Starting phenix.real_space_refine on Fri Mar 15 01:41:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7a_10391/03_2024/6t7a_10391.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7a_10391/03_2024/6t7a_10391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7a_10391/03_2024/6t7a_10391.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7a_10391/03_2024/6t7a_10391.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7a_10391/03_2024/6t7a_10391.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7a_10391/03_2024/6t7a_10391.pdb" } resolution = 3.7 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= 0.003 sd= 0.021 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 190 5.49 5 S 10 5.16 5 C 5889 2.51 5 N 1960 2.21 5 O 2289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 64": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10338 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} 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: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" 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: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1936 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "J" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1959 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "K" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 307 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 178 Time building chain proxies: 5.81, per 1000 atoms: 0.56 Number of scatterers: 10338 At special positions: 0 Unit cell: (85.05, 115.5, 129.15, 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 10 16.00 P 190 15.00 O 2289 8.00 N 1960 7.00 C 5889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 1.2 seconds 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1438 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 8 sheets defined 68.2% alpha, 1.9% beta 93 base pairs and 171 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.965A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.511A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.534A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.769A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 4.227A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.160A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.810A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) 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: 4.184A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.552A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.540A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.585A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.331A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.722A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 31 through 41 removed outlier: 4.046A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 50 through 76 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.809A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) 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: 4.185A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.552A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.540A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.584A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.331A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 3.602A pdb=" N VAL K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 91 through 94 Processing helix chain 'K' and resid 95 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.875A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.264A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.451A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.507A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.375A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 408 hydrogen bonds defined for protein. 