Starting phenix.real_space_refine on Fri Sep 27 13:22:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/09_2024/8han_34597.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/09_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_34597/09_2024/8han_34597.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/09_2024/8han_34597.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/09_2024/8han_34597.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8han_34597/09_2024/8han_34597.cif" } 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. Time to flip 108 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.13, 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 - 3.00 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: 4.06 Conformation dependent library (CDL) restraints added in 1.2 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... Secondary structure from input PDB file: 52 helices and 14 sheets defined 61.5% alpha, 7.5% beta 118 base pairs and 226 stacking pairs defined. Time for finding SS restraints: 6.69 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.555A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.516A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.659A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) 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 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: 4.393A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 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 104 through 123 Processing helix chain 'E' and resid 46 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: 3.583A 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 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.724A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) 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 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.419A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 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 1089 through 1103 Proline residue: K1096 - end of helix Processing helix chain 'K' and resid 1108 through 1112 Processing helix chain 'K' and resid 1116 through 1121 Processing helix chain 'K' and resid 1124 through 1129 removed outlier: 3.512A 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: 4.121A pdb=" N TYR K1153 " --> pdb=" O GLU K1149 " (cutoff:3.500A) Processing helix chain 'K' and resid 1172 through 1197 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 1237 through 1242 removed outlier: 3.502A pdb=" N PHE K1241 " --> pdb=" O CYS K1237 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR K1242 " --> pdb=" O GLU K1238 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1237 through 1242' Processing helix chain 'K' and resid 1292 through 1296 Processing helix chain 'K' and resid 1308 through 1314 Processing helix chain 'K' and resid 1332 through 1350 Processing helix chain 'K' and resid 1445 through 1465 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 1555 removed outlier: 3.752A pdb=" N ASN K1547 " --> pdb=" O ASP K1543 " (cutoff:3.500A) Processing helix chain 'K' and resid 1621 through 1628 Processing helix chain 'K' and resid 1663 through 1674 removed outlier: 3.940A pdb=" N PHE K1667 " --> pdb=" O GLY K1663 " (cutoff:3.500A) 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: 6.604A 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: 6.397A 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: 6.985A 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: 7.005A 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 removed outlier: 3.635A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.202A 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 1211 through 1212 removed outlier: 3.833A pdb=" N LEU K1211 " --> pdb=" O ILE K1221 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1234 through 1236 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: 6.879A pdb=" N ALA K1395 " --> pdb=" O VAL K1362 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER K1364 " --> pdb=" O THR K1393 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR K1393 " --> pdb=" O SER K1364 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP K1366 " --> pdb=" O TYR K1391 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR K1391 " --> pdb=" O ASP K1366 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR K1368 " --> pdb=" O PHE K1389 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE K1389 " --> pdb=" O THR K1368 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU K1396 " --> pdb=" O MET K1412 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET K1412 " --> pdb=" O LEU K1396 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE K1410 " --> pdb=" O ALA K1398 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU K1400 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N CYS K1408 " --> pdb=" O GLU K1400 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE K1402 " --> pdb=" O ASP K1406 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP K1406 " --> pdb=" O ILE K1402 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR K1433 " --> pdb=" O HIS K1413 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN K1415 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE K1431 " --> pdb=" O GLN K1415 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR K1417 " --> pdb=" O VAL K1429 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL K1429 " --> pdb=" O TYR K1417 " (cutoff:3.500A) 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) 586 hydrogen bonds defined for protein. 