024/8cvo_27011_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvo_27011/02_2024/8cvo_27011_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvo_27011/02_2024/8cvo_27011_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvo_27011/02_2024/8cvo_27011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvo_27011/02_2024/8cvo_27011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvo_27011/02_2024/8cvo_27011_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvo_27011/02_2024/8cvo_27011_updated.pdb" } resolution = 2.95 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= 0.031 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 471 5.49 5 Mg 12 5.21 5 S 23 5.16 5 C 9071 2.51 5 N 3239 2.21 5 O 4604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G ASP 182": "OD1" <-> "OD2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J ASP 133": "OD1" <-> "OD2" Residue "J ASP 150": "OD1" <-> "OD2" Residue "J TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "N ASP 12": "OD1" <-> "OD2" Residue "N ASP 69": "OD1" <-> "OD2" Residue "N ASP 77": "OD1" <-> "OD2" Residue "U GLU 73": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17421 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 10090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 10090 Classifications: {'RNA': 471} Modifications used: {'rna2p_pur': 34, 'rna2p_pyr': 37, 'rna3p': 2, 'rna3p_pur': 219, 'rna3p_pyr': 179} Link IDs: {'rna2p': 71, 'rna3p': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Chain: "E" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 482 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "G" Number of atoms: 1670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1670 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 209} 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 Chain: "I" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1225 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 145} Chain: "J" Number of atoms: 1012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1012 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "M" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "S" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 474 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "U" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 658 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 47 Unusual residues: {' MG': 12, 'V7A': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16420 SG CYS S 24 47.536 67.044 47.555 1.00 68.29 S ATOM 16446 SG CYS S 27 46.769 63.105 48.246 1.00 69.39 S ATOM 16552 SG CYS S 40 50.103 65.280 49.667 1.00 69.26 S ATOM 16577 SG CYS S 43 49.456 64.842 46.134 1.00 70.06 S Time building chain proxies: 9.63, per 1000 atoms: 0.55 Number of scatterers: 17421 At special positions: 0 Unit cell: (129.228, 129.228, 124.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 23 16.00 P 471 15.00 Mg 12 11.99 O 4604 8.00 N 3239 7.00 C 9071 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: 10.07 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 101 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 43 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 40 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 24 " pdb="ZN ZN S 101 " - pdb=" SG CYS S 27 " Number of angles added : 6 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 8 sheets defined 38.3% alpha, 17.0% beta 140 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 10.25 Creating SS restraints... Processing helix chain 'E' and resid 79 through 93 removed outlier: 4.174A pdb=" N LYS E 92 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N HIS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 10 No H-bonds generated for 'chain 'G' and resid 7 through 10' Processing helix chain 'G' and resid 28 through 45 Processing helix chain 'G' and resid 73 through 76 No H-bonds generated for 'chain 'G' and resid 73 through 76' Processing helix chain 'G' and resid 81 through 94 Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 129 through 143 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 209 through 214 Processing helix chain 'I' and resid 21 through 30 Processing helix chain 'I' and resid 32 through 34 No H-bonds generated for 'chain 'I' and resid 32 through 34' Processing helix chain 'I' and resid 