Starting phenix.real_space_refine on Tue Apr 9 10:47:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/04_2024/8han_34597_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/04_2024/8han_34597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/04_2024/8han_34597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/04_2024/8han_34597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/04_2024/8han_34597_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/04_2024/8han_34597_updated.pdb" } resolution = 4.2 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= 0.003 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: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 45 5.16 5 C 9330 2.51 5 N 2940 2.21 5 O 3571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A ARG 52": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 72": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 23": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B ARG 40": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 78": "NH1" <-> "NH2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "C ARG 17": "NH1" <-> "NH2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C ARG 29": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 42": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 99": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 67": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "G ARG 20": "NH1" <-> "NH2" Residue "G ARG 29": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 77": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 88": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 79": "NH1" <-> "NH2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "K GLU 1089": "OE1" <-> "OE2" Residue "K GLU 1107": "OE1" <-> "OE2" Residue "K ARG 1173": "NH1" <-> "NH2" Residue "K GLU 1183": "OE1" <-> "OE2" Residue "K GLU 1186": "OE1" <-> "OE2" Residue "K GLU 1188": "OE1" <-> "OE2" Residue "K TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 1267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 1319": "NH1" <-> "NH2" Residue "K GLU 1370": "OE1" <-> "OE2" Residue "K PHE 1410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1513": "OE1" <-> "OE2" Residue "K ASP 1518": "OD1" <-> "OD2" Residue "K TYR 1519": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16180 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 687 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ALY:plan-2': 2, 'ALY:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} 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: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 745 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4134 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 468} Chain breaks: 4 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3016 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 Time building chain proxies: 9.07, per 1000 atoms: 0.56 Number of scatterers: 16180 At special positions: 0 Unit cell: (102.9, 127.89, 158.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 294 15.00 O 3571 8.00 N 2940 7.00 C 9330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 3 sheets defined 54.2% alpha, 5.6% beta 118 base pairs and 226 stacking pairs defined. Time for finding SS restraints: 8.24 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 78 Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.649A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.393A 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 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 105 through 122 Processing helix chain 'E' and resid 46 through 56 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 40 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.662A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) 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 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.419A 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 123 Processing helix chain 'K' and resid 1089 through 1103 Proline residue: K1096 - end of helix Processing helix chain 'K' and resid 1109 through 1111 No H-bonds generated for 'chain 'K' and resid 1109 through 1111' Processing helix chain 'K' and resid 1117 through 1120 No H-bonds generated for 'chain 'K' and resid 1117 through 1120' Processing helix chain 'K' and resid 1125 through 1128 No H-bonds generated for 'chain 'K' and resid 1125 through 1128' Processing helix chain 'K' and resid 1135 through 1144 Processing helix chain 'K' and resid 1150 through 1167 Processing helix chain 'K' and resid 1173 through 1196 removed outlier: 4.042A pdb=" N ASP K1190 " --> pdb=" O GLU K1186 " (cutoff:3.500A) Proline residue: K1191 - end of helix Processing helix chain 'K' and resid 1238 through 1241 No H-bonds generated for 'chain 'K' and resid 1238 through 1241' Processing helix chain 'K' and resid 1292 through 1295 No H-bonds generated for 'chain 