1731 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: 7.86 Time building geometry restraints manager: 4.64 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: 0.00 - 1.66: 23876 1.66 - 3.31: 443 3.31 - 4.97: 37 4.97 - 6.63: 4 6.63 - 8.28: 3 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: 1818 2.76 - 3.29: 15194 3.29 - 3.83: 31831 3.83 - 4.36: 35551 4.36 - 4.90: 52884 Nonbonded interactions: 137278 Sorted by model distance: nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP A 123 " pdb=" NE2 HIS E 113 " model vdw 2.236 3.120 nonbonded pdb=" NH1 ARG C 17 " pdb=" OP2 DG J 48 " model vdw 2.244 3.120 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.274 3.120 nonbonded pdb=" N2 DG I 35 " pdb=" O2 DT J 147 " model vdw 2.277 3.120 ... (remaining 137273 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 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: 1.460 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 42.320 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- 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= 0.151 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 : 1.353 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: 0.2268 time to fit residues: 11.9141 Evaluate side-chains 24 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 136 optimal weight: 10.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1628 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.0985 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= 0.167 Angle : 0.509 5.879 24363 Z= 0.299 Chirality : 0.033 0.150 2714 Planarity : 0.003 0.033 2077 Dihedral : 28.472 170.382 4705 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % 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: 3.04 (0.24), residues: 1230 helix: 2.73 (0.18), residues: 766 sheet: 0.36 (0.63), residues: 66 loop : 0.98 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K1502 HIS 0.005 0.001 HIS A 113 PHE 0.008 0.001 PHE A 67 TYR 0.014 0.001 TYR K1102 ARG 0.005 0.000 ARG G 88 *********************** 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: 0 poor density : 29 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: H 62 MET cc_start: 0.8865 (mmp) cc_final: 0.8661 (mmt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.2308 time to fit residues: 12.3197 Evaluate side-chains 24 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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: 0.4980 chunk 42 optimal weight: 6.9990 chunk 113 optimal weight: 40.0000 chunk 92 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 GLN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17106 Z= 0.322 Angle : 0.642 7.011 24363 Z= 0.374 Chirality : 0.038 0.145 2714 Planarity : 0.005 0.044 2077 Dihedral : 29.274 174.739 4705 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % 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: 2.52 (0.23), residues: 1230 helix: 2.31 (0.18), residues: 763 sheet: 0.13 (0.65), residues: 69 loop : 0.83 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K1158 HIS 0.009 0.002 HIS K1297 PHE 0.013 0.002 PHE G 25 TYR 0.036 0.002 TYR B 88 ARG 0.011 0.001 ARG K1202 *********************** 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 28 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.337 Fit side-chains REVERT: E 120 MET cc_start: 0.8529 (mmp) cc_final: 0.7837 (mmm) REVERT: K 1691 MET cc_start: 0.6936 (ptp) cc_final: 0.5683 (tmm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2419 time to fit residues: 12.6629 Evaluate side-chains 24 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 2.276 ------------------------------------------------------------------------------- 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: 30.0000 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** K1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1343 ASN K1487 HIS K1547 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17106 Z= 0.339 Angle : 0.688 8.417 24363 Z= 0.394 Chirality : 0.039 0.159 2714 Planarity : 0.006 0.126 2077 Dihedral : 30.237 179.371 4705 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: 1.81 (0.18), residues: 765 sheet: 0.12 (0.63), residues: 66 loop : 0.53 