36 through 53 Processing helix chain 'I' and resid 58 through 69 Processing helix chain 'I' and resid 93 through 110 Processing helix chain 'I' and resid 116 through 129 Processing helix chain 'I' and resid 133 through 147 Processing helix chain 'I' and resid 149 through 154 removed outlier: 4.752A pdb=" N HIS I 153 " --> pdb=" O ALA I 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 80 No H-bonds generated for 'chain 'J' and resid 77 through 80' Processing helix chain 'J' and resid 88 through 96 Proline residue: J 93 - end of helix Processing helix chain 'J' and resid 114 through 132 Processing helix chain 'J' and resid 138 through 143 Processing helix chain 'M' and resid 15 through 31 Processing helix chain 'M' and resid 81 through 89 Processing helix chain 'N' and resid 15 through 18 No H-bonds generated for 'chain 'N' and resid 15 through 18' Processing helix chain 'N' and resid 27 through 37 Processing helix chain 'N' and resid 50 through 63 Processing helix chain 'N' and resid 68 through 84 Processing helix chain 'N' and resid 87 through 94 Processing helix chain 'N' and resid 108 through 111 No H-bonds generated for 'chain 'N' and resid 108 through 111' Processing helix chain 'S' and resid 4 through 11 Processing helix chain 'S' and resid 17 through 19 No H-bonds generated for 'chain 'S' and resid 17 through 19' Processing helix chain 'S' and resid 41 through 50 Processing helix chain 'U' and resid 5 through 7 No H-bonds generated for 'chain 'U' and resid 5 through 7' Processing helix chain 'U' and resid 15 through 25 Processing helix chain 'U' and resid 42 through 44 No H-bonds generated for 'chain 'U' and resid 42 through 44' Processing helix chain 'U' and resid 64 through 68 removed outlier: 3.727A pdb=" N VAL U 67 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY U 68 " --> pdb=" O SER U 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 64 through 68' Processing helix chain 'U' and resid 71 through 74 Processing sheet with id= A, first strand: chain 'E' and resid 69 through 76 removed outlier: 3.811A pdb=" N ALA E 40 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 61 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL E 38 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N GLY E 63 " --> pdb=" O GLU E 36 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU E 36 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'G' and resid 97 through 104 removed outlier: 3.504A pdb=" N SER G 53 " --> pdb=" O TYR G 68 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 163 through 170 removed outlier: 3.731A pdb=" N GLY G 147 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP G 180 " --> pdb=" O LYS G 203 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 73 through 78 Processing sheet with id= E, first strand: chain 'J' and resid 48 through 53 removed outlier: 3.606A pdb=" N LYS J 71 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 97 through 101 removed outlier: 3.542A pdb=" N ARG M 11 " --> pdb=" O ASP M 97 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS M 71 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 45 through 52 removed outlier: 3.617A pdb=" N ASN M 47 " --> pdb=" O MET M 67 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'U' and resid 30 through 33 removed outlier: 7.006A pdb=" N THR U 48 " --> pdb=" O ILE U 31 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N THR U 33 " --> pdb=" O THR U 48 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLY U 50 " --> pdb=" O THR U 33 " (cutoff:3.500A) 306 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 353 hydrogen bonds 530 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 9.35 Time building geometry restraints manager: 10.