Starting phenix.real_space_refine on Mon Nov 18 17:24:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/11_2024/8ham_34596.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/11_2024/8ham_34596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/11_2024/8ham_34596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/11_2024/8ham_34596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/11_2024/8ham_34596.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ham_34596/11_2024/8ham_34596.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 330 5.49 5 S 46 5.16 5 C 9835 2.51 5 N 3130 2.21 5 O 3836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 135 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17177 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 720 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ALY:plan-2': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 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: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} 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: "I" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3384 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "J" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3381 Classifications: {'DNA': 165} Link IDs: {'rna3p': 164} Chain: "K" Number of atoms: 4302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4302 Classifications: {'peptide': 517} Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 484} Chain breaks: 4 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: 9.93, per 1000 atoms: 0.58 Number of scatterers: 17177 At special positions: 0 Unit cell: (101.43, 161.7, 124.95, 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 46 16.00 P 330 15.00 O 3836 8.00 N 3130 7.00 C 9835 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 - 3.00 Amino acid : True - 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: 4.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 62.0% alpha, 7.5% beta 129 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 7.09 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.775A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.705A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.356A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.533A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.686A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.559A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.561A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.342A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.943A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 1088 through 1104 Proline residue: K1096 - end of helix removed outlier: 3.514A pdb=" N GLN K1104 " --> pdb=" O ALA K1100 " (cutoff:3.500A) Processing helix chain 'K' and resid 1108 through 1112 Processing helix chain 'K' and resid 1124 through 1129 removed outlier: 3.510A pdb=" N ILE K1128 " --> pdb=" O ASP K1124 " (cutoff:3.500A) Processing helix chain 'K' and resid 1134 through 1145 Processing helix chain 'K' and resid 1149 through 1168 removed outlier: 4.061A pdb=" N TYR K1153 " --> pdb=" O GLU K1149 " (cutoff:3.500A) Processing helix chain 'K' and resid 1172 through 1197 removed outlier: 4.353A 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 1244 Processing helix chain 'K' and resid 1292 through 1296 Processing helix chain 'K' and resid 1308 through 1316 Processing helix chain 'K' and resid 1332 through 1350 Processing helix chain 'K' and resid 1372 through 1380 Processing helix chain 'K' and resid 1443 through 1464 removed outlier: 4.474A pdb=" N THR K1447 " --> pdb=" O ARG K1443 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA K1448 " --> pdb=" O CYS K1444 " (cutoff:3.500A) Processing helix chain 'K' and resid 1495 through 1513 Processing helix chain 'K' and resid 1522 through 1530 Processing helix chain 'K' and resid 1533 through 1537 Processing helix chain 'K' and resid 1543 through 1554 removed outlier: 4.115A pdb=" N ASN K1547 " --> pdb=" O ASP K1543 " (cutoff:3.500A) Processing helix chain 'K' and resid 1617 through 