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP K1502 HIS 0.008 0.002 HIS B 75 PHE 0.024 0.002 PHE E 104 TYR 0.019 0.002 TYR K1153 ARG 0.014 0.001 ARG A 134 *********************** 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 30 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.7355 (mpp) cc_final: 0.7126 (mpp) REVERT: E 120 MET cc_start: 0.8622 (mmp) cc_final: 0.8354 (mmm) REVERT: K 1193 MET cc_start: 0.7325 (tpt) cc_final: 0.7052 (tpt) REVERT: K 1661 MET cc_start: 0.0835 (mmm) cc_final: 0.0600 (mmm) REVERT: K 1691 MET cc_start: 0.6804 (ptp) cc_final: 0.5579 (tmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.3152 time to fit residues: 15.0429 Evaluate side-chains 26 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.281 ------------------------------------------------------------------------------- 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: 8.9990 chunk 82 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 107 optimal weight: 0.0870 chunk 59 optimal weight: 0.3980 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN K1146 GLN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1413 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17106 Z= 0.185 Angle : 0.561 6.471 24363 Z= 0.329 Chirality : 0.035 0.165 2714 Planarity : 0.004 0.035 2077 Dihedral : 30.041 179.039 4705 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 2.44 (0.24), residues: 1230 helix: 2.30 (0.18), residues: 766 sheet: 0.04 (0.64), residues: 68 loop : 0.66 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K1502 HIS 0.011 0.001 HIS K1351 PHE 0.009 0.001 PHE K1397 TYR 0.013 0.001 TYR C 50 ARG 0.005 0.000 ARG A 134 *********************** 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 30 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 1.467 Fit side-chains REVERT: A 120 MET cc_start: 0.7343 (mpp) cc_final: 0.7118 (mpp) REVERT: E 120 MET cc_start: 0.8544 (mmp) cc_final: 0.7870 (mmm) REVERT: K 1193 MET cc_start: 0.7648 (tpt) cc_final: 0.7351 (tpt) REVERT: K 1232 ASN cc_start: -0.1196 (m-40) cc_final: -0.1729 (p0) REVERT: K 1661 MET cc_start: 0.0282 (mmm) cc_final: 0.0078 (mmm) REVERT: K 1691 MET cc_start: 0.6821 (ptp) cc_final: 0.5626 (tmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2639 time to fit residues: 13.7763 Evaluate side-chains 26 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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: 6.9990 chunk 130 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17106 Z= 0.191 Angle : 0.548 6.135 24363 Z= 0.321 Chirality : 0.034 0.148 2714 Planarity : 0.004 0.033 2077 Dihedral : 29.799 179.559 4705 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: 2.62 (0.24), residues: 1230 helix: 2.43 (0.18), residues: 764 sheet: 0.02 (0.64), residues: 69 loop : 0.79 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K1502 HIS 0.007 0.001 HIS B 75 PHE 0.007 0.001 PHE D 65 TYR 0.009 0.001 TYR G 57 ARG 0.003 0.000 ARG A 134 *********************** 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 30 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 1.370 Fit side-chains REVERT: E 120 MET cc_start: 0.8514 (mmp) cc_final: 0.8208 (mmm) REVERT: K 1193 MET cc_start: 0.7495 (tpt) cc_final: 0.7275 (tpt) REVERT: K 1691 MET cc_start: 0.6957 (ptp) cc_final: 0.5875 (tmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2601 time to fit residues: 13.5555 Evaluate side-chains 26 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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: 3.9990 chunk 82 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN ** H 63 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: 0.7730 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17106 Z= 0.275 Angle : 0.610 6.216 24363 Z= 0.352 Chirality : 0.037 0.403 2714 Planarity : 0.005 0.032 2077 Dihedral : 30.168 177.886 4705 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: 2.24 (0.18), residues: 765 sheet: 0.07 (0.64), residues: 66 loop : 0.68 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K1502 HIS 0.011 0.002 HIS B 75 PHE 0.013 0.002 PHE K1397 TYR 0.013 0.002 TYR D 40 ARG 0.005 0.001 ARG G 20 *********************** 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 : 1.446 Fit side-chains REVERT: B 88 TYR cc_start: 0.7231 (m-10) cc_final: 0.6911 (m-10) REVERT: E 120 MET cc_start: 0.8640 (mmp) cc_final: 0.8054 (mmm) REVERT: K 1193 MET cc_start: 0.7651 (tpt) cc_final: 0.7391 (tpt) REVERT: K 1691 MET cc_start: 0.7027 (ptp) cc_final: 0.5806 (tmm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2812 time to fit residues: 13.8610 Evaluate side-chains 26 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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: 8.9990 chunk 43 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN ** H 63 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: 0.7671 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17106 Z= 