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2732 1.33 - 1.45: 7103 1.45 - 1.57: 7908 1.57 - 1.69: 941 1.69 - 1.81: 39 Bond restraints: 18723 Sorted by residual: bond pdb=" CAI V7A A1601 " pdb=" CAL V7A A1601 " ideal model delta sigma weight residual 0.000 1.362 -1.362 2.00e-02 2.50e+03 4.64e+03 bond pdb=" CAH V7A A1601 " pdb=" CAI V7A A1601 " ideal model delta sigma weight residual 0.401 1.448 -1.047 2.00e-02 2.50e+03 2.74e+03 bond pdb=" CAI V7A A1601 " pdb=" CAJ V7A A1601 " ideal model delta sigma weight residual 2.379 1.508 0.871 2.00e-02 2.50e+03 1.90e+03 bond pdb=" CAA V7A A1601 " pdb=" CAF V7A A1601 " ideal model delta sigma weight residual 2.233 1.392 0.841 2.00e-02 2.50e+03 1.77e+03 bond pdb=" CAG V7A A1601 " pdb=" CAJ V7A A1601 " ideal model delta sigma weight residual 0.719 1.525 -0.806 2.00e-02 2.50e+03 1.62e+03 ... (remaining 18718 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.41: 2325 105.41 - 112.55: 10688 112.55 - 119.69: 6272 119.69 - 126.83: 7074 126.83 - 133.97: 1243 Bond angle restraints: 27602 Sorted by residual: angle pdb=" CAD V7A A1601 " pdb=" CAE V7A A1601 " pdb=" CAH V7A A1601 " ideal model delta sigma weight residual 39.59 119.93 -80.34 3.00e+00 1.11e-01 7.17e+02 angle pdb=" CAH V7A A1601 " pdb=" CAI V7A A1601 " pdb=" CAJ V7A A1601 " ideal model delta sigma weight residual 169.27 114.71 54.56 3.00e+00 1.11e-01 3.31e+02 angle pdb=" CAH V7A A1601 " pdb=" CAI V7A A1601 " pdb=" CAL V7A A1601 " ideal model delta sigma weight residual 82.18 125.99 -43.81 3.00e+00 1.11e-01 2.13e+02 angle pdb=" CAE V7A A1601 " pdb=" CAH V7A A1601 " pdb=" CAI V7A A1601 " ideal model delta sigma weight residual 73.96 116.63 -42.67 3.00e+00 1.11e-01 2.02e+02 angle pdb=" CAM V7A A1601 " pdb=" CAL V7A A1601 " pdb=" OAZ V7A A1601 " ideal model delta sigma weight residual 150.73 114.92 35.81 3.00e+00 1.11e-01 1.42e+02 ... (remaining 27597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 10714 35.87 - 71.75: 1181 71.75 - 107.62: 137 107.62 - 143.49: 6 143.49 - 179.36: 8 Dihedral angle restraints: 12046 sinusoidal: 9402 harmonic: 2644 Sorted by residual: dihedral pdb=" O4' C A1013 " pdb=" C1' C A1013 " pdb=" N1 C A1013 " pdb=" C2 C A1013 " ideal model delta sinusoidal sigma weight residual 200.00 48.36 151.64 1 1.50e+01 4.44e-03 8.02e+01 dihedral pdb=" O4' C A1144 " pdb=" C1' C A1144 " pdb=" N1 C A1144 " pdb=" C2 C A1144 " ideal model delta sinusoidal sigma weight residual 200.00 69.94 130.06 1 1.50e+01 4.44e-03 7.01e+01 dihedral pdb=" O4' U A1121 " pdb=" C1' U A1121 " pdb=" N1 U A1121 " pdb=" C2 U A1121 " ideal model delta sinusoidal sigma weight residual 232.00 52.64 179.36 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.830: 3445 0.830 - 1.660: 0 1.660 - 2.490: 0 2.490 - 3.320: 0 3.320 - 4.150: 1 Chirality restraints: 3446 Sorted by residual: chirality pdb=" CAM V7A A1601 " pdb=" CAL V7A A1601 " pdb=" CAN V7A A1601 " pdb=" CAP V7A A1601 " both_signs ideal model delta sigma weight residual False 1.75 -2.40 4.15 2.00e-01 2.50e+01 4.31e+02 chirality pdb=" P G A1184 " pdb=" OP1 G A1184 " pdb=" OP2 G A1184 " pdb=" O5' G A1184 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" P U A1153 " pdb=" OP1 U A1153 " pdb=" OP2 U A1153 " pdb=" O5' U A1153 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.41e+00 ... (remaining 3443 not shown) Planarity restraints: 1766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A 950 " 0.031 2.00e-02 2.50e+03 5.51e-01 6.84e+03 pdb=" C4' 2MG A 950 " 0.423 2.00e-02 2.50e+03 pdb=" O4' 2MG A 950 " 0.584 2.00e-02 2.50e+03 pdb=" C3' 2MG A 950 " -0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG A 950 " -0.540 2.00e-02 2.50e+03 pdb=" C2' 2MG A 950 " -0.218 2.00e-02 2.50e+03 pdb=" O2' 2MG A 950 " 0.893 2.00e-02 2.50e+03 pdb=" C1' 2MG A 950 " 0.237 2.00e-02 2.50e+03 pdb=" N9 2MG A 950 " -0.821 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A 951 " 0.005 2.00e-02 2.50e+03 5.05e-01 5.73e+03 pdb=" C4' 5MC A 951 " 0.414 2.00e-02 2.50e+03 pdb=" O4' 5MC A 951 " 0.520 2.00e-02 2.50e+03 pdb=" C3' 5MC A 951 " -0.574 2.00e-02 2.50e+03 pdb=" O3' 5MC A 951 " -0.447 2.00e-02 2.50e+03 pdb=" C2' 5MC A 951 " -0.250 2.00e-02 2.50e+03 pdb=" O2' 5MC A 951 " 0.812 2.00e-02 2.50e+03 pdb=" C1' 5MC A 951 " 0.254 2.00e-02 2.50e+03 pdb=" N1 5MC A 951 " -0.733 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAH V7A A1601 " 0.298 2.00e-02 2.50e+03 2.47e-01 9.13e+02 pdb=" CAI V7A A1601 " 0.005 2.00e-02 2.50e+03 pdb=" CAJ V7A A1601 " -0.293 2.00e-02 2.50e+03 pdb=" CAL V7A A1601 " -0.018 2.00e-02 2.50e+03 pdb=" CAM V7A A1601 " 0.313 2.00e-02 2.50e+03 pdb=" OAZ V7A A1601 " -0.304 2.00e-02 2.50e+03 ... (remaining 1763 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 527 2.64 - 3.20: 15221 3.20 - 3.77: 34713 3.77 - 4.33: 46835 4.33 - 4.90: 63685 Nonbonded interactions: 160981 Sorted by model distance: nonbonded pdb=" OP2 G A1184 " pdb="MG MG A1604 " model vdw 2.075 2.170 