'K' and resid 1292 through 1295' Processing helix chain 'K' and resid 1309 through 1313 Processing helix chain 'K' and resid 1333 through 1349 Processing helix chain 'K' and resid 1446 through 1464 Processing helix chain 'K' and resid 1496 through 1513 Processing helix chain 'K' and resid 1522 through 1529 Processing helix chain 'K' and resid 1534 through 1536 No H-bonds generated for 'chain 'K' and resid 1534 through 1536' Processing helix chain 'K' and resid 1544 through 1554 Processing helix chain 'K' and resid 1621 through 1627 Processing helix chain 'K' and resid 1664 through 1673 Processing helix chain 'K' and resid 1681 through 1697 Processing sheet with id= A, first strand: chain 'K' and resid 1268 through 1271 Processing sheet with id= B, first strand: chain 'K' and resid 1280 through 1282 Processing sheet with id= C, first strand: chain 'K' and resid 1518 through 1521 removed outlier: 4.082A pdb=" N TRP K1472 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR K1433 " --> pdb=" O TRP K1472 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS K1413 " --> pdb=" O SER K1432 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU K1434 " --> pdb=" O GLY K1411 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY K1411 " --> pdb=" O LEU K1434 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER K1436 " --> pdb=" O PHE K1409 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE K1409 " --> pdb=" O SER K1436 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA K1398 " --> pdb=" O PHE K1409 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY K1411 " --> pdb=" O LEU K1396 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU K1396 " --> pdb=" O GLY K1411 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N HIS K1413 " --> pdb=" O LYS K1394 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS K1394 " --> pdb=" O HIS K1413 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN K1415 " --> pdb=" O ARG K1392 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG K1392 " --> pdb=" O GLN K1415 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N TYR K1417 " --> pdb=" O PRO K1390 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA K1363 " --> pdb=" O ALA K1395 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE K1397 " --> pdb=" O VAL K1361 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL K1361 " --> pdb=" O PHE K1397 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE K1399 " --> pdb=" O VAL K1359 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL K1359 " --> pdb=" O PHE K1399 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU K1401 " --> pdb=" O VAL K1357 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL K1357 " --> pdb=" O GLU K1401 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 558 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 226 stacking parallelities Total time for adding SS restraints: 7.73 Time building geometry restraints manager: 8.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4005 1.34 - 1.46: 4727 1.46 - 1.58: 7722 1.58 - 1.70: 586 1.70 - 1.82: 66 Bond restraints: 17106 Sorted by residual: bond pdb=" NZ ALY B 12 " pdb=" CH ALY B 12 " ideal model delta sigma weight residual 1.343 1.385 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 bond pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" N ARG K1514 " pdb=" CA ARG K1514 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.39e+00 bond pdb=" CH ALY B 12 " pdb=" OH ALY B 12 " ideal model delta sigma weight residual 1.225 1.247 -0.022 2.00e-02 2.50e+03 1.21e+00 ... (remaining 17101 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.78: 1631 105.78 - 112.83: 9314 112.83 - 119.88: 5711 119.88 - 126.92: 6864 126.92 - 133.97: 843 Bond angle restraints: 24363 Sorted by residual: angle pdb=" CA ALY B 16 " pdb=" C ALY B 16 " pdb=" O ALY B 16 " ideal model delta sigma weight residual 120.80 129.08 -8.28 1.70e+00 3.46e-01 2.37e+01 angle pdb=" C ARG E 49 " pdb=" N GLU E 50 " pdb=" CA GLU E 50 " ideal model delta sigma weight residual 120.72 116.05 4.67 1.67e+00 3.59e-01 7.81e+00 angle pdb=" N GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 110.39 114.44 -4.05 1.66e+00 3.63e-01 5.95e+00 angle pdb=" N ALY B 12 " pdb=" CA ALY B 12 " pdb=" CB ALY B 12 " ideal model delta sigma weight residual 110.50 114.61 -4.11 1.70e+00 3.46e-01 5.84e+00 angle pdb=" CB MET E 90 " pdb=" CG MET E 90 " pdb=" SD MET E 90 " ideal model delta sigma weight residual 112.70 119.88 -7.18 3.00e+00 1.11e-01 5.73e+00 ... (remaining 24358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 8167 34.00 - 67.99: 1416 67.99 - 101.99: 28 101.99 - 135.98: 1 135.98 - 169.98: 2 Dihedral angle restraints: 9614 sinusoidal: 5937 harmonic: 3677 Sorted by residual: dihedral pdb=" C4' DT I 136 " pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " pdb=" P DT I 137 " ideal model delta sinusoidal sigma weight residual 220.00 50.02 