0.180 Angle : 0.556 7.273 24363 Z= 0.324 Chirality : 0.034 0.148 2714 Planarity : 0.004 0.034 2077 Dihedral : 30.121 176.162 4705 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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: 2.63 (0.24), residues: 1230 helix: 2.46 (0.18), residues: 766 sheet: -0.05 (0.65), residues: 68 loop : 0.75 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K1502 HIS 0.009 0.001 HIS B 75 PHE 0.007 0.001 PHE K1544 TYR 0.017 0.001 TYR K1102 ARG 0.005 0.000 ARG F 92 *********************** 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 32 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.481 Fit side-chains REVERT: B 88 TYR cc_start: 0.7186 (m-10) cc_final: 0.6928 (m-10) REVERT: E 120 MET cc_start: 0.8469 (mmp) cc_final: 0.7870 (mmm) REVERT: K 1193 MET cc_start: 0.7519 (tpt) cc_final: 0.7293 (tpt) REVERT: K 1232 ASN cc_start: -0.1569 (m-40) cc_final: -0.2092 (p0) REVERT: K 1691 MET cc_start: 0.6959 (ptp) cc_final: 0.5801 (tmm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.2617 time to fit residues: 14.7907 Evaluate side-chains 27 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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: 10.0000 chunk 58 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN F 93 GLN H 84 ASN K1235 HIS ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17106 Z= 0.366 Angle : 0.695 8.109 24363 Z= 0.395 Chirality : 0.040 0.162 2714 Planarity : 0.005 0.043 2077 Dihedral : 30.733 178.137 4705 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: 1.97 (0.24), residues: 1230 helix: 1.94 (0.18), residues: 760 sheet: -0.39 (0.65), residues: 69 loop : 0.53 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K1502 HIS 0.009 0.002 HIS B 75 PHE 0.011 0.002 PHE H 65 TYR 0.017 0.002 TYR K1539 ARG 0.010 0.001 ARG B 45 *********************** 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 28 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.366 Fit side-chains REVERT: B 88 TYR cc_start: 0.7427 (m-10) cc_final: 0.7075 (m-10) REVERT: E 120 MET cc_start: 0.8749 (mmp) cc_final: 0.8150 (mmm) REVERT: K 1193 MET cc_start: 0.7314 (tpt) cc_final: 0.7069 (tpt) REVERT: K 1691 MET cc_start: 0.7017 (ptp) cc_final: 0.5830 (tmm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2633 time to fit residues: 12.8791 Evaluate side-chains 25 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.415 ------------------------------------------------------------------------------- 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: 0.9980 chunk 99 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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** ** K1438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 17106 Z= 0.340 Angle : 0.689 7.817 24363 Z= 0.392 Chirality : 0.039 0.156 2714 Planarity : 0.005 0.031 2077 Dihedral : 31.167 173.350 4705 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.56 (0.23), residues: 1230 helix: 1.66 (0.18), residues: 764 sheet: -0.62 (0.63), residues: 75 loop : 0.28 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K1502 HIS 0.010 0.002 HIS B 75 PHE 0.013 0.002 PHE H 65 TYR 0.017 0.002 TYR D 40 ARG 0.005 0.001 ARG A 134 ********************** 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 27 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 1.352 Fit side-chains revert: symmetry clash REVERT: B 58 LEU cc_start: 0.8832 (tp) cc_final: 0.8344 (pp) REVERT: E 120 MET cc_start: 0.8857 (mmp) cc_final: 0.8282 (mmm) REVERT: K 1691 MET cc_start: 0.7074 (ptp) cc_final: 0.5773 (tmm) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.2685 time to fit residues: 12.7543 Evaluate side-chains 24 residues out of total 1089 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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: 0.0970 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN K1438 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.043603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.031490 restraints weight = 227561.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.031506 restraints weight = 133173.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.031776 restraints weight = 84628.238| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17106 Z= 0.186 Angle : 0.594 7.960 24363 Z= 0.343 Chirality : 0.035 0.147 2714 Planarity : 0.004 0.036 2077 Dihedral : 30.637 172.822 4705 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % 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: 2.15 (0.24), residues: 1230 helix: 2.16 (0.18), residues: 770 sheet: -0.29 (0.68), residues: 64 loop : 0.35 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K1502 HIS 0.009 0.001 HIS B 75 PHE 0.031 0.002 PHE K1399 TYR 0.013 0.001 TYR K1102 ARG 0.006 0.000 ARG K1530 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1953.96 seconds wall clock time: 36 minutes 45.52 seconds (2205.52 seconds total)