nonbonded pdb=" OP2 A A1095 " pdb="MG MG A1612 " model vdw 2.211 2.170 nonbonded pdb=" O VAL J 85 " pdb=" NE2 GLN J 88 " model vdw 2.223 2.520 nonbonded pdb=" N2 G A1163 " pdb=" O6 G A1167 " model vdw 2.226 2.520 nonbonded pdb=" OP2 U A 945 " pdb=" O2' C A1209 " model vdw 2.241 2.440 ... (remaining 160976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 0.010 Extract box with map and model: 8.980 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 64.410 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.140 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:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 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 : 0.022 1.362 18723 Z= 1.271 Angle : 1.083 80.341 27602 Z= 0.473 Chirality : 0.085 4.150 3446 Planarity : 0.019 0.551 1766 Dihedral : 23.013 179.364 10348 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.57 % Favored : 93.66 % Rotamer: Outliers : 1.47 % Allowed : 0.53 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.29), residues: 915 helix: 1.21 (0.28), residues: 367 sheet: -0.15 (0.39), residues: 173 loop : -0.81 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 22 HIS 0.004 0.001 HIS J 86 PHE 0.018 0.002 PHE S 37 TYR 0.024 0.002 TYR N 64 ARG 0.008 0.000 ARG N 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 284 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7211 (m-80) cc_final: 0.6856 (m-80) REVERT: E 78 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7794 (mt-10) REVERT: E 85 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8196 (ttpt) REVERT: G 161 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7940 (mmm) REVERT: I 123 GLU cc_start: 0.9045 (tp30) cc_final: 0.8834 (mm-30) REVERT: J 79 ASP cc_start: 0.9016 (t0) cc_final: 0.8655 (t0) REVERT: J 80 TYR cc_start: 0.9076 (t80) cc_final: 0.8754 (t80) REVERT: M 20 SER cc_start: 0.9191 (p) cc_final: 0.8970 (p) REVERT: M 46 LYS cc_start: 0.8416 (tptm) cc_final: 0.8163 (tppp) REVERT: M 76 ILE cc_start: 0.8875 (mm) cc_final: 0.8551 (mm) REVERT: S 46 GLU cc_start: 0.8188 (pt0) cc_final: 0.7962 (pt0) outliers start: 11 outliers final: 3 residues processed: 290 average time/residue: 1.4606 time to fit residues: 468.4404 Evaluate side-chains 221 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 217 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 111 ASP Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 66 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN G 97 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 HIS N 52 GLN ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.428 18723 Z= 0.349 Angle : 1.020 69.960 27602 Z= 0.448 Chirality : 0.049 1.708 3446 Planarity : 0.006 0.123 1766 Dihedral : 23.768 177.856 8540 Min Nonbonded Distance : 1.594 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.57 % Favored : 93.77 % Rotamer: Outliers : 4.01 % Allowed : 18.85 % Favored : 77.14 % 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: 0.30 (0.29), residues: 915 helix: 1.26 (0.28), residues: 373 sheet: 0.00 (0.39), residues: 176 loop : -0.74 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 200 HIS 0.005 0.001 HIS N 46 PHE 0.013 0.002 PHE U 74 TYR 0.016 0.002 TYR J 103 ARG 0.007 0.001 ARG N 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 215 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7158 (m-80) cc_final: 0.6817 (m-80) REVERT: E 85 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8219 (ttpt) REVERT: E 89 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: G 161 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7816 (mmm) REVERT: I 123 GLU cc_start: 0.9095 (tp30) cc_final: 0.8781 (mm-30) REVERT: J 80 TYR cc_start: 0.9071 (t80) cc_final: 0.8767 (t80) REVERT: J 169 GLN cc_start: 0.9438 (tt0) cc_final: 0.9223 (tt0) REVERT: M 20 SER cc_start: 0.9211 (p) cc_final: 0.8929 (p) REVERT: M 76 ILE cc_start: 0.9040 (mm) cc_final: 0.8820 (mm) outliers start: 30 outliers final: 16 residues processed: 226 average time/residue: 1.3121 time to fit residues: 330.3838 Evaluate side-chains 222 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain U residue 39 MET Chi-restraints excluded: chain U residue 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 134 optimal weight: 0.0980 chunk 110 optimal weight: 5.9990 chunk 123 optimal weight: 