169.98 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA J 59 " pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " pdb=" P DA J 60 " ideal model delta sinusoidal sigma weight residual 220.00 62.06 157.94 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" CG ARG H 33 " pdb=" CD ARG H 33 " pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " ideal model delta sinusoidal sigma weight residual -180.00 -135.34 -44.66 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 9611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1995 0.030 - 0.060: 537 0.060 - 0.089: 108 0.089 - 0.119: 61 0.119 - 0.149: 13 Chirality restraints: 2714 Sorted by residual: chirality pdb=" CA MET K1095 " pdb=" N MET K1095 " pdb=" C MET K1095 " pdb=" CB MET K1095 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.94e-01 chirality pdb=" P DA J 60 " pdb=" OP1 DA J 60 " pdb=" OP2 DA J 60 " pdb=" O5' DA J 60 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 2711 not shown) Planarity restraints: 2077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 105 " -0.021 2.00e-02 2.50e+03 1.09e-02 2.67e+00 pdb=" N1 DC I 105 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DC I 105 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC I 105 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DC I 105 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 105 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 105 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 105 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 105 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO D 103 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 151 " 0.012 2.00e-02 2.50e+03 7.46e-03 1.67e+00 pdb=" N9 DG I 151 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DG I 151 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 151 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 151 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 151 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG I 151 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 151 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 151 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG I 151 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 151 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 151 " -0.001 2.00e-02 2.50e+03 ... (remaining 2074 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1833 2.76 - 3.29: 15251 3.29 - 3.83: 31930 3.83 - 4.36: 35687 4.36 - 4.90: 52909 Nonbonded interactions: 137610 Sorted by model distance: nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.219 2.440 nonbonded pdb=" OD1 ASP A 123 " pdb=" NE2 HIS E 113 " model vdw 2.236 2.520 nonbonded pdb=" NH1 ARG C 17 " pdb=" OP2 DG J 48 " model vdw 2.244 2.520 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.274 2.520 nonbonded pdb=" N2 DG I 35 " pdb=" O2 DT J 147 " model vdw 2.277 2.520 ... (remaining 137605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 45 through 134) selection = (chain 'E' and resid 45 through 134) } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and resid 21 through 102) } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 31 and (name N or name CA or name C or name O or name CB \ )) or resid 32 through 124)) selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 19 through 162) selection = (chain 'J' and resid 19 through 162) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 4.300 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 53.760 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17106 Z= 0.147 Angle : 0.536 8.284 24363 Z= 0.330 Chirality : 0.032 0.149 2714 Planarity : 0.003 0.035 2077 Dihedral : 24.993 169.976 7240 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.88 (0.24), residues: 1230 helix: 2.68 (0.18), residues: 756 sheet: 0.28 (0.63), residues: 66 loop : 0.81 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1502 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE K1484 TYR 0.019 0.001 TYR K1102 ARG 0.007 0.000 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.8444 (mmp) cc_final: 0.8209 (mmp) REVERT: H 62 MET cc_start: 0.8783 (mmp) cc_final: 0.8516 (mmt) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2456 time to fit residues: 12.7534 Evaluate side-chains 24 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17106 Z= 0.261 Angle : 0.589 6.408 24363 Z= 0.342 Chirality : 0.036 0.155 2714 Planarity : 0.004 0.033 2077 Dihedral : 28.831 171.298 4705 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.09 % Allowed : 2.41 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.80 (0.23), residues: 1230 helix: 2.56 (0.18), residues: 759 sheet: 0.18 (0.63), residues: 68 loop : 0.91 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K1502 HIS 0.009 0.001 HIS B 75 PHE 0.008 0.001 PHE K1667 TYR 0.020 0.002 TYR K1503 ARG 0.005 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 1.527 Fit