1209 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 216 hydrogen bonds 432 hydrogen bond angles 0 basepair planarities 93 basepair parallelities 171 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 5.10 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: 1653 1.33 - 1.44: 3477 1.44 - 1.56: 5364 1.56 - 1.68: 378 1.68 - 1.80: 20 Bond restraints: 10892 Sorted by residual: bond pdb=" C3' DT I 87 " pdb=" O3' DT I 87 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.32e+00 bond pdb=" C ILE K 96 " pdb=" N PRO K 97 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.36e-02 5.41e+03 2.75e+00 bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.492 1.418 0.074 5.00e-02 4.00e+02 2.19e+00 bond pdb=" CA ILE F 26 " pdb=" C ILE F 26 " ideal model delta sigma weight residual 1.523 1.542 -0.018 1.27e-02 6.20e+03 2.11e+00 bond pdb=" CB ASN G 110 " pdb=" CG ASN G 110 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.09e+00 ... (remaining 10887 not shown) Histogram of bond angle deviations from ideal: 96.29 - 103.88: 653 103.88 - 111.47: 5248 111.47 - 119.06: 3850 119.06 - 126.65: 5108 126.65 - 134.23: 605 Bond angle restraints: 15464 Sorted by residual: angle pdb=" N ILE F 34 " pdb=" CA ILE F 34 " pdb=" C ILE F 34 " ideal model delta sigma weight residual 112.96 107.02 5.94 1.00e+00 1.00e+00 3.53e+01 angle pdb=" CA ARG F 23 " pdb=" C ARG F 23 " pdb=" N ASP F 24 " ideal model delta sigma weight residual 119.63 115.90 3.73 8.10e-01 1.52e+00 2.12e+01 angle pdb=" C ARG F 23 " pdb=" CA ARG F 23 " pdb=" CB ARG F 23 " ideal model delta sigma weight residual 116.63 111.29 5.34 1.16e+00 7.43e-01 2.12e+01 angle pdb=" C LYS K 88 " pdb=" N MET K 89 " pdb=" CA MET K 89 " ideal model delta sigma weight residual 122.54 115.16 7.38 1.65e+00 3.67e-01 2.00e+01 angle pdb=" CA LYS H 27 " pdb=" CB LYS H 27 " pdb=" CG LYS H 27 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 ... (remaining 15459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 4324 19.65 - 39.31: 919 39.31 - 58.96: 783 58.96 - 78.61: 52 78.61 - 98.26: 17 Dihedral angle restraints: 6095 sinusoidal: 3789 harmonic: 2306 Sorted by residual: dihedral pdb=" CA LYS D 27 " pdb=" C LYS D 27 " pdb=" N ARG D 28 " pdb=" CA ARG D 28 " ideal model delta harmonic sigma weight residual 180.00 152.71 27.29 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA LYS H 27 " pdb=" C LYS H 27 " pdb=" N ARG H 28 " pdb=" CA ARG H 28 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 6092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1240 0.048 - 0.096: 373 0.096 - 0.144: 85 0.144 - 0.191: 15 0.191 - 0.239: 2 Chirality restraints: 1715 Sorted by residual: chirality pdb=" CB THR C 59 " pdb=" CA THR C 59 " pdb=" OG1 THR C 59 " pdb=" CG2 THR C 59 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB THR G 59 " pdb=" CA THR G 59 " pdb=" OG1 THR G 59 " pdb=" CG2 THR G 59 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" C PRO C 80 " pdb=" CB PRO C 80 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1712 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" C ASP F 24 " -0.069 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.026 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 60 " 0.028 2.00e-02 2.50e+03 1.50e-02 5.64e+00 pdb=" N1 DT I 60 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT I 60 " -0.014 2.00e-02 2.50e+03 pdb=" O2 DT I 60 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 60 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 60 " 0.008 2.00e-02 2.50e+03 pdb=" O4 DT I 60 " 0.013 2.00e-02 2.50e+03 pdb=" C5 DT I 60 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 60 " -0.012 2.00e-02 2.50e+03 pdb=" C6 DT I 60 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO C 80 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 0.73 - 1.57: 3 1.57 - 2.40: 27 2.40 - 3.23: 8880 3.23 - 4.07: 29627 4.07 - 4.90: 48132 Warning: very small nonbonded interaction distances. Nonbonded interactions: 86669 Sorted by model distance: nonbonded pdb=" CG GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 0.733 3.520 nonbonded pdb=" CB GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 0.902 3.520 nonbonded pdb=" CG GLU E 73 " pdb=" CG ASN F 25 " model vdw 1.472 3.670 nonbonded pdb=" CD GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 1.995 3.350 nonbonded pdb=" CB GLU E 73 " pdb=" CG ASN F 25 " model vdw 2.044 3.670 ... (remaining 86664 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 16 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.100 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: 1.160 Check model and map are aligned: 0.170 Set scattering table: 0.090 Process input model: 