0.0470 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 86 HIS N 59 HIS ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.432 18723 Z= 0.261 Angle : 0.969 69.243 27602 Z= 0.423 Chirality : 0.044 1.487 3446 Planarity : 0.006 0.112 1766 Dihedral : 23.615 178.973 8535 Min Nonbonded Distance : 1.573 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.03 % Favored : 94.32 % Rotamer: Outliers : 4.28 % Allowed : 22.59 % Favored : 73.13 % 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: 0.38 (0.29), residues: 915 helix: 1.30 (0.28), residues: 371 sheet: 0.14 (0.40), residues: 179 loop : -0.72 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 200 HIS 0.006 0.001 HIS N 46 PHE 0.011 0.001 PHE G 129 TYR 0.012 0.001 TYR S 21 ARG 0.007 0.000 ARG G 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 230 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7352 (m-80) cc_final: 0.6973 (m-80) REVERT: E 85 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8248 (ttpt) REVERT: G 141 MET cc_start: 0.8982 (mmt) cc_final: 0.8683 (mmt) REVERT: I 72 SER cc_start: 0.8614 (m) cc_final: 0.8378 (m) REVERT: I 74 GLU cc_start: 0.7974 (pp20) cc_final: 0.7767 (pp20) REVERT: I 75 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8771 (m) REVERT: I 123 GLU cc_start: 0.8965 (tp30) cc_final: 0.8694 (mm-30) REVERT: I 149 ARG cc_start: 0.7674 (tmm-80) cc_final: 0.7458 (tmm-80) REVERT: J 80 TYR cc_start: 0.9156 (t80) cc_final: 0.8724 (t80) REVERT: M 20 SER cc_start: 0.9110 (p) cc_final: 0.8867 (p) REVERT: M 68 ARG cc_start: 0.8855 (mtp85) cc_final: 0.8520 (mtp85) REVERT: S 37 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.8313 (p90) outliers start: 32 outliers final: 19 residues processed: 244 average time/residue: 1.3002 time to fit residues: 354.6821 Evaluate side-chains 226 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 205 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.432 18723 Z= 0.274 Angle : 0.967 69.119 27602 Z= 0.420 Chirality : 0.043 1.475 3446 Planarity : 0.006 0.114 1766 Dihedral : 23.547 179.370 8532 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.57 % Favored : 93.88 % Rotamer: Outliers : 5.08 % Allowed : 25.40 % Favored : 69.52 % 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: 0.48 (0.29), residues: 915 helix: 1.32 (0.28), residues: 371 sheet: 0.30 (0.40), residues: 175 loop : -0.65 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 200 HIS 0.003 0.001 HIS M 15 PHE 0.009 0.001 PHE G 129 TYR 0.020 0.001 TYR J 170 ARG 0.006 0.000 ARG G 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 216 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7456 (m-80) cc_final: 0.7050 (m-80) REVERT: E 85 LYS cc_start: 0.8765 (ttmt) cc_final: 0.8279 (ttpt) REVERT: G 17 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: G 138 GLN cc_start: 0.8306 (tp40) cc_final: 0.7986 (tm-30) REVERT: G 141 MET cc_start: 0.8862 (mmt) cc_final: 0.8657 (mmt) REVERT: G 142 ASN cc_start: 0.8628 (m-40) cc_final: 0.8282 (m-40) REVERT: I 123 GLU cc_start: 0.8971 (tp30) cc_final: 0.8722 (mm-30) REVERT: I 149 ARG cc_start: 0.7655 (tmm-80) cc_final: 0.7419 (tmm-80) REVERT: J 130 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8863 (t0) REVERT: M 20 SER cc_start: 0.9099 (p) cc_final: 0.8852 (p) REVERT: M 68 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8551 (mtp85) REVERT: N 16 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7517 (tt0) REVERT: N 115 LYS cc_start: 0.8538 (ptpp) cc_final: 0.8309 (ptmm) outliers start: 38 outliers final: 23 residues processed: 235 average time/residue: 1.2447 time to fit residues: 327.9291 Evaluate side-chains 229 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 130 ASN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 98 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 38 SER Chi-restraints excluded: chain U residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN I 96 GLN J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.431 18723 Z= 0.476 Angle : 1.036 68.516 27602 Z= 0.460 Chirality : 0.048 1.432 3446 Planarity : 0.007 0.119 1766 Dihedral : 23.567 178.747 8532 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.90 % Favored : 93.66 % Rotamer: Outliers : 6.68 % Allowed : 26.20 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 915 helix: 1.23 (0.28), residues: 371 sheet: 0.09 (0.39), residues: 181 loop : -0.70 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP U 34 HIS 0.005 0.001 HIS S 31 PHE 0.015 0.002 PHE U 74 TYR 0.026 0.002 TYR J 103 ARG 0.007 0.001 ARG I 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 203 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7639 (m-80) cc_final: 0.7328 (m-80) REVERT: E 85 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8226 (ttpt) REVERT: G 142 ASN cc_start: 0.8691 (m-40) cc_final: 0.8423 (m-40) REVERT: I 74 GLU cc_start: 0.7900 (pp20) cc_final: 0.7676 (pp20) REVERT: J 130 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8875 (t0) REVERT: M 20 SER cc_start: 0.9113 (p) cc_final: 0.8844 (p) REVERT: M 68 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8411 (mtp85) REVERT: M 76 ILE cc_start: 0.9012 (mm) cc_final: 0.8803 (mm) REVERT: N 16 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: S 35 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8316 (mtt180) REVERT: S 37 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8193 (p90) outliers start: 50 outliers final: 32 residues processed: 228 average time/residue: 1.2314 time to fit residues: 316.5852 Evaluate side-chains 234 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 66 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 130 ASN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 137 SER Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 56 LEU Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain U residue 38 SER Chi-restraints excluded: chain U residue 48 THR Chi-restraints excluded: chain U residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.431 18723 Z= 0.301 Angle : 0.983 68.848 27602 Z= 0.431 Chirality : 0.044 1.468 3446 Planarity : 0.006 0.114 1766 Dihedral : 23.538 178.928 8532 Min Nonbonded Distance : 1.573 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.59 % Favored : 94.97 % Rotamer: Outliers : 6.02 % Allowed : 27.81 % Favored : 66.18 % 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: 0.44 (0.29), residues: 915 helix: 1.35 (0.28), residues: 371 sheet: 0.13 (0.40), residues: 181 loop : -0.67 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 200 HIS 0.003 0.001 HIS M 15 PHE 0.009 0.001 PHE G 129 TYR 0.021 0.002 TYR J 170 ARG 0.008 0.000 ARG G 48 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 209 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7637 (m-80) cc_final: 0.7234 (m-80) REVERT: E 85 LYS cc_start: 0.8739 (ttmt) cc_final: 0.8283 (ttpt) REVERT: G 142 ASN cc_start: 0.8646 (m-40) cc_final: 0.8407 (m-40) REVERT: I 74 GLU cc_start: 0.7905 (pp20) cc_final: 0.7642 (pp20) REVERT: J 130 ASN cc_start: 0.9112 (OUTLIER) cc_final: 0.8875 (t0) REVERT: M 20 SER cc_start: 0.9110 (p) cc_final: 0.8838 (p) REVERT: M 68 ARG cc_start: 0.8891 (mtp85) cc_final: 0.8598 (mtp85) REVERT: M 100 ILE cc_start: 0.8693 (mm) cc_final: 0.8442 (mt) REVERT: N 16 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: S 37 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8258 (p90) outliers start: 45 outliers final: 29 residues processed: 233 average time/residue: 1.2749 time to fit residues: 333.3975 Evaluate side-chains 230 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 130 ASN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 33 THR Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain U residue 38 SER Chi-restraints excluded: chain U residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 27 GLN J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.432 18723 Z= 0.301 Angle : 0.983 68.897 27602 Z= 0.430 Chirality : 0.044 1.462 3446 Planarity : 0.006 0.114 1766 Dihedral : 23.496 179.606 8532 Min Nonbonded Distance : 1.571 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.46 % Favored : 94.21 % Rotamer: Outliers : 5.75 % Allowed : 28.88 % Favored : 65.37 % 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: 0.43 (0.29), residues: 915 helix: 1.37 (0.28), residues: 370 sheet: 0.16 (0.40), residues: 175 loop : -0.71 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 200 HIS 0.004 0.001 HIS M 15 PHE 0.008 0.001 PHE G 129 TYR 0.017 0.001 TYR G 202 ARG 0.005 0.000 ARG G 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7508 (m-80) cc_final: 0.7059 (m-80) REVERT: E 85 