1629 Processing helix chain 'K' and resid 1664 through 1675 Processing helix chain 'K' and resid 1680 through 1698 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.712A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.768A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.294A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.540A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.122A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 1205 through 1206 removed outlier: 3.526A pdb=" N ASP K1276 " --> pdb=" O PHE K1206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1234 through 1237 Processing sheet with id=AB4, first strand: chain 'K' and resid 1280 through 1282 Processing sheet with id=AB5, first strand: chain 'K' and resid 1357 through 1370 removed outlier: 6.529A pdb=" N ALA K1395 " --> pdb=" O VAL K1362 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER K1364 " --> pdb=" O THR K1393 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR K1393 " --> pdb=" O SER K1364 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP K1366 " --> pdb=" O TYR K1391 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR K1391 " --> pdb=" O ASP K1366 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR K1368 " --> pdb=" O PHE K1389 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE K1389 " --> pdb=" O THR K1368 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K1396 " --> pdb=" O MET K1412 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE K1410 " --> pdb=" O ALA K1398 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLU K1400 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N CYS K1408 " --> pdb=" O GLU K1400 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE K1402 " --> pdb=" O ASP K1406 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP K1406 " --> pdb=" O ILE K1402 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN K1415 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ILE K1431 " --> pdb=" O GLN K1415 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR K1417 " --> pdb=" O VAL K1429 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL K1429 " --> pdb=" O TYR K1417 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP K1472 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N TYR K1433 " --> pdb=" O TRP K1472 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP K1518 " --> pdb=" O HIS K1636 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 310 hydrogen bonds 620 hydrogen bond angles 0 basepair planarities 129 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 7.92 Time building geometry restraints manager: 5.07 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: 3318 1.33 - 1.45: 5725 1.45 - 1.57: 8432 1.57 - 1.69: 658 1.69 - 1.81: 68 Bond restraints: 18201 Sorted by residual: bond pdb=" NZ ALY B 16 " pdb=" CH ALY B 16 " ideal model delta sigma weight residual 1.343 1.385 -0.042 2.00e-02 2.50e+03 4.45e+00 bond pdb=" NZ ALY B 12 " pdb=" CH ALY B 12 " ideal model delta sigma weight residual 1.343 1.384 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.70e+00 bond pdb=" C LEU D 101 " pdb=" N LEU D 102 " ideal model delta sigma weight residual 1.329 1.352 -0.024 1.60e-02 3.91e+03 2.20e+00 bond pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.69e+00 ... (remaining 18196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 25591 2.07 - 4.14: 381 4.14 - 6.22: 17 6.22 - 8.29: 4 8.29 - 10.36: 1 Bond angle restraints: 25994 Sorted by residual: angle pdb=" CA LEU K1507 " pdb=" CB LEU K1507 " pdb=" CG LEU K1507 " ideal model delta sigma weight residual 116.30 105.94 10.36 3.50e+00 8.16e-02 8.76e+00 angle pdb=" C ASN B 64 " pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta sigma weight residual 122.97 120.31 2.66 9.80e-01 1.04e+00 7.38e+00 angle pdb=" C PHE K1544 " pdb=" N TRP K1545 " pdb=" CA TRP K1545 " ideal model delta sigma weight residual 120.09 123.41 -3.32 1.25e+00 6.40e-01 7.04e+00 angle pdb=" CB MET K1290 " pdb=" CG MET K1290 " pdb=" SD MET K1290 " ideal model delta sigma weight residual 112.70 120.41 -7.71 3.00e+00 1.11e-01 