side-chains REVERT: E 120 MET cc_start: 0.7903 (mmm) cc_final: 0.7576 (mmm) REVERT: K 1193 MET cc_start: 0.7790 (tpt) cc_final: 0.7584 (tpt) REVERT: K 1691 MET cc_start: 0.6688 (ptp) cc_final: 0.5419 (tmm) outliers start: 1 outliers final: 0 residues processed: 29 average time/residue: 0.2500 time to fit residues: 13.1250 Evaluate side-chains 25 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17106 Z= 0.168 Angle : 0.512 6.532 24363 Z= 0.301 Chirality : 0.033 0.143 2714 Planarity : 0.003 0.045 2077 Dihedral : 28.957 176.064 4705 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.98 (0.24), residues: 1230 helix: 2.76 (0.18), residues: 755 sheet: 0.17 (0.63), residues: 68 loop : 0.87 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K1502 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE K1397 TYR 0.008 0.001 TYR D 40 ARG 0.006 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 1.534 Fit side-chains REVERT: E 120 MET cc_start: 0.7901 (mmm) cc_final: 0.7412 (mmm) REVERT: K 1691 MET cc_start: 0.6655 (ptp) cc_final: 0.5414 (tmm) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2548 time to fit residues: 13.6658 Evaluate side-chains 25 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** K1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1231 GLN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17106 Z= 0.348 Angle : 0.684 9.477 24363 Z= 0.392 Chirality : 0.039 0.158 2714 Planarity : 0.005 0.039 2077 Dihedral : 29.866 177.027 4705 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.09 % Allowed : 3.61 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.90 (0.23), residues: 1230 helix: 1.82 (0.18), residues: 756 sheet: 0.04 (0.65), residues: 66 loop : 0.55 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K1502 HIS 0.013 0.002 HIS D 109 PHE 0.012 0.002 PHE K1399 TYR 0.016 0.002 TYR C 39 ARG 0.008 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 1.417 Fit side-chains REVERT: A 120 MET cc_start: 0.6784 (mpp) cc_final: 0.6244 (mpp) REVERT: E 120 MET cc_start: 0.8277 (mmm) cc_final: 0.7729 (mmm) REVERT: K 1691 MET cc_start: 0.6786 (ptp) cc_final: 0.5514 (tmm) outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.2664 time to fit residues: 14.2695 Evaluate side-chains 25 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 30.0000 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 59 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 89 ASN ** K1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1231 GLN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1343 ASN K1349 GLN K1487 HIS K1547 ASN K1628 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 17106 Z= 0.379 Angle : 0.711 7.636 24363 Z= 0.408 Chirality : 0.040 0.180 2714 Planarity : 0.005 0.038 2077 Dihedral : 30.818 177.285 4705 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.24 (0.23), residues: 1230 helix: 1.35 (0.18), residues: 747 sheet: -0.44 (0.64), residues: 68 loop : 0.26 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP K1502 HIS 0.015 0.003 HIS K1438 PHE 0.028 0.002 PHE E 104 TYR 0.021 0.002 TYR C 39 ARG 0.011 0.001 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 1.495 Fit side-chains REVERT: E 120 MET cc_start: 0.8281 (mmm) cc_final: 0.7721 (mmm) REVERT: K 1193 MET cc_start: 0.7548 (tpt) cc_final: 0.7271 (tpt) REVERT: K 1691 MET cc_start: 0.7039 (ptp) cc_final: 0.5873 (tmm) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.3048 time to fit residues: 14.2374 Evaluate side-chains 24 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1146 GLN ** K1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17106 Z= 0.243 Angle : 0.601 6.955 24363 Z= 0.350 Chirality : 0.036 0.221 2714 Planarity : 0.004 0.034 2077 Dihedral : 30.674 176.189 4705 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 1.82 (0.24), residues: 1230 helix: 1.91 (0.19), residues: 742 sheet: -0.17 (0.65), residues: 66 loop : 0.29 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K1502 HIS 0.007 0.001 HIS K1485 PHE 0.008 0.001 PHE K1399 TYR 0.014 0.002 TYR K1102 ARG 0.006 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.538 Fit side-chains REVERT: E 120 MET cc_start: 0.8257 (mmm) cc_final: 0.7630 (mmm) REVERT: K 1193 MET cc_start: 0.7403 (tpt) cc_final: 0.7006 (tpt) REVERT: K 1691 MET cc_start: 0.7012 (ptp) cc_final: 0.5849 (tmm) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2939 time to fit residues: 12.8559 Evaluate side-chains 23 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1231 GLN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17106 Z= 0.203 Angle : 0.572 7.152 24363 Z= 0.334 Chirality : 0.035 0.149 2714 Planarity : 0.004 0.054 2077 Dihedral : 30.419 175.770 4705 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.14 (0.24), residues: 1230 helix: 2.18 (0.18), residues: 750 sheet: -0.34 (0.64), residues: 68 loop : 0.41 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K1502 HIS 0.009 0.001 