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8349 (ttpp) REVERT: G 138 GLN cc_start: 0.8291 (tp40) cc_final: 0.8079 (tm-30) REVERT: G 142 ASN cc_start: 0.8590 (m-40) cc_final: 0.8280 (m110) REVERT: I 74 GLU cc_start: 0.7998 (pp20) cc_final: 0.7783 (pp20) REVERT: J 130 ASN cc_start: 0.9103 (OUTLIER) cc_final: 0.8853 (t0) REVERT: M 20 SER cc_start: 0.9103 (p) cc_final: 0.8833 (p) REVERT: M 68 ARG cc_start: 0.8888 (mtp85) cc_final: 0.8401 (mtp85) REVERT: M 100 ILE cc_start: 0.8717 (mm) cc_final: 0.8458 (mt) REVERT: N 16 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: N 115 LYS cc_start: 0.8515 (ptpp) cc_final: 0.8300 (ptmm) REVERT: S 37 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.8258 (p90) outliers start: 43 outliers final: 29 residues processed: 231 average time/residue: 1.2160 time to fit residues: 315.3402 Evaluate side-chains 236 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 130 ASN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 9 LEU Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain U residue 38 SER Chi-restraints excluded: chain U residue 48 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.0170 chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.1980 chunk 12 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 120 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.432 18723 Z= 0.304 Angle : 0.987 68.877 27602 Z= 0.432 Chirality : 0.044 1.466 3446 Planarity : 0.006 0.114 1766 Dihedral : 23.480 179.786 8532 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.14 % Favored : 94.54 % Rotamer: Outliers : 4.95 % Allowed : 30.08 % Favored : 64.97 % 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: 0.41 (0.29), residues: 915 helix: 1.34 (0.28), residues: 369 sheet: 0.20 (0.40), residues: 175 loop : -0.71 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 200 HIS 0.004 0.001 HIS M 15 PHE 0.008 0.001 PHE G 129 TYR 0.024 0.002 TYR J 170 ARG 0.007 0.000 ARG N 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 202 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7461 (m-80) cc_final: 0.7025 (m-80) REVERT: E 85 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8102 (ttpp) REVERT: E 92 LYS cc_start: 0.8800 (ptpp) cc_final: 0.8380 (pmtt) REVERT: G 142 ASN cc_start: 0.8581 (m-40) cc_final: 0.8314 (m110) REVERT: G 180 ASP cc_start: 0.8637 (t0) cc_final: 0.7815 (p0) REVERT: I 74 GLU cc_start: 0.7952 (pp20) cc_final: 0.7683 (pp20) REVERT: M 20 SER cc_start: 0.9128 (p) cc_final: 0.8855 (p) REVERT: M 68 ARG cc_start: 0.8883 (mtp85) cc_final: 0.8417 (mtp85) REVERT: M 100 ILE cc_start: 0.8718 (mm) cc_final: 0.8455 (mt) REVERT: N 16 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: N 17 VAL cc_start: 0.9340 (OUTLIER) cc_final: 0.9093 (p) REVERT: N 115 LYS cc_start: 0.8500 (ptpp) cc_final: 0.8271 (ptmm) REVERT: S 37 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.8199 (p90) outliers start: 37 outliers final: 29 residues processed: 220 average time/residue: 1.1851 time to fit residues: 293.3664 Evaluate side-chains 231 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 42 ASP Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain S residue 32 SER Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 38 SER Chi-restraints excluded: chain U residue 48 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.0670 chunk 96 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 80 optimal weight: 0.1980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.432 18723 Z= 0.274 Angle : 0.980 68.998 27602 Z= 0.428 Chirality : 0.043 1.480 3446 Planarity : 0.006 0.113 1766 Dihedral : 23.456 179.798 8532 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.70 % Favored : 94.97 % Rotamer: Outliers : 4.28 % Allowed : 30.75 % Favored : 64.97 % 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: 0.40 (0.29), residues: 915 helix: 1.34 (0.28), residues: 368 sheet: 0.15 (0.39), residues: 176 loop : -0.71 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 70 HIS 0.004 0.001 HIS M 15 PHE 0.010 0.001 PHE U 74 TYR 0.019 0.001 TYR G 202 ARG 0.006 0.000 ARG N 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 204 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7473 (m-80) cc_final: 0.6990 (m-80) REVERT: E 85 LYS cc_start: 0.8753 (ttmt) cc_final: 0.8413 (ttpp) REVERT: E 92 LYS cc_start: 0.8774 (ptpp) cc_final: 