6.60e+00 angle pdb=" C LEU D 101 " pdb=" N LEU D 102 " pdb=" CA LEU D 102 " ideal model delta sigma weight residual 120.49 116.91 3.58 1.42e+00 4.96e-01 6.35e+00 ... (remaining 25989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.73: 8639 34.73 - 69.46: 1510 69.46 - 104.19: 30 104.19 - 138.92: 2 138.92 - 173.65: 2 Dihedral angle restraints: 10183 sinusoidal: 6423 harmonic: 3760 Sorted by residual: dihedral pdb=" CA LYS B 20 " pdb=" C LYS B 20 " pdb=" N VAL B 21 " pdb=" CA VAL B 21 " ideal model delta harmonic sigma weight residual -180.00 -151.44 -28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA MET K1412 " pdb=" C MET K1412 " pdb=" N HIS K1413 " pdb=" CA HIS K1413 " ideal model delta harmonic sigma weight residual 180.00 159.34 20.66 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 10180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2234 0.034 - 0.069: 512 0.069 - 0.103: 98 0.103 - 0.137: 41 0.137 - 0.172: 1 Chirality restraints: 2886 Sorted by residual: chirality pdb=" CA ILE K1635 " pdb=" N ILE K1635 " pdb=" C ILE K1635 " pdb=" CB ILE K1635 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-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 -2.48 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CB VAL B 43 " pdb=" CA VAL B 43 " pdb=" CG1 VAL B 43 " pdb=" CG2 VAL B 43 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 2883 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 103 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO E 121 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 30 " -0.007 2.00e-02 2.50e+03 1.12e-02 2.84e+00 pdb=" N1 DC J 30 " 0.007 2.00e-02 2.50e+03 pdb=" C2 DC J 30 " -0.026 2.00e-02 2.50e+03 pdb=" O2 DC J 30 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC J 30 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DC J 30 " -0.002 2.00e-02 2.50e+03 pdb=" N4 DC J 30 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC J 30 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC J 30 " 0.006 2.00e-02 2.50e+03 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3218 2.79 - 3.32: 16302 3.32 - 3.84: 34004 3.84 - 4.37: 38628 4.37 - 4.90: 55646 Nonbonded interactions: 147798 Sorted by model distance: nonbonded pdb=" ND2 ASN E 108 " pdb=" O GLY F 42 " model vdw 2.260 3.120 nonbonded pdb=" N GLY C 44 " pdb=" O ILE D 89 " model vdw 2.268 3.120 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.296 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.304 3.040 nonbonded pdb=" NH2 ARG G 35 " pdb=" OP2 DT I 129 " model vdw 2.309 3.120 ... (remaining 147793 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 19 through 102) selection = chain 'F' } 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 10 through 171) selection = (chain 'J' and resid 10 through 171) } 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: 0.700 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 44.300 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 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 0.049 18201 Z= 0.155 Angle : 0.565 10.362 25994 Z= 0.351 Chirality : 0.033 0.172 2886 Planarity : 0.004 0.047 2162 Dihedral : 25.163 173.648 7755 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.08 (0.23), residues: 1258 helix: 1.94 (0.18), residues: 772 sheet: 0.25 (0.61), residues: 77 loop : 0.68 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1472 HIS 0.009 0.001 HIS K1451 PHE 0.024 0.001 PHE K1410 TYR 0.016 0.001 TYR K1227 ARG 0.006 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 1.579 Fit side-chains REVERT: A 97 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 124 ILE cc_start: 0.9712 (mt) cc_final: 0.9507 (tp) REVERT: B 84 MET cc_start: 0.7405 (tpp) cc_final: 0.7030 (mmm) REVERT: D 59 MET cc_start: 0.9014 (tpp) cc_final: 0.8581 (tpp) REVERT: K 1502 TRP cc_start: 0.4260 (t60) cc_final: 0.3669 (t60) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.2983 time to fit residues: 26.3523 Evaluate side-chains 42 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 63 optimal weight: 0.0270 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 