33.580 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.040 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 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 : 0.006 0.074 10892 Z= 0.375 Angle : 0.870 9.233 15464 Z= 0.526 Chirality : 0.048 0.239 1715 Planarity : 0.006 0.058 1327 Dihedral : 26.125 98.264 4657 Min Nonbonded Distance : 0.733 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.81 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.23), residues: 829 helix: -1.95 (0.16), residues: 569 sheet: None (None), residues: 0 loop : -1.70 (0.34), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.009 0.002 PHE D 62 TYR 0.027 0.002 TYR F 98 ARG 0.007 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.9019 (t80) cc_final: 0.8623 (t80) REVERT: B 59 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8236 (mtpt) REVERT: B 60 VAL cc_start: 0.9049 (m) cc_final: 0.8010 (p) REVERT: B 63 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7510 (mt-10) REVERT: B 92 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7676 (ttp80) REVERT: C 73 ASN cc_start: 0.8815 (t0) cc_final: 0.8556 (t0) REVERT: C 84 GLN cc_start: 0.8744 (tp40) cc_final: 0.8352 (tp-100) REVERT: D 85 THR cc_start: 0.9519 (m) cc_final: 0.9088 (p) REVERT: E 86 SER cc_start: 0.8750 (m) cc_final: 0.8499 (m) REVERT: E 124 ILE cc_start: 0.9285 (mt) cc_final: 0.8917 (mp) REVERT: F 59 LYS cc_start: 0.8804 (tttm) cc_final: 0.8597 (tttm) REVERT: F 60 VAL cc_start: 0.9172 (p) cc_final: 0.8677 (m) REVERT: F 70 VAL cc_start: 0.9486 (t) cc_final: 0.8584 (t) REVERT: F 71 THR cc_start: 0.9268 (p) cc_final: 0.8683 (p) REVERT: G 56 GLU cc_start: 0.8182 (tt0) cc_final: 0.7931 (tt0) REVERT: G 71 ARG cc_start: 0.8832 (ttp-170) cc_final: 0.8617 (ttp80) REVERT: H 51 ILE cc_start: 0.8660 (tt) cc_final: 0.8417 (tt) REVERT: H 73 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7633 (mm-30) REVERT: H 80 TYR cc_start: 0.8678 (m-10) cc_final: 0.7979 (m-10) REVERT: H 85 THR cc_start: 0.9140 (m) cc_final: 0.8620 (p) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3398 time to fit residues: 144.1722 Evaluate side-chains 232 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 89 ASN C 112 GLN D 92 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN H 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10892 Z= 0.234 Angle : 0.632 7.534 15464 Z= 0.371 Chirality : 0.037 0.163 1715 Planarity : 0.004 0.034 1327 Dihedral : 29.175 87.364 3109 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.58 % Allowed : 16.80 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.27), residues: 829 helix: 0.21 (0.20), residues: 579 sheet: None (None), residues: 0 loop : -1.18 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.008 0.001 PHE F 100 TYR 0.019 0.002 TYR D 80 ARG 0.007 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 264 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.7372 (mtt) cc_final: 0.7071 (mtt) REVERT: B 67 ARG cc_start: 0.8599 (ttm110) cc_final: 0.8392 (ttm110) REVERT: B 92 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7646 (ttp80) REVERT: C 64 GLU cc_start: 0.8064 (tt0) cc_final: 0.7825 (tm-30) REVERT: C 84 GLN cc_start: 0.8710 (tp40) cc_final: 0.8314 (tp40) REVERT: C 104 GLN cc_start: 0.8199 (tp-100) cc_final: 0.7870 (mm-40) REVERT: D 77 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9066 (mp) REVERT: D 85 THR cc_start: 0.9515 (m) cc_final: 0.9288 (p) REVERT: D 117 LYS cc_start: 0.9280 (mmmt) cc_final: 0.8969 (mtpt) REVERT: E 86 SER cc_start: 0.8829 (m) cc_final: 0.8496 (p) REVERT: E 120 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7396 (mtt) REVERT: F 70 VAL cc_start: 0.9451 (t) cc_final: 0.8682 (m) REVERT: F 88 TYR cc_start: 0.8680 (m-10) cc_final: 0.7970 (m-10) REVERT: G 56 GLU cc_start: 0.8537 (tt0) cc_final: 0.8133 (tt0) REVERT: H 34 TYR cc_start: 0.8868 (m-80) cc_final: 0.8592 (m-10) REVERT: H 73 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7927 (tp30) REVERT: H 80 TYR cc_start: 0.8418 (m-10) cc_final: 0.7997 (m-10) REVERT: H 82 LYS cc_start: 0.9121 (mppt) cc_final: 0.8912 (mmtm) REVERT: H 85 THR cc_start: 0.9201 (m) cc_final: 0.8772 (p) outliers start: 23 outliers final: 14 residues processed: 270 average time/residue: 0.2637 time to fit residues: 94.0902 