0.8471 (pmtt) REVERT: G 17 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8064 (m-30) REVERT: G 180 ASP cc_start: 0.8602 (t0) cc_final: 0.7886 (p0) REVERT: G 203 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8234 (mmtp) REVERT: I 74 GLU cc_start: 0.7915 (pp20) cc_final: 0.7620 (pp20) REVERT: M 20 SER cc_start: 0.9138 (p) cc_final: 0.8869 (p) REVERT: M 68 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8414 (mtp85) REVERT: N 16 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: N 17 VAL cc_start: 0.9322 (OUTLIER) cc_final: 0.9084 (p) REVERT: N 115 LYS cc_start: 0.8399 (ptpp) cc_final: 0.8198 (ptmm) REVERT: S 37 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8105 (p90) REVERT: U 66 MET cc_start: 0.8985 (mtp) cc_final: 0.8737 (mtp) outliers start: 32 outliers final: 21 residues processed: 220 average time/residue: 1.2217 time to fit residues: 301.6166 Evaluate side-chains 222 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 205 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 90 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 125 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 HIS ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.432 18723 Z= 0.275 Angle : 0.983 69.050 27602 Z= 0.429 Chirality : 0.043 1.482 3446 Planarity : 0.006 0.113 1766 Dihedral : 23.430 179.384 8530 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.14 % Favored : 94.54 % Rotamer: Outliers : 3.61 % Allowed : 32.89 % Favored : 63.50 % 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: 0.42 (0.29), residues: 915 helix: 1.32 (0.28), residues: 365 sheet: 0.23 (0.39), residues: 179 loop : -0.69 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 70 HIS 0.003 0.001 HIS M 15 PHE 0.009 0.001 PHE G 129 TYR 0.021 0.002 TYR G 202 ARG 0.007 0.000 ARG G 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 TYR cc_start: 0.7498 (m-80) cc_final: 0.7043 (m-80) REVERT: E 92 LYS cc_start: 0.8770 (ptpp) cc_final: 0.8468 (pmtt) REVERT: G 17 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: G 180 ASP cc_start: 0.8623 (t0) cc_final: 0.7951 (p0) REVERT: G 203 LYS cc_start: 0.8515 (mmtp) cc_final: 0.8209 (mmtp) REVERT: I 74 GLU cc_start: 0.7853 (pp20) cc_final: 0.7563 (pp20) REVERT: M 20 SER cc_start: 0.9126 (p) cc_final: 0.8861 (p) REVERT: M 68 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8431 (mtp85) REVERT: N 16 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: N 17 VAL cc_start: 0.9318 (OUTLIER) cc_final: 0.9101 (p) REVERT: S 37 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7979 (p90) outliers start: 27 outliers final: 19 residues processed: 217 average time/residue: 1.2743 time to fit residues: 310.4613 Evaluate side-chains 222 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 199 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 134 SER Chi-restraints excluded: chain J residue 100 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 125 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 16 GLU Chi-restraints excluded: chain N residue 17 VAL Chi-restraints excluded: chain N residue 94 SER Chi-restraints excluded: chain S residue 37 PHE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN J 86 HIS ** J 88 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 = 0.3417 r_free = 0.3417 target = 0.093016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.066138 restraints weight = 39013.601| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.69 r_work: 0.2770 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.431 18723 Z= 0.573 Angle : 1.095 68.386 27602 Z= 0.494 Chirality : 0.051 1.445 3446 Planarity : 0.007 0.119 1766 Dihedral : 23.580 178.674 8530 Min Nonbonded Distance : 1.566 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.34 % Favored : 93.33 % Rotamer: Outliers : 4.28 % Allowed : 32.49 % Favored : 63.24 % 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: 0.17 (0.29), residues: 915 helix: 1.10 (0.28), residues: 363 sheet: -0.02 (0.39), residues: 174 loop : -0.72 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP J 70 HIS 0.008 0.002 HIS S 31 PHE 0.019 0.002 PHE G 192 TYR 0.032 0.002 TYR J 103 ARG 0.009 0.001 ARG I 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5845.87 seconds wall clock time: 105 minutes 30.19 seconds (6330.19 seconds total)