141 optimal weight: 0.7980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18201 Z= 0.164 Angle : 0.529 8.330 25994 Z= 0.312 Chirality : 0.034 0.157 2886 Planarity : 0.004 0.045 2162 Dihedral : 28.753 172.997 5132 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.62 (0.23), residues: 1258 helix: 2.40 (0.18), residues: 784 sheet: 0.33 (0.59), residues: 79 loop : 0.81 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K1545 HIS 0.006 0.001 HIS E 113 PHE 0.017 0.001 PHE D 65 TYR 0.016 0.001 TYR C 50 ARG 0.004 0.000 ARG K1441 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8575 (mtm) cc_final: 0.8340 (mtp) REVERT: C 72 ASP cc_start: 0.8904 (m-30) cc_final: 0.8584 (m-30) REVERT: E 97 GLU cc_start: 0.7634 (mt-10) cc_final: 0.6763 (mt-10) REVERT: H 61 ILE cc_start: 0.9430 (mm) cc_final: 0.9132 (mm) REVERT: K 1502 TRP cc_start: 0.4183 (t60) cc_final: 0.3750 (t60) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2800 time to fit residues: 26.5245 Evaluate side-chains 40 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 117 optimal weight: 40.0000 chunk 96 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 141 optimal weight: 0.0570 chunk 153 optimal weight: 7.9990 chunk 126 optimal weight: 9.9990 chunk 140 optimal weight: 40.0000 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN C 104 GLN E 39 HIS E 108 ASN F 64 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN K1113 GLN K1266 GLN ** K1291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1310 ASN K1415 GLN ** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 18201 Z= 0.357 Angle : 0.726 10.250 25994 Z= 0.410 Chirality : 0.041 0.183 2886 Planarity : 0.006 0.049 2162 Dihedral : 29.859 169.184 5132 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.18 % Allowed : 3.15 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.89 (0.23), residues: 1258 helix: 1.82 (0.18), residues: 782 sheet: 0.29 (0.58), residues: 79 loop : 0.47 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K1545 HIS 0.012 0.002 HIS F 75 PHE 0.026 0.002 PHE G 25 TYR 0.032 0.002 TYR K1298 ARG 0.008 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 1.417 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8276 (pt0) cc_final: 0.7629 (mt-10) REVERT: A 120 MET cc_start: 0.8560 (mtm) cc_final: 0.8120 (mtp) REVERT: C 56 GLU cc_start: 0.8202 (tt0) cc_final: 0.7463 (tt0) REVERT: E 97 GLU cc_start: 0.8464 (mt-10) cc_final: 0.7546 (mt-10) REVERT: F 84 MET cc_start: 0.8343 (tpp) cc_final: 0.8031 (tpp) REVERT: H 61 ILE cc_start: 0.9553 (mm) cc_final: 0.9246 (mm) REVERT: H 62 MET cc_start: 0.9173 (tpt) cc_final: 0.8872 (tpp) REVERT: K 1502 TRP cc_start: 0.4612 (t60) cc_final: 0.3906 (t60) outliers start: 2 outliers final: 1 residues processed: 51 average time/residue: 0.3053 time to fit residues: 25.0175 Evaluate side-chains 34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 40.0000 chunk 106 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN K1146 GLN K1291 HIS K1698 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18201 Z= 0.259 Angle : 0.597 10.002 25994 Z= 0.348 Chirality : 0.036 0.159 2886 Planarity : 0.004 0.048 2162 Dihedral : 29.794 169.513 5132 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.27 (0.23), residues: 1258 helix: 2.11 (0.18), residues: 783 sheet: 0.41 (0.58), residues: 77 loop : 0.63 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K1545 HIS 0.008 0.001 HIS B 75 PHE 0.020 0.002 PHE A 104 TYR 0.020 0.002 TYR K1102 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8572 (mtm) cc_final: 0.8052 (mtp) REVERT: E 97 GLU cc_start: 0.7967 (mt-10) cc_final: 0.6716 (mt-10) REVERT: F 84 MET cc_start: 0.8152 (tpp) cc_final: 0.7876 (tpp) REVERT: H 59 MET cc_start: 0.8477 (tpp) cc_final: 0.8251 (tpp) REVERT: H 61 ILE cc_start: 0.9579 (mm) cc_final: 0.9227 (mm) REVERT: H 62 MET cc_start: 0.9048 (tpt) cc_final: 0.8809 (tpp) REVERT: K 1502 TRP cc_start: 0.3934 (t60) cc_final: 0.3596 (t60) REVERT: K 1691 MET cc_start: 0.5592 (ppp) cc_final: 0.5342 (ppp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2667 time to fit residues: 