Evaluate side-chains 252 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 236 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 48 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 78 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN C 104 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10892 Z= 0.243 Angle : 0.617 7.228 15464 Z= 0.365 Chirality : 0.037 0.150 1715 Planarity : 0.004 0.031 1327 Dihedral : 29.014 87.398 3109 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.98 % Allowed : 20.37 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.28), residues: 829 helix: 1.32 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.81 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.011 0.001 PHE A 84 TYR 0.032 0.002 TYR D 80 ARG 0.004 0.001 ARG F 36 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 257 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 THR cc_start: 0.9227 (m) cc_final: 0.8996 (p) REVERT: A 120 MET cc_start: 0.7736 (mtt) cc_final: 0.7463 (mtt) REVERT: B 92 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7748 (ttp80) REVERT: C 36 LYS cc_start: 0.9313 (mmmt) cc_final: 0.8886 (mmmm) REVERT: C 84 GLN cc_start: 0.8663 (tp40) cc_final: 0.8290 (tp40) REVERT: D 77 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9072 (mp) REVERT: D 85 THR cc_start: 0.9478 (m) cc_final: 0.9159 (p) REVERT: D 90 GLU cc_start: 0.8685 (mp0) cc_final: 0.8374 (mp0) REVERT: D 105 LYS cc_start: 0.8990 (ptpp) cc_final: 0.8255 (ptpp) REVERT: E 124 ILE cc_start: 0.9262 (mt) cc_final: 0.8962 (mt) REVERT: E 133 GLU cc_start: 0.7103 (pt0) cc_final: 0.6871 (pt0) REVERT: F 88 TYR cc_start: 0.8738 (m-10) cc_final: 0.7671 (m-10) REVERT: G 56 GLU cc_start: 0.8613 (tt0) cc_final: 0.8222 (tt0) REVERT: H 34 TYR cc_start: 0.8891 (m-80) cc_final: 0.8647 (m-10) REVERT: H 80 TYR cc_start: 0.8431 (m-10) cc_final: 0.8106 (m-10) REVERT: H 82 LYS cc_start: 0.9176 (mppt) cc_final: 0.8850 (mmtm) REVERT: H 83 ARG cc_start: 0.8610 (mmt-90) cc_final: 0.8388 (tpp-160) REVERT: H 85 THR cc_start: 0.9143 (m) cc_final: 0.8633 (p) outliers start: 32 outliers final: 23 residues processed: 269 average time/residue: 0.2722 time to fit residues: 96.0392 Evaluate side-chains 255 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 231 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN C 89 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10892 Z= 0.283 Angle : 0.652 8.334 15464 Z= 0.380 Chirality : 0.038 0.154 1715 Planarity : 0.004 0.031 1327 Dihedral : 28.972 89.156 3109 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.91 % Allowed : 23.64 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.29), residues: 829 helix: 1.85 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.60 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.007 0.001 PHE F 100 TYR 0.035 0.002 TYR B 88 ARG 0.005 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 248 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8636 (tptt) cc_final: 0.8406 (tptt) REVERT: B 84 MET cc_start: 0.6650 (tpp) cc_final: 0.6226 (tpp) REVERT: C 84 GLN cc_start: 0.8674 (tp40) cc_final: 0.8267 (tp40) REVERT: D 35 SER cc_start: 0.9156 (m) cc_final: 0.8867 (t) REVERT: D 77 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9130 (mp) REVERT: D 85 THR cc_start: 0.9533 (m) cc_final: 0.9282 (p) REVERT: D 90 GLU cc_start: 0.8682 (mp0) cc_final: 0.8285 (mp0) REVERT: D 102 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7539 (mm-30) REVERT: D 105 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8672 (ptpp) REVERT: E 82 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8650 (mm) REVERT: F 88 TYR cc_start: 0.8736 (m-10) cc_final: 0.7881 (m-10) REVERT: G 56 GLU cc_start: 0.8669 (tt0) cc_final: 0.8271 (tt0) REVERT: H 82 LYS cc_start: 0.9284 (mppt) cc_final: 0.8842 (mmtm) REVERT: H 83 ARG cc_start: 0.8711 (mmt-90) cc_final: 0.8479 (tpp-160) REVERT: H 85 THR cc_start: 0.9132 (m) cc_final: 0.8824 (p) outliers start: 38 outliers final: 26 residues processed: 262 average time/residue: 0.2715 time to fit residues: 93.3783 Evaluate side-chains 254 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 226 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 78 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 89 