HIS B 75 PHE 0.008 0.001 PHE K1544 TYR 0.018 0.002 TYR B 88 ARG 0.006 0.000 ARG K1498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.655 Fit side-chains REVERT: B 88 TYR cc_start: 0.7694 (m-10) cc_final: 0.7345 (m-10) REVERT: E 120 MET cc_start: 0.8233 (mmm) cc_final: 0.7647 (mmm) REVERT: K 1193 MET cc_start: 0.7449 (tpt) cc_final: 0.7041 (tpt) REVERT: K 1691 MET cc_start: 0.6986 (ptp) cc_final: 0.5844 (tmm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2732 time to fit residues: 13.3894 Evaluate side-chains 25 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 91 optimal weight: 0.0470 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 131 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17106 Z= 0.165 Angle : 0.546 6.641 24363 Z= 0.320 Chirality : 0.034 0.176 2714 Planarity : 0.003 0.035 2077 Dihedral : 30.033 175.328 4705 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.48 (0.24), residues: 1230 helix: 2.46 (0.19), residues: 753 sheet: -0.34 (0.63), residues: 68 loop : 0.54 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K1502 HIS 0.008 0.001 HIS B 75 PHE 0.008 0.001 PHE K1544 TYR 0.012 0.001 TYR K1102 ARG 0.005 0.000 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.446 Fit side-chains REVERT: B 88 TYR cc_start: 0.7446 (m-10) cc_final: 0.7195 (m-10) REVERT: D 62 MET cc_start: 0.8595 (mmm) cc_final: 0.8281 (mmm) REVERT: E 120 MET cc_start: 0.8310 (mmm) cc_final: 0.7690 (mmm) REVERT: K 1193 MET cc_start: 0.7401 (tpt) cc_final: 0.7006 (tpt) REVERT: K 1691 MET cc_start: 0.6982 (ptp) cc_final: 0.5968 (tmm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2672 time to fit residues: 13.2516 Evaluate side-chains 25 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 88 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1235 HIS ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17106 Z= 0.231 Angle : 0.573 7.277 24363 Z= 0.334 Chirality : 0.035 0.152 2714 Planarity : 0.004 0.034 2077 Dihedral : 30.134 176.426 4705 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.39 (0.24), residues: 1230 helix: 2.37 (0.18), residues: 759 sheet: -0.37 (0.65), residues: 68 loop : 0.50 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K1502 HIS 0.009 0.001 HIS B 75 PHE 0.025 0.001 PHE K1397 TYR 0.013 0.001 TYR D 40 ARG 0.009 0.000 ARG K1530 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.484 Fit side-chains REVERT: E 120 MET cc_start: 0.8354 (mmm) cc_final: 0.7732 (mmm) REVERT: K 1193 MET cc_start: 0.7456 (tpt) cc_final: 0.7052 (tpt) REVERT: K 1661 MET cc_start: 0.0611 (tpt) cc_final: 0.0064 (tmm) REVERT: K 1691 MET cc_start: 0.6949 (ptp) cc_final: 0.5848 (tmm) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2881 time to fit residues: 12.7783 Evaluate side-chains 23 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 94 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17106 Z= 0.230 Angle : 0.588 7.610 24363 Z= 0.342 Chirality : 0.036 0.150 2714 Planarity : 0.004 0.051 2077 Dihedral : 30.417 174.044 4705 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.14 (0.24), residues: 1230 helix: 2.22 (0.18), residues: 754 sheet: -0.54 (0.63), residues: 74 loop : 0.36 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K1502 HIS 0.009 0.002 HIS B 75 PHE 0.016 0.001 PHE K1397 TYR 0.012 0.002 TYR C 39 ARG 0.009 0.000 ARG K1530 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.445 Fit side-chains REVERT: A 120 MET cc_start: 0.7197 (mpp) cc_final: 0.6786 (mpp) REVERT: E 120 MET cc_start: 0.8369 (mmm) cc_final: 0.7743 (mmm) REVERT: K 1193 MET cc_start: 0.7457 (tpt) cc_final: 0.7042 (tpt) REVERT: K 1385 MET cc_start: 0.5972 (tpp) cc_final: 0.4553 (ppp) REVERT: K 1691 MET cc_start: 0.7031 (ptp) cc_final: 0.5951 (tmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.3017 time to fit residues: 13.9857 Evaluate side-chains 24 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 122 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.043331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.030649 restraints weight = 229815.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.031132 restraints weight = 124709.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.031455 restraints weight = 83889.089| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.6470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17106 Z= 0.223 Angle : 0.588 8.580 24363 Z= 0.340 Chirality : 0.035 0.147 2714 Planarity : 0.004 0.033 2077 Dihedral : 30.412 174.704 4705 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.19 (0.24), residues: 1230 helix: 2.26 (0.18), residues: 756 sheet: -0.59 (0.62), residues: 74 loop : 0.38 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K1502 HIS 0.009 0.001 HIS B 75 PHE 0.011 0.001 PHE K1397 TYR 0.013 0.001 TYR D 40 ARG 0.006 0.000 ARG H 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.28 seconds wall clock time: 41 minutes 39.12 seconds (2499.12 seconds total)