20.8709 Evaluate side-chains 35 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.5980 chunk 85 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 30.0000 chunk 62 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 135 optimal weight: 30.0000 chunk 38 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: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN G 38 ASN K1628 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 18201 Z= 0.386 Angle : 0.699 9.449 25994 Z= 0.399 Chirality : 0.040 0.255 2886 Planarity : 0.005 0.044 2162 Dihedral : 30.193 166.492 5132 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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 (0.23), residues: 1258 helix: 1.77 (0.18), residues: 783 sheet: -0.01 (0.56), residues: 79 loop : 0.49 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K1545 HIS 0.007 0.002 HIS F 75 PHE 0.018 0.002 PHE K1267 TYR 0.016 0.002 TYR H 42 ARG 0.009 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 120 MET cc_start: 0.8496 (mtm) cc_final: 0.7871 (mtp) REVERT: E 97 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7170 (mt-10) REVERT: F 84 MET cc_start: 0.8113 (tpp) cc_final: 0.7476 (tpp) REVERT: H 61 ILE cc_start: 0.9602 (mm) cc_final: 0.9301 (mm) REVERT: H 62 MET cc_start: 0.9224 (tpt) cc_final: 0.8999 (tpp) REVERT: K 1502 TRP cc_start: 0.4805 (t60) cc_final: 0.4407 (t60) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2893 time to fit residues: 21.4651 Evaluate side-chains 34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 24 GLN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18201 Z= 0.170 Angle : 0.566 8.276 25994 Z= 0.334 Chirality : 0.035 0.150 2886 Planarity : 0.004 0.043 2162 Dihedral : 30.086 171.714 5132 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.30 (0.24), residues: 1258 helix: 2.21 (0.18), residues: 784 sheet: 0.05 (0.57), residues: 79 loop : 0.56 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K1502 HIS 0.006 0.001 HIS B 75 PHE 0.014 0.001 PHE K1410 TYR 0.010 0.001 TYR C 57 ARG 0.004 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 120 MET cc_start: 0.8565 (mtm) cc_final: 0.7980 (mtp) REVERT: E 106 ASP cc_start: 0.8945 (m-30) cc_final: 0.8740 (m-30) REVERT: F 84 MET cc_start: 0.7649 (tpp) cc_final: 0.7118 (tpp) REVERT: H 61 ILE cc_start: 0.9573 (mm) cc_final: 0.9265 (mm) REVERT: H 62 MET cc_start: 0.9116 (tpt) cc_final: 0.8914 (tpp) REVERT: K 1385 MET cc_start: 0.4740 (ttt) cc_final: 0.4527 (ttt) REVERT: K 1502 TRP cc_start: 0.4411 (t60) cc_final: 0.4034 (t60) REVERT: K 1691 MET cc_start: 0.5364 (ppp) cc_final: 0.5125 (ppp) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.2589 time to fit residues: 24.3662 Evaluate side-chains 39 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 20.0000 chunk 17 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.050 18201 Z= 0.445 Angle : 0.739 10.216 25994 Z= 0.419 Chirality : 0.042 0.163 2886 Planarity : 0.005 0.051 2162 Dihedral : 30.500 167.347 5132 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.54 (0.23), residues: 1258 helix: 1.61 (0.18), residues: 786 sheet: 0.24 (0.63), residues: 67 loop : 0.12 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K1545 HIS 0.010 0.002 HIS F 75 PHE 0.021 0.002 PHE H 65 TYR 0.017 0.002 TYR D 40 ARG 0.009 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 1.831 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8500 (mtm) cc_final: 0.7805 (mtp) REVERT: E 110 CYS cc_start: 0.9160 (m) cc_final: 0.8893 (m) REVERT: F 84 MET cc_start: 0.8182 (tpp) cc_final: 0.7484 (tpp) REVERT: H 61 ILE cc_start: 0.9603 (mm) cc_final: 0.9331 (mm) REVERT: H 62 MET cc_start: 0.9214 (tpt) cc_final: 0.9009 (tpp) REVERT: K 1691 MET cc_start: 0.5801 (ppp) cc_final: 0.5582 (ppp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.3093 time to fit residues: 19.5640 Evaluate side-chains 28 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18201 Z= 0.217 Angle : 0.588 8.950 25994 Z= 0.346 Chirality : 0.035 0.151 2886 Planarity : 0.004 0.052 2162 Dihedral : 30.430 172.864 5132 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.99 (0.24), residues: 1258 helix: 1.99 (0.18), residues: 789 sheet: 0.26 (0.64), residues: 67 loop : 0.28 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K1676 HIS 0.006 0.001 HIS B 75 PHE 0.021 0.002 PHE K1410 TYR 0.014 0.001 TYR D 40 ARG 0.003 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 1.647 Fit side-chains REVERT: A 97 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 106 ASP cc_start: 0.8747 (m-30) cc_final: 0.8416 (m-30) REVERT: A 120 MET cc_start: 0.8479 (mtm) cc_final: 0.7844 (mtp) REVERT: F 84 MET cc_start: 0.7712 (tpp) cc_final: 0.7121 (tpp) REVERT: H 61 ILE cc_start: 0.9556 (mm) cc_final: 0.9294 (mm) REVERT: H 62 MET cc_start: 0.9158 (tpt) cc_final: 0.8947 (tpp) REVERT: K 1502 TRP cc_start: 0.4181 (t60) cc_final: 0.3908 (t60) REVERT: K 1691 MET cc_start: 0.5769 (ppp) cc_final: 0.5529 (ppp) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2493 time to fit residues: 18.9989 Evaluate side-chains 34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 144 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 18201 Z= 0.422 Angle : 0.729 10.208 25994 Z= 0.415 Chirality : 0.041 0.178 2886 Planarity : 0.005 0.060 2162 Dihedral : 30.789 170.351 5132 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.44 (0.23), residues: 1258 helix: 1.55 (0.18), residues: 785 sheet: 0.22 (0.65), residues: 67 loop : 0.03 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K1545 HIS 0.011 0.002 HIS F 75 PHE 0.023 0.003 PHE H 65 TYR 0.013 0.002 TYR E 99 ARG 0.008 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8413 (mtm) cc_final: 0.7782 (mtp) REVERT: F 84 MET cc_start: 0.8114 (tpp) cc_final: 0.7405 (tpp) REVERT: H 61 ILE cc_start: 0.9592 (mm) cc_final: 0.9290 (mm) REVERT: H 62 MET cc_start: 0.9248 (tpt) cc_final: 0.9027 (tpp) REVERT: K 1691 MET cc_start: 0.5825 (ppp) cc_final: 0.5594 (ppp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.2384 time to fit residues: 14.7704 Evaluate side-chains 28 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 143 optimal weight: 0.0670 chunk 123 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18201 Z= 0.299 Angle : 0.649 11.971 25994 Z= 0.374 Chirality : 0.037 0.169 2886 Planarity : 0.005 0.051 2162 Dihedral : 30.790 173.061 5132 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.64 (0.24), residues: 1258 helix: 1.73 (0.18), residues: 789 sheet: 0.19 (0.65), residues: 67 loop : 0.08 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K1676 HIS 0.007 0.001 HIS F 75 PHE 0.026 0.002 PHE K1410 TYR 0.016 0.001 TYR H 40 ARG 0.005 0.000 ARG F 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 1.381 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8397 (mtm) cc_final: 0.7829 (mtp) REVERT: F 84 MET cc_start: 0.8020 (tpp) cc_final: 0.7306 (tpp) REVERT: H 61 ILE cc_start: 0.9512 (mm) cc_final: 0.9125 (mm) REVERT: H 62 MET cc_start: 0.9208 (tpt) cc_final: 0.8979 (tpp) REVERT: K 1691 MET cc_start: 0.6051 (ppp) cc_final: 0.5763 (ppp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2507 time to fit residues: 15.5620 Evaluate side-chains 29 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.058521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037565 restraints weight = 166108.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.037512 restraints weight = 89985.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.037889 restraints weight = 59941.928| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.6316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18201 Z= 0.193 Angle : 0.585 8.478 25994 Z= 0.342 Chirality : 0.035 0.171 2886 Planarity : 0.004 0.051 2162 Dihedral : 30.529 173.769 5132 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 2.01 (0.24), residues: 1258 helix: 2.05 (0.18), residues: 788 sheet: 0.16 (0.65), residues: 67 loop : 0.19 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K1676 HIS 0.007 0.001 HIS B 75 PHE 0.025 0.002 PHE K1410 TYR 0.013 0.001 TYR C 57 ARG 0.005 0.000 ARG F 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2230.07 seconds wall clock time: 42 minutes 56.08 seconds (2576.08 seconds total)