ASN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10892 Z= 0.243 Angle : 0.629 9.050 15464 Z= 0.366 Chirality : 0.037 0.160 1715 Planarity : 0.004 0.030 1327 Dihedral : 28.878 89.895 3109 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.98 % Allowed : 24.11 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.29), residues: 829 helix: 2.25 (0.21), residues: 574 sheet: None (None), residues: 0 loop : -0.37 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.010 0.001 PHE E 78 TYR 0.041 0.002 TYR D 80 ARG 0.005 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.6766 (tpp) cc_final: 0.6329 (tpp) REVERT: C 64 GLU cc_start: 0.8171 (tt0) cc_final: 0.7818 (tm-30) REVERT: C 84 GLN cc_start: 0.8685 (tp40) cc_final: 0.8313 (tp40) REVERT: D 35 SER cc_start: 0.9126 (m) cc_final: 0.8831 (t) REVERT: D 85 THR cc_start: 0.9519 (m) cc_final: 0.9262 (p) REVERT: D 90 GLU cc_start: 0.8690 (mp0) cc_final: 0.8261 (mp0) REVERT: D 102 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7594 (mm-30) REVERT: D 105 LYS cc_start: 0.8876 (ptpp) cc_final: 0.8611 (ptpp) REVERT: E 82 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8392 (mm) REVERT: F 88 TYR cc_start: 0.8717 (m-10) cc_final: 0.7965 (m-10) REVERT: G 56 GLU cc_start: 0.8673 (tt0) cc_final: 0.8377 (tt0) REVERT: H 82 LYS cc_start: 0.9297 (mppt) cc_final: 0.8887 (mmtm) outliers start: 32 outliers final: 21 residues processed: 256 average time/residue: 0.2604 time to fit residues: 87.7508 Evaluate side-chains 249 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 227 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 0.0770 overall best weight: 3.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 89 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10892 Z= 0.245 Angle : 0.641 9.851 15464 Z= 0.371 Chirality : 0.037 0.160 1715 Planarity : 0.004 0.030 1327 Dihedral : 28.789 89.767 3109 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.75 % Allowed : 25.35 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.29), residues: 829 helix: 2.42 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.31 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.009 0.001 PHE E 78 TYR 0.059 0.002 TYR D 80 ARG 0.006 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 235 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8309 (tp) cc_final: 0.8092 (tp) REVERT: C 36 LYS cc_start: 0.9158 (tmmt) cc_final: 0.8939 (tptt) REVERT: C 64 GLU cc_start: 0.8153 (tt0) cc_final: 0.7766 (tm-30) REVERT: C 75 LYS cc_start: 0.8853 (mmmm) cc_final: 0.8461 (mmmm) REVERT: C 84 GLN cc_start: 0.8700 (tp40) cc_final: 0.8250 (tp-100) REVERT: D 35 SER cc_start: 0.9095 (m) cc_final: 0.8699 (t) REVERT: D 85 THR cc_start: 0.9524 (m) cc_final: 0.9275 (p) REVERT: D 90 GLU cc_start: 0.8732 (mp0) cc_final: 0.8240 (mp0) REVERT: D 105 LYS cc_start: 0.8902 (ptpp) cc_final: 0.8682 (ptpp) REVERT: F 88 TYR cc_start: 0.8720 (m-10) cc_final: 0.7953 (m-10) REVERT: G 56 GLU cc_start: 0.8709 (tt0) cc_final: 0.8448 (tt0) REVERT: H 82 LYS cc_start: 0.9297 (mppt) cc_final: 0.8842 (mmtm) REVERT: H 83 ARG cc_start: 0.8679 (mmt-90) cc_final: 0.7967 (mmt90) outliers start: 37 outliers final: 29 residues processed: 250 average time/residue: 0.2815 time to fit residues: 91.4638 Evaluate side-chains 249 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 10 optimal weight: 0.3980 chunk 53 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 57 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 89 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10892 Z= 0.218 Angle : 0.640 9.958 15464 Z= 0.368 Chirality : 0.036 0.163 1715 Planarity : 0.003 0.030 1327 Dihedral : 28.694 89.778 3109 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 4.82 % Allowed : 27.84 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.29), residues: 829 helix: 2.47 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -0.11 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.005 0.001 PHE E 67 TYR 0.071 0.002 TYR D 80 ARG 0.009 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8422 (tpp) cc_final: 0.8163 (tpp) REVERT: B 20 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7927 (tppp) REVERT: B 22 LEU cc_start: 0.8331 (tp) cc_final: 0.8118 (tp) REVERT: C 36 LYS cc_start: 0.9181 (tmmt) cc_final: 0.8957 (tptt) REVERT: C 64 GLU cc_start: 0.8100 (tt0) cc_final: 0.7781 (tm-30) REVERT: C 75 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8527 (mmmm) REVERT: C 84 GLN cc_start: 0.8672 (tp40) cc_final: 0.8245 (tp40) REVERT: D 35 SER cc_start: 0.9132 (m) cc_final: 0.8705 (t) REVERT: D 85 THR cc_start: 0.9491 (m) cc_final: 0.9219 (p) REVERT: D 90 GLU cc_start: 0.8704 (mp0) cc_final: 0.8217 (mp0) REVERT: E 125 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8191 (mm-40) REVERT: E 133 GLU cc_start: 0.7533 (pm20) cc_final: 0.7114 (pm20) REVERT: F 53 GLU cc_start: 0.7966 (pt0) cc_final: 0.7664 (pt0) REVERT: F 88 TYR cc_start: 0.8676 (m-10) cc_final: 0.7906 (m-10) REVERT: G 15 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7885 (ptmm) REVERT: G 56 GLU cc_start: 0.8702 (tt0) cc_final: 0.8417 (tt0) REVERT: G 57 TYR cc_start: 0.9187 (t80) cc_final: 0.8951 (t80) REVERT: H 82 LYS cc_start: 0.9312 (mppt) cc_final: 0.8859 (mmtm) REVERT: H 83 ARG cc_start: 0.8668 (mmt-90) cc_final: 0.8026 (mmt90) outliers start: 31 outliers final: 21 residues processed: 250 average time/residue: 0.3375 time to fit residues: 111.8285 Evaluate side-chains 243 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** C 73 ASN C 89 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.5708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10892 Z= 0.205 Angle : 0.660 11.037 15464 Z= 0.374 Chirality : 0.037 0.182 1715 Planarity : 0.004 0.045 1327 Dihedral : 28.584 89.861 3109 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.35 % Allowed : 28.15 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.29), residues: 829 helix: 2.46 (0.21), residues: 571 sheet: None (None), residues: 0 loop : -0.02 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.013 0.001 PHE E 78 TYR 0.068 0.002 TYR D 80 ARG 0.012 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 229 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7128 (tm-30) REVERT: A 120 MET cc_start: 0.8403 (tpp) cc_final: 0.8175 (tpp) REVERT: B 22 LEU cc_start: 0.8324 (tp) cc_final: 0.8108 (tp) REVERT: C 64 GLU cc_start: 0.8121 (tt0) cc_final: 0.7756 (tm-30) REVERT: C 75 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8562 (mmmm) REVERT: C 84 GLN cc_start: 0.8652 (tp40) cc_final: 0.8204 (tp40) REVERT: D 35 SER cc_start: 0.9141 (m) cc_final: 0.8820 (t) REVERT: D 85 THR cc_start: 0.9465 (m) cc_final: 0.9185 (p) REVERT: D 90 GLU cc_start: 0.8711 (mp0) cc_final: 0.8257 (mp0) REVERT: E 125 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8287 (mm-40) REVERT: F 88 TYR cc_start: 0.8609 (m-10) cc_final: 0.7816 (m-10) REVERT: G 56 GLU cc_start: 0.8687 (tt0) cc_final: 0.8422 (tt0) REVERT: H 37 TYR cc_start: 0.8837 (m-80) cc_final: 0.8636 (m-80) REVERT: H 68 GLU cc_start: 0.8399 (tp30) cc_final: 0.7810 (tp30) REVERT: H 82 LYS cc_start: 0.9316 (mppt) cc_final: 0.8922 (mmtm) REVERT: H 83 ARG cc_start: 0.8676 (mmt-90) cc_final: 0.7973 (mmt90) outliers start: 28 outliers final: 25 residues processed: 240 average time/residue: 0.2552 time to fit residues: 80.6563 Evaluate side-chains 244 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 87 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 92 optimal weight: 40.0000 overall best weight: 3.7590 ------------------------------------------------------------------------------- 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** C 73 ASN D 106 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10892 Z= 0.257 Angle : 0.706 13.247 15464 Z= 0.395 Chirality : 0.038 0.216 1715 Planarity : 0.004 0.058 1327 Dihedral : 28.626 89.697 3109 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.89 % Allowed : 29.39 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.29), residues: 829 helix: 2.39 (0.22), residues: 572 sheet: None (None), residues: 0 loop : 0.14 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 113 PHE 0.005 0.001 PHE F 100 TYR 0.083 0.003 TYR B 88 ARG 0.014 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 219 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7143 (tm-30) REVERT: C 35 ARG cc_start: 0.8032 (ttm-80) cc_final: 0.7699 (tpt170) REVERT: C 64 GLU cc_start: 0.8171 (tt0) cc_final: 0.7813 (tm-30) REVERT: C 75 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8550 (mmmm) REVERT: C 84 GLN cc_start: 0.8626 (tp40) cc_final: 0.8202 (tp40) REVERT: D 35 SER cc_start: 0.9034 (m) cc_final: 0.8537 (t) REVERT: D 76 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8394 (ttm-80) REVERT: D 85 THR cc_start: 0.9481 (m) cc_final: 0.9175 (p) REVERT: D 90 GLU cc_start: 0.8770 (mp0) cc_final: 0.8293 (mp0) REVERT: F 88 TYR cc_start: 0.8656 (m-10) cc_final: 0.7787 (m-10) REVERT: G 56 GLU cc_start: 0.8719 (tt0) cc_final: 0.8433 (tt0) REVERT: G 57 TYR cc_start: 0.9209 (t80) cc_final: 0.8960 (t80) REVERT: H 39 TYR cc_start: 0.8728 (t80) cc_final: 0.8466 (t80) REVERT: H 68 GLU cc_start: 0.8384 (tp30) cc_final: 0.7801 (tp30) REVERT: H 82 LYS cc_start: 0.9324 (mppt) cc_final: 0.8916 (mmtm) REVERT: H 83 ARG cc_start: 0.8709 (mmt-90) cc_final: 0.8153 (mmt90) outliers start: 25 outliers final: 23 residues processed: 231 average time/residue: 0.2492 time to fit residues: 76.5221 Evaluate side-chains 241 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 218 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 50.0000 chunk 88 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 0.0000 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 81 optimal weight: 30.0000 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10892 Z= 0.246 Angle : 0.712 13.845 15464 Z= 0.396 Chirality : 0.038 0.183 1715 Planarity : 0.004 0.060 1327 Dihedral : 28.634 89.302 3109 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.89 % Allowed : 29.55 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.29), residues: 829 helix: 2.42 (0.21), residues: 572 sheet: None (None), residues: 0 loop : 0.19 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.005 0.001 PHE E 84 TYR 0.086 0.003 TYR B 88 ARG 0.014 0.001 ARG B 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1658 Ramachandran restraints generated. 829 Oldfield, 0 Emsley, 829 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 73 GLU cc_start: 0.8823 (tm-30) cc_final: 0.8535 (pp20) REVERT: C 35 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7655 (tpt170) REVERT: C 64 GLU cc_start: 0.8131 (tt0) cc_final: 0.7765 (tm-30) REVERT: C 75 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8657 (mmmm) REVERT: C 84 GLN cc_start: 0.8641 (tp40) cc_final: 0.8205 (tp40) REVERT: D 35 SER cc_start: 0.9061 (m) cc_final: 0.8646 (t) REVERT: D 90 GLU cc_start: 0.8753 (mp0) cc_final: 0.8285 (mp0) REVERT: E 125 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8315 (mm-40) REVERT: F 88 TYR cc_start: 0.8640 (m-10) cc_final: 0.7826 (m-10) REVERT: G 56 GLU cc_start: 0.8723 (tt0) cc_final: 0.8422 (tt0) REVERT: G 57 TYR cc_start: 0.9227 (t80) cc_final: 0.8991 (t80) REVERT: H 44 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8511 (tm-30) REVERT: H 82 LYS cc_start: 0.9359 (mppt) cc_final: 0.8953 (mmtm) REVERT: H 83 ARG cc_start: 0.8712 (mmt-90) cc_final: 0.8198 (mmt90) outliers start: 25 outliers final: 23 residues processed: 232 average time/residue: 0.2526 time to fit residues: 78.4670 Evaluate side-chains 238 residues out of total 714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 215 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 0.0980 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 14 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN D 81 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.073478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.052937 restraints weight = 37804.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.054653 restraints weight = 19309.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055789 restraints weight = 12945.666| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10892 Z= 0.266 Angle : 0.735 14.101 15464 Z= 0.407 Chirality : 0.038 0.182 1715 Planarity : 0.004 0.061 1327 Dihedral : 28.650 89.398 3109 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.67 % Allowed : 29.86 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.29), residues: 829 helix: 2.45 (0.21), residues: 568 sheet: None (None), residues: 0 loop : 0.22 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.006 0.001 PHE F 100 TYR 0.105 0.003 TYR D 80 ARG 0.014 0.001 ARG B 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2132.98 seconds wall clock time: 38 minutes 59.73 seconds (2339.73 seconds total)